Index (LOCI Javadocs 0-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

a - Variable in class loci.visbio.util.Segment2D: Endpoints.
About - Class in loci.checks: Displays a small information dialog about this package.
About - Class in ome.xml.version: Displays a small information dialog about the project.
About() - Constructor for class ome.xml.version.About
about() - Static method in class ome.xml.version.About
abs(int) - Static method in class loci.visbio.util.Docker: Integer absolute value function.
Abstract - Variable in class loci.niche.MODSForm
AbstractNode - Class in loci.multithreadedplugin: This abstract base class handles interaction with the NodeScheduler.
AbstractNode() - Constructor for class loci.multithreadedplugin.AbstractNode
AbstractPipelineProcessor - Class in loci.chainableplugin: This is the abstract base class for a chainable processor.
AbstractPipelineProcessor() - Constructor for class loci.chainableplugin.AbstractPipelineProcessor
AbstractPlugin - Class in loci.deepzoom.workflow.plugin: Abstract base class for plugin.
AbstractPlugin() - Constructor for class loci.deepzoom.workflow.plugin.AbstractPlugin
AbstractPlugin - Class in loci.multiinstanceplugin: Abstract base class for plugin.
AbstractPlugin() - Constructor for class loci.multiinstanceplugin.AbstractPlugin
accept(File) - Method in class LineLength
accept(File) - Method in class loci.sonification.Sonification
actionPerformed(ActionEvent) - Method in class loci.apps.MultiLUT: Handles button press events.
actionPerformed(ActionEvent) - Method in class loci.slim.ColorWidget: Handles checkbox and button presses.
actionPerformed(ActionEvent) - Method in class loci.slim.MouseBehaviorButtons: Handles checkbox and button presses.
actionPerformed(ActionEvent) - Method in class loci.slim.SlimData: Handles OK button press.
actionPerformed(ActionEvent) - Method in class loci.slim.SlimPlotter: Handles checkbox and button presses.
actionPerformed(ActionEvent) - Method in class loci.slim.TwoDPane: Handles checkbox presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.BioTask: Toggles the stop button.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.CollapseWidget: Applies changes to this dimensional collapse transform's parameters.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.DataControls: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.ExportPane: Handles button press events.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.ProjectionWidget: Applies changes to this projection's parameters.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.SamplingWidget: Applies changes to this data sampling's parameters.
actionPerformed(ActionEvent) - Method in class loci.visbio.data.SendToIJPane
actionPerformed(ActionEvent) - Method in class loci.visbio.data.SpectralWidget: Applies changes to this spectral mapping's parameters.
actionPerformed(ActionEvent) - Method in class loci.visbio.ext.FunctionWidget: Applies changes to this data sampling's parameters.
actionPerformed(ActionEvent) - Method in class loci.visbio.OrthoStack
actionPerformed(ActionEvent) - Method in class loci.visbio.overlays.OverlayWidget: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.overlays.StatsOptionsPane: Change selection state of check boxes depending on button pressed.
actionPerformed(ActionEvent) - Method in class loci.visbio.state.ResolutionToggleOption: Handles checkbox toggles.
actionPerformed(ActionEvent) - Method in class loci.visbio.state.SpreadsheetLaunchOption: Responds to changes in checkbox state.
actionPerformed(ActionEvent) - Method in class loci.visbio.SystemControls: Handles action events.
actionPerformed(ActionEvent) - Method in class loci.visbio.SystemManager: Outputs current RAM usage to console.
actionPerformed(ActionEvent) - Method in class loci.visbio.util.BreakawayPanel: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.util.DialogPane: Handles button press events.
actionPerformed(ActionEvent) - Method in class loci.visbio.util.FontChooserPane: Handles GUI events.
actionPerformed(ActionEvent) - Method in class loci.visbio.util.WizardPane: Handles button press events.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.BioSlideWidget: Called when previous or next button is pushed.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.CapturePanel: Called when a button is pressed.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.ColorPane: Handles GUI events.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.DisplayControls: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.DisplayWindow: Handles button presses.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.SliceToggler: Handles GUI events.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.StackPanel: Handles button presses and combo box selections.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.TransformPanel: Handles button presses and combo box selections.
actionPerformed(ActionEvent) - Method in class loci.visbio.view.ViewPanel: Handles button presses and combo box selections.
actionPerformed(ActionEvent) - Method in class loci.visbio.VisBioFrame: Internal method enabling logic managers to access their own methods via VisBio's menu system.
actionPerformed(ActionEvent) - Method in class TestMem
actualSampleRate - Variable in class de.sciss.jcollider.Server.Status
add() - Method in class de.sciss.jcollider.OSCResponderNode: Adds the node to the list of actively listening nodes.
add(String) - Method in class loci.deepzoom.util.xmllight.XMLWriter: Adds an embedded XML string with proper indent.
add(IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Adds a component to the workflow in phase I.
add(IModule) - Method in class loci.deepzoom.workflow.WorkFlow
add(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Adds two N-D vectors.
add2D - Variable in class loci.visbio.view.DisplayControls: Button for adding a 2D display to the list.
add3D - Variable in class loci.visbio.view.DisplayControls: Button for adding a 3D display to the list.
addActionListener(ActionListener) - Method in class de.sciss.jcollider.gui.EZSlider
addAfterMsg(Node) - Method in class de.sciss.jcollider.Group
addAfterMsg(Node, String[], float[]) - Method in class de.sciss.jcollider.Synth
addAxis(String) - Method in class loci.visbio.view.TransformHandler: Notifies the transform panel of a new dimensional axis.
addAxis(String) - Method in class loci.visbio.view.TransformPanel: Adds a dimensional axis.
addBeforeMsg(Node) - Method in class de.sciss.jcollider.Group
addBeforeMsg(Node, String[], float[]) - Method in class de.sciss.jcollider.Synth
addBooleanOption(String, String, char, String, boolean) - Method in class loci.visbio.state.OptionManager: Adds an option allowing the user to toggle a check box.
addBuf(Buffer) - Method in class de.sciss.jcollider.Server: For internal use by Buffer objects.
addCurveListener(CurveListener) - Method in class loci.slim.fit.CurveCollection
addCurveListener(CurveListener) - Method in interface loci.slim.fit.CurveReporter
addCustomOption(String, Component) - Method in class loci.visbio.state.OptionManager: Adds a custom GUI component to VisBio's options dialog.
addData(DataTransform) - Method in class loci.visbio.data.DataControls: Adds a data object to the data object tree.
addData(DataTransform) - Method in class loci.visbio.data.DataManager: Adds a data object to the list.
addDisplay(DisplayWindow) - Method in class loci.visbio.view.DisplayControls: Adds a display to the list of current displays.
addDisplay(DisplayWindow) - Method in class loci.visbio.view.DisplayManager: Adds a display to the list of current displays.
addDoWhenBooted(Server.CompletionAction) - Method in class de.sciss.jcollider.Server: Registers an action to be executed after the boot process is complete.
addEndTag(String) - Method in class loci.deepzoom.util.xmllight.XMLWriter: Ends a tag.
addHelpTopic(String, String) - Method in class loci.visbio.help.HelpManager: Adds a new help topic.
addImageToStack(ImagePlus, ImageProcessor, ImageStack) - Method in class loci.apps.flow.Find_Particle_Areas
addItem(String, ScalarType) - Method in class loci.visbio.view.BioColorWidget: Adds a scalar to the list of available choices.
addItemListener(ItemListener) - Method in class loci.visbio.view.BioColorWidget: Adds an item listener to this widget.
addListener(NumberListener) - Method in class de.sciss.jcollider.gui.NumberField: Register a NumberListener which will be informed about changes of the gadgets content.
addListener(NodeListener) - Method in class de.sciss.jcollider.NodeWatcher: Registers a listener to be informed about node status changes.
addListener(ServerListener) - Method in class de.sciss.jcollider.Server: Registers a listener to be informed about server status changes.
addListOption(String, String, String, String[]) - Method in class loci.visbio.state.OptionManager: Adds an option allowing the user to select from a dropdown list.
addManager(LogicManager) - Method in class loci.visbio.VisBioFrame: Adds a logic manager to the VisBio interface.
addNode(OSCResponderNode) - Method in class de.sciss.jcollider.OSCMultiResponder
addNumericOption(String, String, String, String, int) - Method in class loci.visbio.state.OptionManager: Adds an option allowing the user to enter a numerical value.
addNumericOption(String, String, String, String, double) - Method in class loci.visbio.state.OptionManager: Adds an option allowing the user to enter a numerical value.
addObject(OverlayObject) - Method in class loci.visbio.overlays.OverlayTransform: Adds an overlay object at the current dimensional position.
addObject(OverlayObject, int[]) - Method in class loci.visbio.overlays.OverlayTransform: Adds an overlay object at the given dimensional position.
addOption(String, BioOption) - Method in class loci.visbio.state.OptionManager: Adds an option to VisBio's options dialog.
addOption(String, BioOption) - Method in class loci.visbio.state.OptionPane: Adds an option with a boolean value to the specified tab.
addOutputListener(OutputListener) - Method in class loci.visbio.util.OutputConsole
addPanel(ControlPanel, int, int, int, int) - Method in class loci.visbio.PanelManager: Adds a new control panel.
addPanel(ControlPanel, int, int, int, int, String, String) - Method in class loci.visbio.PanelManager: Adds a new control panel.
addReplaceMsg(Node) - Method in class de.sciss.jcollider.Group
addReplaceMsg(Node, String[], float[]) - Method in class de.sciss.jcollider.Synth
addRow(JPanel, String, double, String) - Static method in class loci.slim.SlimData
addSpawnListener(SpawnListener) - Method in class loci.visbio.util.InstanceServer: Adds an application instance spawn listener.
addStringOption(String, String, String, String, String) - Method in class loci.visbio.state.OptionManager: Adds an option allowing the user to enter a string.
addTab(String) - Method in class loci.visbio.state.OptionPane: Initializes a tab with the given name.
addTag(String) - Method in class loci.deepzoom.util.xmllight.XMLWriter: Starts a new tag.
addTagWithContent(String, String) - Method in class loci.deepzoom.util.xmllight.XMLWriter: Adds a tag with some content on a single line.
addTask(BioTask) - Method in class loci.visbio.TaskControls: Adds a task to the tasks pane.
addToHeadMsg(Group) - Method in class de.sciss.jcollider.Group
addToHeadMsg(Group, String[], float[]) - Method in class de.sciss.jcollider.Synth
addTool(OverlayTool) - Method in class loci.visbio.overlays.OverlayWidget: Adds the given overlay tool to the overlay widget.
addTopic(String, String) - Method in class loci.visbio.help.HelpWindow: Adds the given topic to the list, from the given source file.
addToTailMsg(Group) - Method in class de.sciss.jcollider.Group
addToTailMsg(Group, String[], float[]) - Method in class de.sciss.jcollider.Synth
addTransform(DataTransform, int) - Method in class loci.visbio.view.BioSlideWidget: Adds a transform to the list affected by this slider.
addTransform(DataTransform) - Method in class loci.visbio.view.DisplayWindow: Links the given data transform to the display.
addTransform(DataTransform) - Method in class loci.visbio.view.StackHandler: Links the given data transform to the display.
addTransform(DataTransform) - Method in class loci.visbio.view.TransformHandler: Links the given data transform to the display.
addTransform(DataTransform) - Method in class loci.visbio.view.TransformPanel: Adds the given data transform to the list.
addTransformListener(TransformListener) - Method in class loci.visbio.data.DataTransform: Adds the given listener to the list of listeners.
addTSB(TransientSelectBox) - Method in class loci.visbio.overlays.OverlayTransform: Adds a transient selection box.
addWindow(Window) - Method in class loci.visbio.util.Docker: Adds a window to the dockable group.
addWindow(Window, int) - Method in class loci.visbio.util.Docker: Adds a window to the dockable group, at the given docking priority.
addWindow(Window) - Method in class loci.visbio.WindowManager: Registers a window with the window manager.
addWindow(Window, boolean) - Method in class loci.visbio.WindowManager: Registers a window with the window manager.
adjoin(float[][], float[][]) - Static method in class loci.visbio.overlays.OverlayUtil: Connects a pair of VisAD-style 2D arrays of points.
ADJUST - Static variable in class loci.visbio.overlays.PolylineTool
ADJUST_TAIL - Static variable in class loci.visbio.overlays.PolylineTool
adjustColorTable(float[][], float[], boolean) - Static method in class loci.visbio.util.ColorUtil: Ensures the color table is of the proper type (RGB or RGBA).
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.visbio.OrthoStack
after(Node) - Static method in class de.sciss.jcollider.Group
after(Node, String) - Static method in class de.sciss.jcollider.Synth
after(Node, String, String[], float[]) - Static method in class de.sciss.jcollider.Synth
align(EZSlider[]) - Static method in class de.sciss.jcollider.gui.EZSlider
alive - Variable in class loci.slim.fit.CurveRenderer
alive - Variable in class loci.slim.fit.RendererSwitcher
alive - Variable in class loci.visbio.util.InstanceServer: Whether this instance server is still listening for spawn events.
alive - Variable in class loci.visbio.view.TransformLink: Whether this link is still active.
alloc(int) - Method in interface de.sciss.jcollider.BlockAllocator: Allocates a new bus.
alloc(Server, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns a new mono Buffer with given number of frames.
alloc(Server, int, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns a new Buffer with given number of channels and frames.
alloc(Server, int, int, Buffer.CompletionFunction) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns a new Buffer with given number of channels and frames.
alloc(Server, int, int, Buffer.CompletionFunction, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns a new Buffer with given number of channels and frames.
alloc() - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor.
alloc(OSCMessage) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor.
alloc(Server, Object) - Static method in class de.sciss.jcollider.Bus
alloc(Server, Object, int) - Static method in class de.sciss.jcollider.Bus
alloc() - Method in class de.sciss.jcollider.Bus
alloc() - Method in class de.sciss.jcollider.ContiguousBlockAllocator
alloc(int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator
alloc() - Method in class de.sciss.jcollider.NodeIDAllocator
alloc(int) - Method in class de.sciss.jcollider.PowerOfTwoAllocator
allocConsecutive(int, Server, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns an array of neighbouring single channel Buffer objects with given number of frames.
allocConsecutive(int, Server, int, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns an array of neighbouring Buffer objects with given number of channels and frames.
allocConsecutive(int, Server, int, int, Buffer.CompletionFunction) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns an array of neighbouring Buffer objects with given number of channels and frames.
allocConsecutive(int, Server, int, int, Buffer.CompletionFunction, int) - Static method in class de.sciss.jcollider.Buffer: Allocates and returns an array of neighbouring Buffer objects with given number of channels and frames.
allocMsg() - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_alloc message to allocate the buffer created with the basic new constructor.
allocMsg(OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_alloc message to allocate the buffer created with the basic new constructor.
allocPerm() - Method in class de.sciss.jcollider.NodeIDAllocator
allocRead(String) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in a sound file.
allocRead(String, long) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in a sound file.
allocRead(String, long, int) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in a sound file.
allocRead(String, long, int, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in a sound file.
allocReadChannel(String, long, int, int[]) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in selected channels of a sound file.
allocReadChannel(String, long, int, int[], OSCMessage) - Method in class de.sciss.jcollider.Buffer: Allocates the buffer created with the basic new constructor, by reading in selected channels of a sound file.
allocReadChannelMsg(String, long, int, int[]) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocReadChannel message to allocate the buffer created with the basic new constructor, by reading in selected channels from a sound file.
allocReadChannelMsg(String, long, int, int[], OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocReadChannel message to allocate the buffer created with the basic new constructor, by reading in selected channels from a sound file.
allocReadMsg(String) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocRead message to allocate the buffer created with the basic new constructor, by reading in a sound file.
allocReadMsg(String, long) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocRead message to allocate the buffer created with the basic new constructor, by reading in a sound file.
allocReadMsg(String, long, int) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocRead message to allocate the buffer created with the basic new constructor, by reading in a sound file.
allocReadMsg(String, long, int, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_allocRead message to allocate the buffer created with the basic new constructor, by reading in a sound file.
ALLOW_3D - Static variable in class loci.visbio.util.DisplayUtil: Flag for enabling or disabling Java3D, for debugging.
allowCurveFit - Variable in class loci.slim.SlimData
ALPHA_TYPE - Static variable in class loci.visbio.overlays.OverlayTransform: MathType for alpha color mappings.
always - Variable in class loci.visbio.util.MessagePane: Checkbox within dialog.
analyzeIndividualParticles() - Method in class loci.apps.flow.Find_Particle_Areas
analyzeSingleStack() - Method in class loci.apps.flow.Find_Particle_Areas
ANGLE - Static variable in class loci.visbio.overlays.OverlayArrow
animate - Variable in class loci.visbio.view.TransformPanel: Button for toggling status of animation.
animating - Variable in class loci.visbio.view.TransformHandler: Flag indicating status of animation.
animAxis - Variable in class loci.visbio.view.TransformHandler: Dimensional axis to use for animation.
animBox - Variable in class loci.visbio.view.TransformPanel: List of axes for animation.
animSync - Variable in class loci.visbio.view.TransformHandler: Synchronization object for animation.
animThread - Variable in class loci.visbio.view.TransformHandler: Thread responsible for animation.
AperioScannerInterpreter - Class in loci.apps.SlideScannerImport
AperioScannerInterpreter(String, String) - Constructor for class loci.apps.SlideScannerImport.AperioScannerInterpreter
append(String) - Method in class de.sciss.jcollider.gui.LogTextArea: This method is public because of the superclass method.
applyMatrix(double[]) - Method in class loci.visbio.view.ViewHandler: Applies the given matrix transform to the display.
applyTo(Window) - Method in class loci.visbio.WindowState: Applies this state to the given window.
APPROVE_OPTION - Static variable in class loci.visbio.util.DialogPane: Return value if approve (ok) is chosen.
ar(String, int) - Static method in class de.sciss.jcollider.UGen: Constructs a new audio rate UGen with zero arguments and a required explict output channel number.
ar(String) - Static method in class de.sciss.jcollider.UGen: Constructs a new audio rate UGen with zero arguments.
ar(String, int, GraphElem) - Static method in class de.sciss.jcollider.UGen: Constructs a new audio rate UGen with one given argument and an explicit number of output channels.
ar(String, GraphElem) - Static method in class de.sciss.jcollider.UGen: Constructs a new audio rate UGen with one given argument
ar(String, int, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, int, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, int, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, int, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ar(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ArbitrarySlice - Class in loci.visbio.data: A transform for slicing a stack of images in 3D.
ArbitrarySlice() - Constructor for class loci.visbio.data.ArbitrarySlice: Creates an uninitialized arbitrary slice.
ArbitrarySlice(DataTransform, String) - Constructor for class loci.visbio.data.ArbitrarySlice: Creates an overlay object for the given transform.
ARC - Static variable in class loci.visbio.overlays.OverlayNodedObject: Computed (X, Y) pairs for top 1/2 of a unit circle.
ARC - Static variable in class loci.visbio.overlays.OverlayOval: Computed (X, Y) pairs for top 1/2 of a unit circle.
ARC - Static variable in class loci.visbio.overlays.OverlayUtil: Computed (X, Y) pairs for top 1/2 of a unit circle.
AREA - Static variable in class loci.visbio.overlays.OverlayBox
AREA - Static variable in class loci.visbio.overlays.OverlayOval
areBoundsEditable() - Method in class loci.visbio.overlays.OverlayNodedObject: True iff this overlay can be resized using X1, X2, Y1, Y2 entry boxes.
areBoundsEditable() - Method in class loci.visbio.overlays.OverlayObject: True iff this overlay can be resized using X1, X2, Y1, Y2 entry boxes.
areDifferent(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Tests whether two arrays of floats are different.
areOpposite(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Tests whether two vectors are coordinate-wise opposite.
areSame(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Tests whether two arrays of floats are identical.
Arg(String, float, float, float, boolean) - Constructor for class de.sciss.jcollider.UGenInfo.Arg
Arg(String, float, boolean) - Constructor for class de.sciss.jcollider.UGenInfo.Arg
args - Variable in class de.sciss.jcollider.UGenInfo: Array of the input argument definitions
args - Variable in class loci.visbio.util.SpawnEvent: The arguments passed from the spawned application instance.
array(GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen: Assembles two graph elements (such as UGens, or Constants) into one array which in turn can be used for multichannel expansion when passed as an argument to one of the UGen constructor methods
array(GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen: Assembles three graph elements (such as UGens, or Constants) into one array which in turn can be used for multichannel expansion when passed as an argument to one of the UGen constructor methods
array(GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen: Assembles four graph elements (such as UGens, or Constants) into one array which in turn can be used for multichannel expansion when passed as an argument to one of the UGen constructor methods
array(GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen: Assembles five graph elements (such as UGens, or Constants) into one array which in turn can be used for multichannel expansion when passed as an argument to one of the UGen constructor methods
ARRAY_TYPE - Static variable in class loci.jvmlink.ConnThread
arraysEqual(Object[], Object[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two Object arrays are component-wise equal.
arraysEqual(boolean[], boolean[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two boolean arrays are component-wise equal.
arraysEqual(byte[], byte[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two byte arrays are component-wise equal.
arraysEqual(char[], char[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two char arrays are component-wise equal.
arraysEqual(double[], double[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two double arrays are component-wise equal.
arraysEqual(float[], float[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two float arrays are component-wise equal.
arraysEqual(int[], int[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two int arrays are component-wise equal.
arraysEqual(long[], long[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two long arrays are component-wise equal.
arraysEqual(short[], short[]) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two short arrays are component-wise equal.
arrayToString(Object[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of Objects into a String.
arrayToString(boolean[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of booleans into a String.
arrayToString(byte[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of bytes into a String.
arrayToString(char[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of chars into a String.
arrayToString(double[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of doubles into a String.
arrayToString(float[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of floats into a String.
arrayToString(int[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of ints into a String.
arrayToString(long[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of longs into a String.
arrayToString(short[]) - Static method in class loci.visbio.util.ObjectUtil: Converts the given array of shorts into a String.
arrow - Variable in class loci.visbio.overlays.ArrowTool: Arrow currently being drawn.
ArrowTool - Class in loci.visbio.overlays: ArrowTool is the tool for creating arrow overlays.
ArrowTool(OverlayTransform) - Constructor for class loci.visbio.overlays.ArrowTool: Constructs an arrow overlay creation tool.
asArray(GraphElem) - Static method in class de.sciss.jcollider.GraphElemArray
Ascii - Class in <Unnamed>: Outputs the readable ASCII table from 32 to 127.
Ascii() - Constructor for class Ascii
aspectX - Variable in class loci.visbio.view.ViewPanel: Aspect ratio X component text field.
aspectY - Variable in class loci.visbio.view.ViewPanel: Aspect ratio Y component text field.
aspectZ - Variable in class loci.visbio.view.ViewPanel: Aspect ratio Z component text field.
associate(String, String) - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Used for plugin chaining.
associate(String, String) - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Associates a unique input image name for some other launcher to our output image name.
associate(String, String) - Method in interface loci.multiinstanceplugin.IPluginLauncher: Used for plugin chaining.
associate(String, String) - Method in class loci.multiinstanceplugin.PluginLauncher: Associates a unique input image name for some other launcher to our output image name.
associate(String, String) - Method in class loci.multithreadedplugin.AbstractNode: When chaining associates a named output with a named input tied to a particular instance of chained subclass.
associate(String, String) - Method in interface loci.multithreadedplugin.IScheduledNode: For this instance, maps my outgoing data name to a full name which includes the destination instance id and destination incoming name.
asTarget() - Method in class de.sciss.jcollider.Server: Returns a group representation of the server, which at the moment is a synonym for getDefaultGroup.
asUGenInputs() - Method in class de.sciss.jcollider.Constant
asUGenInputs() - Method in interface de.sciss.jcollider.GraphElem
asUGenInputs() - Method in class de.sciss.jcollider.GraphElemArray
asUGenInputs() - Method in class de.sciss.jcollider.UGen
asUGenInputs() - Method in class de.sciss.jcollider.UGenChannel: Returns this as an array
attachROIStoImage(ImagePlus, ArrayList<ArrayList<Float>>) - Static method in class loci.apps.SlideScannerImport.MiniBioformatsTool
audio(Server) - Static method in class de.sciss.jcollider.Bus
audio(Server, int) - Static method in class de.sciss.jcollider.Bus
AUTHOR - Static variable in class loci.visbio.VisBio: Application authors.
AUTO_THUMBS - Static variable in class loci.visbio.data.DataManager: String for thumbnail auto-generation option.
AutoLoginHandler - Class in loci.wiscscan.auth: Helper class for managing secure Kerberos logins.
AutoLoginHandler(Credentials) - Constructor for class loci.wiscscan.auth.AutoLoginHandler: This is the constructor which takes in the username and password to send the JAAS call.
autoSize - Variable in class loci.visbio.util.BreakawayPanel: Flag indicating whether owner window gets intelligently resized.
avgCPU - Variable in class de.sciss.jcollider.Server.Status
axes - Variable in class loci.visbio.data.CollapseWidget: Dropdown combo box listing available dimensions for collapse.
axes - Variable in class loci.visbio.data.ProjectionWidget: Dropdown combo box listing available dimensions for projection.
axes - Variable in class loci.visbio.data.SliceWidget: Dropdown combo box listing available dimensions to slice through.
axis - Variable in class loci.visbio.data.ArbitrarySlice: Dimensional axis to slice through.
axis - Variable in class loci.visbio.data.CollapseTransform: Dimensional axis to collapse.
axis - Variable in class loci.visbio.data.ProjectionTransform: Dimensional axis to project.
axisValid - Variable in class loci.visbio.view.StackLink: Flag indicating whether stackAxis is valid.

B

b - Variable in class loci.visbio.util.Segment2D: Endpoints.
back - Variable in class loci.visbio.util.WizardPane: Wizard's back button.
BackupTools - Class in loci.backup.github: Utility class for use with GitHubBackup wrappers, such as the GitHubBackupGUI and GitHubBackupMojo.
BackupTools() - Constructor for class loci.backup.github.BackupTools
BareBonesBrowserLaunch - Class in com.centerkey.utils: Bare Bones Browser Launch for Java
Utility class to open a web page from a Swing application in the user's default browser.
Supports: Mac OS X, GNU/Linux, Unix, Windows XP/Vista/7
Example Usage: String url = "http://www.google.com/"; BareBonesBrowserLaunch.openURL(url); Latest Version: www.centerkey.com/java/browser
Author: Dem Pilafian
Public Domain Software -- Free to Use as You Like
BareBonesBrowserLaunch() - Constructor for class com.centerkey.utils.BareBonesBrowserLaunch
BARF - Static variable in class loci.visbio.overlays.OverlayIO
basicNew(Server) - Static method in class de.sciss.jcollider.Group
basicNew(Server, int) - Static method in class de.sciss.jcollider.Group
basicNew(String, Server) - Static method in class de.sciss.jcollider.Synth
basicNew(String, Server, int) - Static method in class de.sciss.jcollider.Synth
bc - Variable in class loci.slim.SlimTypes
bcUnits - Variable in class loci.slim.SlimTypes
bcv - Variable in class loci.slim.SlimTypes
bcvFunc - Variable in class loci.slim.SlimTypes
bcvFuncFit - Variable in class loci.slim.SlimTypes
bcvFuncRes - Variable in class loci.slim.SlimTypes
before(Node) - Static method in class de.sciss.jcollider.Group
before(Node, String) - Static method in class de.sciss.jcollider.Synth
before(Node, String, String[], float[]) - Static method in class de.sciss.jcollider.Synth
begin - Variable in class loci.visbio.view.SliceToggler: Starting slice index.
BEGIN_EXTEND - Static variable in class loci.visbio.overlays.PolylineTool
beginTree(DetailAST) - Method in class loci.checks.BlankLinesCheck
BIGNAME - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: create a server name box
Binary - Class in <Unnamed>: Attempts to convert a string of zeroes and ones into readable text using a variety of encodings.
Binary() - Constructor for class Binary
BinaryDiff - Class in <Unnamed>: Compares two binary files, outputting their differences in human-readable form.
BinaryDiff() - Constructor for class BinaryDiff
binRadius - Variable in class loci.slim.SlimData
binsToPico(float) - Method in class loci.slim.SlimData: Converts value in histogram bins to picoseconds.
bio - Variable in class loci.visbio.LogicManager: VisBio frame.
BioArrowButton - Class in loci.visbio.util: BioArrowButton is a simple arrow button of fixed size.
BioArrowButton(int) - Constructor for class loci.visbio.util.BioArrowButton: Constructs a new arrow button of default size.
BioArrowButton(int, int) - Constructor for class loci.visbio.util.BioArrowButton: Constructs a new slider widget.
BioColorWidget - Class in loci.visbio.view: BioColorWidget is a widget for controlling mappings from range scalars to color scalars.
BioColorWidget(int) - Constructor for class loci.visbio.view.BioColorWidget: Constructs a new color widget.
BioComboBox - Class in loci.visbio.util: An extension of JComboBox that makes the widget slightly wider than normal, to work around a bug in the Windows and GTK Look and Feels where combo boxes are slightly too narrow.
BioComboBox() - Constructor for class loci.visbio.util.BioComboBox: Constructs a new combo box.
BioComboBox(String[]) - Constructor for class loci.visbio.util.BioComboBox: Constructs a new combo box.
BioDropHandler - Class in loci.visbio: BioDropHandler provides drag and drop support for handling file drops into VisBio.
BioDropHandler(VisBioFrame) - Constructor for class loci.visbio.BioDropHandler: Constructs a new transfer handler for VisBio file drops.
BioOption - Class in loci.visbio.state: BioOption represents an option in the VisBio Options dialog.
BioOption(String) - Constructor for class loci.visbio.state.BioOption: Constructs a new option.
BioSlideWidget - Class in loci.visbio.view: BioSlideWidget is a widget for exploring one dimension of a dataset.
BioSlideWidget(DataTransform, int) - Constructor for class loci.visbio.view.BioSlideWidget: Constructs a new slider widget from the given transform and index.
BioTask - Class in loci.visbio: BioTask is a panel representing a particular VisBio task.
BioTask(TaskManager, String) - Constructor for class loci.visbio.BioTask: Constructs a new VisBio task.
BlankLinesCheck - Class in loci.checks: A Checkstyle check for identifying multiple consecutive blank lines.
BlankLinesCheck() - Constructor for class loci.checks.BlankLinesCheck
BlockAllocator - Interface in de.sciss.jcollider: The BlockAllocator interface allows the use of different implementations of allocators for audio and control busses by the Server class.
BlockAllocator.Block - Interface in de.sciss.jcollider: This sub interface describes a class which represents a block of indices in a BlockAllocator.
BlockAllocator.Factory - Interface in de.sciss.jcollider: This sub interface describes a class which is capable of producing a new BlockAllocator.
blue - Variable in class loci.visbio.view.ColorHandler: Red, green and blue components of images.
blue - Variable in class loci.visbio.view.ColorPane: Color map widgets.
BLUE_TYPE - Static variable in class loci.visbio.overlays.OverlayTransform: MathType for blue color mappings.
BOOLEAN_TYPE - Static variable in class loci.jvmlink.ConnThread
BooleanOption - Class in loci.visbio.state: BooleanOption is a true-or-false option in the VisBio Options dialog.
BooleanOption(String, char, String, boolean) - Constructor for class loci.visbio.state.BooleanOption: Constructs a new option.
boot() - Method in class de.sciss.jcollider.Server: Starts booting a local server and establishes the ping-thread when done
boot(boolean) - Method in class de.sciss.jcollider.Server: Starts booting a local server.
BOOTQUIT - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: create a boot/quit button
bootThread - Variable in class de.sciss.jcollider.Server
bottom - Variable in class loci.visbio.util.BreakawayPanel: Arrow buttons.
boundingBox - Variable in class loci.visbio.view.ViewHandler: Whether bounding box is visible.
boundingBoxOverlapsBoundingBoxOf(Segment2D) - Method in class loci.visbio.util.Segment2D: Whether another segment meets the bounding box of this segment.
BOUNDS - Static variable in class loci.visbio.overlays.OverlayNodedObject: The names of the statistics this object reports.
bounds - Variable in class loci.visbio.overlays.PointerTool: Array of the bounds of the OverlayObjects at the current dimensional position.
box - Variable in class loci.visbio.overlays.BoxTool: Box currently being drawn.
box - Variable in class loci.visbio.view.BioColorWidget: Combo box listing available range components.
BoxTool - Class in loci.visbio.overlays: BoxTool is the tool for creating box overlays.
BoxTool(OverlayTransform) - Constructor for class loci.visbio.overlays.BoxTool: Constructs a box overlay creation tool.
BreakawayPanel - Class in loci.visbio.util: BreakawayPanel is a container with arrows for controlling which edge of its parent container it borders, or whether it floats in a separate window.
BreakawayPanel(Container, String, boolean) - Constructor for class loci.visbio.util.BreakawayPanel: Creates a new breakaway panel.
brightness - Variable in class loci.visbio.view.ColorHandler: Brightness and contrast of images.
brightness - Variable in class loci.visbio.view.ColorPane: Slider for level of brightness.
brightnessValue - Variable in class loci.visbio.view.ColorPane: Label for current brightness value.
BrowserLauncher - Class in loci.visbio.util: BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
bType - Variable in class loci.slim.SlimTypes
Buffer - Class in de.sciss.jcollider: Mimics SCLang's Buffer class, that is, it's a client side representation of an audio buffer
Buffer(Server, int, int) - Constructor for class de.sciss.jcollider.Buffer: Creates a new Buffer with given number of frames and channels.
Buffer(Server, int, int, int) - Constructor for class de.sciss.jcollider.Buffer: Creates a new Buffer with given number of frames and channels.
Buffer.CompletionAction - Interface in de.sciss.jcollider: Interface describing an action to take place after an asynchronous buffer command is completed.
Buffer.CompletionFunction - Interface in de.sciss.jcollider: Interface describing an function that creates an OSC message used as a completion message in asynchronous buffer commands.
bufferArray - Variable in class de.sciss.jcollider.Server
bufInfoResponder - Variable in class de.sciss.jcollider.Server
buildGroup(int, Vector) - Method in class loci.visbio.util.Docker: Recursively builds a list of windows docked together into a group.
buildList(String) - Method in class loci.jar2lib.ClassList: Builds the list of Java classes contained in the given JAR file.
buildMenuItems(DefaultMutableTreeNode) - Method in class loci.visbio.view.TransformPanel: Builds a JMenu from the children of the given tree node.
buildNodesSets(RealTupleType, float[][], float) - Static method in class loci.visbio.overlays.OverlayUtil: Given a set of nodes, creates a UnionSet of Gridded2DSets to highlight the nodes.
burnDelay - Variable in class loci.visbio.view.TransformHandler: Default burn-in delay in milliseconds.
BurnInRenderer - Class in loci.slim.fit: Curve renderer implementation that delivers increasingly high resolution lifetime image renderings, then continually improves the lifetime image based on RCSE minimization thereafter.
BurnInRenderer(CurveCollection) - Constructor for class loci.slim.fit.BurnInRenderer
burnNow - Variable in class loci.visbio.view.TransformLink: Whether a full-resolution burn-in should occur immediately.
burnThread - Variable in class loci.visbio.view.TransformLink: Separate thread for managing full-resolution burn-in.
burnTime - Variable in class loci.visbio.view.TransformLink: Next clock time a full-resolution burn-in should occur.
Bus - Class in de.sciss.jcollider: Mimics SCLang's Bus class, that is, it's a client side representation of an audio or control bus
Bus(Server) - Constructor for class de.sciss.jcollider.Bus: Creates an mono audio bus on the server at index 0.
Bus(Server, Object) - Constructor for class de.sciss.jcollider.Bus
Bus(Server, Object, int) - Constructor for class de.sciss.jcollider.Bus
Bus(Server, Object, int, int) - Constructor for class de.sciss.jcollider.Bus
Bus.GetCompletionAction - Interface in de.sciss.jcollider: Interface describing an action to take place after an asynchronous bus query is completed.
BUTTON_SIZE - Static variable in class loci.visbio.util.BioArrowButton: Default size for arrow buttons.
buttonGroup - Variable in class loci.visbio.overlays.OverlayWidget: Button group ensuring only one tool can be selected at a time.
BUTTONS - Static variable in class de.sciss.jcollider.gui.NodeTreePanel: Flag for the constructor: create a button bar to message the nodes.
buttons - Variable in class loci.visbio.overlays.OverlayWidget: List of buttons for each overlay tool.
bv - Variable in class loci.slim.SlimTypes
BYTE_ORDER - Static variable in class loci.jvmlink.ConnThread
BYTE_TYPE - Static variable in class loci.jvmlink.ConnThread

C

c - Variable in class de.sciss.jcollider.Server
c - Variable in class loci.slim.fit.RendererSwitcher
cache - Variable in class loci.visbio.data.ThumbnailHandler: Thumbnail disk cache for faster thumbnail retrieval.
cache - Variable in class loci.visbio.view.TransformHandler: Cache of full-resolution data in memory.
cachedPos - Variable in class loci.visbio.view.TransformLink: Last cached dimensional position of the link.
calcTrialRatio(double, int, double) - Static method in class loci.apps.flow.FlowCyto
call() - Method in class loci.backup.github.CreateOrphanBranchCommand
call(String) - Method in class loci.visbio.VisBioFrame: This method executes action commands of the form "loci.visbio.data.DataManager.importData(param)" by stripping off the fully qualified class name, checking VisBio's list of logic managers for one of that class, and calling the given method on that object, optionally with the given String parameter.
canBeFilled() - Method in class loci.visbio.overlays.OverlayArrow: True iff this overlay supports the filled parameter.
canBeFilled() - Method in class loci.visbio.overlays.OverlayBox: True iff this overlay supports the filled parameter.
canBeFilled() - Method in class loci.visbio.overlays.OverlayNodedObject: True iff this overlay supports the filled parameter.
canBeFilled() - Method in class loci.visbio.overlays.OverlayObject: True iff this overlay supports the filled parameter.
canBeFilled() - Method in class loci.visbio.overlays.OverlayOval: True iff this overlay supports the filled parameter.
cancel - Variable in class loci.visbio.util.DialogPane: Cancel button.
CANCEL_OPTION - Static variable in class loci.visbio.util.DialogPane: Return value if cancel is chosen.
cancelShutdown() - Method in class loci.visbio.ExitManager: Trip flag indicating shutdown process should not continue.
canDisplay2D() - Method in class loci.visbio.data.DataTransform: Gets whether this data object can be displayed in 2D.
canDisplay3D() - Method in class loci.visbio.data.DataTransform: Gets whether this data object can be displayed in 3D.
canDisplay3D() - Method in class loci.visbio.data.ImageTransform: Gets whether this data object can be displayed in 3D.
canDo3D() - Static method in class loci.visbio.util.DisplayUtil: Whether this JVM supports 3D displays.
canImport(JComponent, DataFlavor[]) - Method in class loci.visbio.BioDropHandler: Determines whether a drop operation is legal with the given flavors.
CaptureHandler - Class in loci.visbio.view: Provides logic for capturing display screenshots and movies.
CaptureHandler(DisplayWindow) - Constructor for class loci.visbio.view.CaptureHandler: Creates a display capture handler.
captureHandler - Variable in class loci.visbio.view.DisplayWindow: Handles logic for capturing the display screenshots and movies.
captureImage(ProjectionControl, double[], DisplayImpl) - Method in class loci.visbio.view.CaptureHandler: Takes a snapshot of the given display with the specified projection matrix.
captureMovie(Vector, double, int, boolean, boolean) - Method in class loci.visbio.view.CaptureHandler: Creates a movie of the given transformation sequence.
CapturePanel - Class in loci.visbio.view: Provides GUI controls for a display capture handler.
CapturePanel(CaptureHandler) - Constructor for class loci.visbio.view.CapturePanel: Constructs a window for capturing display screenshots and movies.
cDummyFunc - Variable in class loci.slim.SlimTypes
centerWindow(Window) - Static method in class loci.visbio.util.SwingUtil: Centers the given window on the screen.
centerWindow(Window, Window) - Static method in class loci.visbio.util.SwingUtil: Centers the given window within the specified parent window.
centerWindow(Rectangle, Window) - Static method in class loci.visbio.util.SwingUtil: Centers the given window within the specified bounds.
chain(IProcessor) - Method in class loci.chainableplugin.AbstractPipelineProcessor: Chains this processor to another.
chain(IProcessor) - Method in interface loci.chainableplugin.IPipelineProcessor: Called from outside the processor before processing begins.
chain(IPluginLauncher, String, IPluginLauncher, String) - Method in class loci.deepzoom.workflow.plugin.PluginScheduler: Chains the named image from one plugin to another.
chain(IPluginLauncher, String, IPluginLauncher, String) - Method in class loci.multiinstanceplugin.PluginScheduler: Chains the named image from one plugin to another.
chain(IScheduledNode, String, IScheduledNode, String) - Method in class loci.multithreadedplugin.NodeScheduler: Chains the named data from one plugin to another.
chainNext(String, IPluginLauncher, String) - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Chains this plugin to the next one.
chainNext(String, IPluginLauncher, String) - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Chains this launcher to next one.
chainNext(ILinkedPlugin) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains default output of this node to default input of next.
chainNext(String, ILinkedPlugin) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains named output of this node to default input of next.
chainNext(ILinkedPlugin, String) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains default output of this node to named input of next.
chainNext(String, ILinkedPlugin, String) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains named output of this node to named output of next.
chainNext(String, IPluginLauncher, String) - Method in interface loci.multiinstanceplugin.IPluginLauncher: Chains this plugin to the next one.
chainNext(ILinkedPlugin) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains default output of this node to default input of next.
chainNext(String, ILinkedPlugin) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains named output of this node to default input of next.
chainNext(ILinkedPlugin, String) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains default output of this node to named input of next.
chainNext(String, ILinkedPlugin, String) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains named output of this node to named output of next.
chainNext(String, IPluginLauncher, String) - Method in class loci.multiinstanceplugin.PluginLauncher: Chains this launcher to next one.
chainNext(IScheduledNode) - Method in class loci.multithreadedplugin.AbstractNode: Chains default output of this node to default input of next node.
chainNext(String, IScheduledNode) - Method in class loci.multithreadedplugin.AbstractNode: Chains named output of this node to default input of next node.
chainNext(IScheduledNode, String) - Method in class loci.multithreadedplugin.AbstractNode: Chains default output of this node to named input of next node.
chainNext(String, IScheduledNode, String) - Method in class loci.multithreadedplugin.AbstractNode: Chains named output of this node to named input of next node.
chainNext(IScheduledNode) - Method in interface loci.multithreadedplugin.INode: Chains default output of this node to default input of next.
chainNext(String, IScheduledNode) - Method in interface loci.multithreadedplugin.INode: Chains named output of this node to default input of next.
chainNext(IScheduledNode, String) - Method in interface loci.multithreadedplugin.INode: Chains default output of this node to named input of next.
chainNext(String, IScheduledNode, String) - Method in interface loci.multithreadedplugin.INode: Chains named output of this node to named output of next.
chainPrevious(String, IPluginLauncher, String) - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Chains this plugin to the previous one.
chainPrevious(String, IPluginLauncher, String) - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Chains this launcher to previous one.
chainPrevious(ILinkedPlugin) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains default input of this node to default output of previous.
chainPrevious(String, ILinkedPlugin) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains named input of this node to default output of previous.
chainPrevious(ILinkedPlugin, String) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains default input of this node to named output of previous.
chainPrevious(String, ILinkedPlugin, String) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Chains named input of this node to named output of previous.
chainPrevious(String, IPluginLauncher, String) - Method in interface loci.multiinstanceplugin.IPluginLauncher: Chains this plugin to the previous one.
chainPrevious(ILinkedPlugin) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains default input of this node to default output of previous.
chainPrevious(String, ILinkedPlugin) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains named input of this node to default output of previous.
chainPrevious(ILinkedPlugin, String) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains default input of this node to named output of previous.
chainPrevious(String, ILinkedPlugin, String) - Method in class loci.multiinstanceplugin.LinkedPlugin: Chains named input of this node to named output of previous.
chainPrevious(String, IPluginLauncher, String) - Method in class loci.multiinstanceplugin.PluginLauncher: Chains this launcher to previous one.
chainPrevious(IScheduledNode) - Method in class loci.multithreadedplugin.AbstractNode: Chains default input of this node to default output of previous node.
chainPrevious(String, IScheduledNode) - Method in class loci.multithreadedplugin.AbstractNode: Chains named input of this node to default output of previous node.
chainPrevious(IScheduledNode, String) - Method in class loci.multithreadedplugin.AbstractNode: Chains default input of this node to named output of previous node.
chainPrevious(String, IScheduledNode, String) - Method in class loci.multithreadedplugin.AbstractNode: Chains named input of this node to named output of previous node.
chainPrevious(IScheduledNode) - Method in interface loci.multithreadedplugin.INode: Chains default input of this node to default output of previous.
chainPrevious(String, IScheduledNode) - Method in interface loci.multithreadedplugin.INode: Chains named input of this node to default output of previous.
chainPrevious(IScheduledNode, String) - Method in interface loci.multithreadedplugin.INode: Chains default input of this node to named output of previous.
chainPrevious(String, IScheduledNode, String) - Method in interface loci.multithreadedplugin.INode: Chains named input of this node to named output of previous.
CHANGED - Static variable in class de.sciss.jcollider.gui.NumberEvent: returned by getID() : the number changed
changed(int) - Method in class de.sciss.jcollider.Server
changedUpdate(DocumentEvent) - Method in class loci.slim.ColorWidget
changedUpdate(DocumentEvent) - Method in class loci.slim.SlimPlotter
changedUpdate(DocumentEvent) - Method in class loci.slim.TwoDPane
changedUpdate(DocumentEvent) - Method in class loci.visbio.overlays.OverlayWidget
changedUpdate(DocumentEvent) - Method in class loci.visbio.view.ColorPane: Handles text field changes.
changedUpdate(DocumentEvent) - Method in class loci.visbio.view.ViewPanel: Handles text field changes.
channels - Variable in class loci.slim.SlimData
CHAR_TYPE - Static variable in class loci.jvmlink.ConnThread
checkBoxes - Variable in class loci.visbio.overlays.StatsOptionsPane: All of the check boxes contained in all tabs.
checkCrash() - Method in class loci.visbio.state.StateManager: Saves an initial VisBio state, then checks to see if VisBio crashed last time, and if so, asks the user whether to restore the previous state.
checkFile(String) - Static method in class UnusedImports
checkMessage(Component, String, boolean, JPanel, String) - Method in class loci.visbio.state.OptionManager: Checks whether to display a message using the given panel, and does so if necessary.
checkMessage(Component, String, MessagePane) - Method in class loci.visbio.state.OptionManager: Checks whether to display a message using the given message pane, and does so if necessary.
checkout(ObjectId) - Method in class loci.backup.github.CreateOrphanBranchCommand
checkout(RevTree, RevTree) - Method in class loci.backup.github.CreateOrphanBranchCommand
checkoutStartPoint() - Method in class loci.backup.github.CreateOrphanBranchCommand
checkSave() - Method in class loci.visbio.state.StateManager: Checks whether the program state has been saved, and if not, prompts the user to save.
checkVisualization() - Method in class loci.visbio.help.HelpManager: Prompts user for whether to visualize the currently selected data object.
checkWarning(Component, String, boolean, String) - Method in class loci.visbio.state.OptionManager: Checks whether to display a warning with the given text, and does so if necessary.
children() - Method in class de.sciss.jcollider.Group
children() - Method in class de.sciss.jcollider.Synth
CHILL - Static variable in class loci.visbio.overlays.FreeformTool: Constant for "wait" mode.
chooseFile() - Static method in class loci.plugins.stitching.TileUtils: Prompts the user to choose a file.
chooseFont - Variable in class loci.visbio.overlays.OverlayWidget: Button for bringing up font chooser.
chooser - Static variable in class loci.visbio.util.SwingUtil
CIRC - Static variable in class loci.visbio.overlays.OverlayOval
classes() - Method in class loci.jar2lib.ClassList: Gets the list of Java classes.
ClassList - Class in loci.jar2lib: A ClassList is a list of Java classes from a particular JAR file.
ClassList(String) - Constructor for class loci.jar2lib.ClassList: Constructs a list of Java classes corresponding to those in the given JAR file.
className - Variable in class de.sciss.jcollider.UGenInfo: Name of the ugen class
CLASSNAME - Static variable in class loci.deepzoom.workflow.PluginModule
cleanMemory() - Method in class loci.visbio.SystemManager: Calls the Java garbage collector to free wasted memory.
clear() - Method in class de.sciss.jcollider.NodeWatcher: Removes all nodes from the list of known nodes.
clear() - Method in interface loci.chainableplugin.IPropertyCollection: Clears the map.
clear() - Method in class loci.chainableplugin.PropertyCollection: Clears all the properties.
clear() - Method in interface loci.deepzoom.workflow.IWorkFlow: Clears wiring.
clear() - Method in class loci.deepzoom.workflow.WorkFlow
clear() - Method in class loci.visbio.data.ThumbnailCache: Wipes the thumbnail disk cache.
clear() - Method in class loci.visbio.data.ThumbnailHandler: Clears thumbnails from memory, restarting background generation if auto-generation is enabled.
CLEAR - Static variable in class loci.visbio.util.ColorUtil: RealType for indicating nothing mapped to a color component.
clearWhenDone - Variable in class loci.visbio.view.TransformLink: Whether a TRANSFORM_DONE event should clear the status message.
clipboard - Variable in class loci.visbio.overlays.OverlayTransform: Clipboard stores overlays grabbed with the copy function.
clipboardPos - Variable in class loci.visbio.overlays.OverlayTransform: Dimensional position of overlays stored in the clipboard.
cloneMenuBar(JMenuBar) - Static method in class loci.visbio.util.SwingUtil: Creates a copy of this menu bar, whose contents update automatically whenever the original menu bar changes.
cloneMenuItem(JMenuItem) - Static method in class loci.visbio.util.SwingUtil: Creates a copy of this menu item, whose contents update automatically whenever the original menu item changes.
close() - Method in class de.sciss.jcollider.Buffer
close(OSCMessage) - Method in class de.sciss.jcollider.Buffer
close() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
close() - Method in class loci.visbio.data.Dataset: Close all open ids.
CLOSE_LOOP - Static variable in class loci.visbio.overlays.PolylineTool
closeAllWindows() - Static method in class loci.apps.flow.FlowCyto
CloseLine(int, int, int) - Method in interface loci.apps.flow.Find_Particle_Areas.MPFC_Ctrl
closeMsg() - Method in class de.sciss.jcollider.Buffer
closeMsg(OSCMessage) - Method in class de.sciss.jcollider.Buffer
collabName() - Static method in class loci.backup.github.ResumePoint
collapse(FlatField[], RealType[]) - Static method in class loci.visbio.data.CollapseTransform: Collapses the given fields.
collapse - Variable in class loci.visbio.data.CollapseWidget: Associated dimensional collapse transform.
collapse(FieldImpl) - Static method in class loci.visbio.util.DataUtil: Collapses a field from the form (z -> ((x, y) -> (v1, ..., vn))) into the form ((x, y, z) -> (v1, ..., vn)).
CollapseTransform - Class in loci.visbio.data: CollapseTransform converts a dimensional axis into a series of range components.
CollapseTransform() - Constructor for class loci.visbio.data.CollapseTransform: Creates an uninitialized dimensional collapse.
CollapseTransform(DataTransform, String, int) - Constructor for class loci.visbio.data.CollapseTransform: Creates a dimensional collapse from the given transform.
CollapseWidget - Class in loci.visbio.data: CollapseWidget is a set of GUI controls for a dimensional collapse transform.
CollapseWidget(CollapseTransform) - Constructor for class loci.visbio.data.CollapseWidget: Creates a new dimensional collapse widget.
collSelectedNodes - Variable in class de.sciss.jcollider.gui.NodeTreePanel
color - Variable in class loci.visbio.data.Dataset: Types mapped to color components (RGBA).
color - Variable in class loci.visbio.overlays.OverlayObject: Color of this overlay.
color - Variable in class loci.visbio.overlays.OverlayWidget: Button for choosing overlay color.
color - Variable in class loci.visbio.view.BioColorWidget: Label naming color component.
COLOR_DETAIL - Static variable in class loci.visbio.util.ColorUtil: Resolution of color tables.
COLOR_NAMES - Static variable in class loci.visbio.view.BioColorWidget: List of color component names.
ColorHandler - Class in loci.visbio.view: Provides logic for controlling a TransformLink's color settings.
ColorHandler(TransformLink) - Constructor for class loci.visbio.view.ColorHandler: Creates a color handler for the given transform link.
colorHandler - Variable in class loci.visbio.view.TransformLink: Associated handler for managing this link's color settings.
colorModel - Variable in class loci.visbio.view.ColorHandler: Color model (RGB_MODEL, HSV_MODEL or COMPOSITE_MODEL).
colorPane - Variable in class loci.visbio.view.ColorHandler: Dialog pane for adjusting color settings.
ColorPane - Class in loci.visbio.view: ColorPane is a dialog pane for adjusting color settings.
ColorPane(ColorHandler) - Constructor for class loci.visbio.view.ColorPane: Constructs a dialog for adjusting color parameters.
colorTables - Variable in class loci.visbio.view.ColorHandler: Color tables.
colorToHex(Color) - Static method in class loci.visbio.util.ColorUtil: Gets a hexidecimal representation for this color.
colorToString(Color) - Static method in class loci.visbio.util.ObjectUtil: Writes the given color object to the given output stream.
ColorUtil - Class in loci.visbio.util: ColorUtil contains useful color table functions.
ColorWidget - Class in loci.slim: VisAD color widget with min/max override and LUT buttons.
ColorWidget(ScalarMap) - Constructor for class loci.slim.ColorWidget
ColorWidget(ScalarMap, String) - Constructor for class loci.slim.ColorWidget
com.centerkey.utils - package com.centerkey.utils
commitComments() - Static method in class loci.backup.github.ResumePoint
compare(File, File) - Static method in class CompareTrees
compareTo(Object) - Method in class de.sciss.jcollider.UGenInfo
CompareTrees - Class in <Unnamed>: Compares the paths specified as command line arguments, outputting all differences between them (i.e., files and directories present in one path but not in the other).
CompareTrees() - Constructor for class CompareTrees
completion(Buffer) - Method in interface de.sciss.jcollider.Buffer.CompletionAction: Executes the completion action.
completion(Buffer) - Method in interface de.sciss.jcollider.Buffer.CompletionFunction: Queries the creation of the completion message.
completion(Bus, float[]) - Method in interface de.sciss.jcollider.Bus.GetCompletionAction: Executes the completion action.
completion(Server) - Method in interface de.sciss.jcollider.Server.CompletionAction: Requests the implementing class to perform any action it wishes.
componentHidden(ComponentEvent) - Method in class loci.visbio.util.Docker: Called when a window is hidden.
componentMoved(ComponentEvent) - Method in class loci.visbio.util.Docker: Called when a window is moved.
componentResized(ComponentEvent) - Method in class loci.visbio.util.Docker: Called when a window is resized.
components - Variable in class loci.slim.fit.CurveFitter
componentShown(ComponentEvent) - Method in class loci.visbio.util.Docker: Called when a window is shown.
composite - Variable in class loci.visbio.view.ColorPane: Color model options.
COMPOSITE_MODEL - Static variable in class loci.visbio.util.ColorUtil: Composite RGB color space model.
compute - Variable in class loci.visbio.data.ArbitrarySlice: Flag indicating whether arbitrary slice should actually be computed.
computeAlphaTable(int, int) - Static method in class loci.visbio.util.ColorUtil: Computes alpha table component from the given transparency settings.
computeColorTables(ScalarMap[], int, int, int, RealType, RealType, RealType) - Static method in class loci.visbio.util.ColorUtil: Computes color tables from the given color settings.
computeCorners(float, float, float, float, float, float) - Static method in class loci.visbio.overlays.OverlayLine: Helper method for computing coordinates of two corner points of the rectangular selection grid for a line or arrow overlay.
computeCursor() - Method in class loci.visbio.view.StackLink: Computes range values at the current cursor location.
computeCursor() - Method in class loci.visbio.view.TransformLink: Computes range values at the current cursor location.
computeCurves() - Method in class loci.slim.fit.CurveCollection: Computes subsamplings.
computeData(boolean) - Method in class loci.visbio.view.StackLink: Computes the reference data at the current position, utilizing thumbnails as appropriate.
computeData(boolean) - Method in class loci.visbio.view.TransformLink: Computes the reference data at the current position, utilizing thumbnails as appropriate.
computeDistance(Rectangle, Rectangle) - Method in class loci.visbio.util.Docker: Computes the distance rectangle A must snap to adjoin rectangle B.
computeDistance(Window, Window) - Method in class loci.visbio.util.Docker: Computes the distance window A must snap to adjoin window B.
computeDragDist(DisplayImpl, int, int) - Method in class loci.visbio.overlays.FreeformExtension: Computes distance between mouse drag and tip of extension.
computeFWHMs - Variable in class loci.slim.SlimData
computeLength() - Method in class loci.visbio.overlays.OverlayNodedObject: Computes length of curve.
computePtOnSegment(float[], float[], float) - Static method in class loci.visbio.util.MathUtil: Computes a point along the line segment a[]-b[] based on the parameter weight.
computeSnap(Window, Vector) - Method in class loci.visbio.util.Docker: Computes the X and Y distances the docked group should snap.
computeTextBounds() - Method in class loci.visbio.overlays.OverlayText
computeThumb(int[]) - Method in class loci.visbio.data.SamplingThumbHandler: Computes a thumbnail for the given dimensional position.
computeThumb(int[]) - Method in class loci.visbio.data.ThumbnailHandler: Computes a thumbnail for the given dimensional position.
configureOverlay(OverlayObject) - Method in class loci.visbio.overlays.OverlayTransform: Configures the given overlay to match the current settings.
configureScrollPane(JScrollPane) - Static method in class loci.visbio.util.SwingUtil: Configures a scroll pane's properties to always show horizontal and vertical scroll bars.
connectTo(OverlayFreeform) - Method in class loci.visbio.overlays.OverlayNodedObject: Creates a new freeform by connecting the tail of this freeform to the head of the freeform supplied.
ConnThread - Class in loci.jvmlink: Thread for managing a client/server socket connection.
ConnThread(Socket, JVMLinkServer) - Constructor for class loci.jvmlink.ConnThread
CONSOLE - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: create a console panel.
ConsoleManager - Class in loci.visbio: ConsoleManager is the manager encapsulating VisBio's console output logic.
ConsoleManager(VisBioFrame) - Constructor for class loci.visbio.ConsoleManager: Constructs an exit manager.
ConsoleStream(OutputStream) - Constructor for class loci.slim.fit.LMCurveFitter.ConsoleStream
Constant - Class in de.sciss.jcollider: A Constant is a wrapper for a constant in a UGen graph.
Constant(float) - Constructor for class de.sciss.jcollider.Constant
constant - Variable in class loci.visbio.view.ColorPane: Opacity model options.
CONSTANT_ALPHA - Static variable in class loci.visbio.util.ColorUtil: Constant alpha value transparency model.
Constants - Interface in de.sciss.jcollider: A utility interface that different classes can implements to gain access to commonly used constants.
constrain(double) - Method in class de.sciss.jcollider.gui.ControlSpec
ContiguousBlockAllocator - Class in de.sciss.jcollider: Quite a 1:1 translation from the SClang class written by James Harkins, this class is a robust allocator for busses in a dynamic environment.
ContiguousBlockAllocator(int) - Constructor for class de.sciss.jcollider.ContiguousBlockAllocator
ContiguousBlockAllocator(int, int) - Constructor for class de.sciss.jcollider.ContiguousBlockAllocator
ContiguousBlockAllocator.Factory - Class in de.sciss.jcollider
contrast - Variable in class loci.visbio.view.ColorHandler: Brightness and contrast of images.
contrast - Variable in class loci.visbio.view.ColorPane: Slider for level of contrast.
contrastValue - Variable in class loci.visbio.view.ColorPane: Label for current contrast value.
control(Server) - Static method in class de.sciss.jcollider.Bus
control(Server, int) - Static method in class de.sciss.jcollider.Bus
Control - Class in de.sciss.jcollider: Class for the Control UGen.
Control(String, Object, int, UGenInput[], int) - Constructor for class de.sciss.jcollider.Control
controlChanged(ScalarMapControlEvent) - Method in class loci.slim.ColorWidget
ControlDesc - Class in de.sciss.jcollider: A descriptor class for a control UGen, similar to SClang's ControlName class.
ControlDesc(String, Object, float, float) - Constructor for class de.sciss.jcollider.ControlDesc
ControlDesc(String, Object, float) - Constructor for class de.sciss.jcollider.ControlDesc
ControlPanel - Class in loci.visbio: ControlPanel is the superclass of all control panel types.
ControlPanel(LogicManager, String, String) - Constructor for class loci.visbio.ControlPanel: Constructs a control panel.
controls - Variable in class loci.visbio.data.ArbitrarySlice: Controls for the arbitrary slice.
controls - Variable in class loci.visbio.data.CollapseTransform: Controls for this dimensional collapse.
controls - Variable in class loci.visbio.data.DataSampling: Controls for this data sampling.
controls - Variable in class loci.visbio.data.Dataset: Controls for this dataset.
controls - Variable in class loci.visbio.data.ProjectionTransform: Controls for this maximum intensity projection.
controls - Variable in class loci.visbio.data.SpectralTransform: Controls for this spectral mapping.
controls - Variable in class loci.visbio.ext.ExternalFunction: Controls for this external function transform.
controls - Variable in class loci.visbio.overlays.OverlayTransform: Controls for creating overlays.
controls - Variable in class loci.visbio.view.DisplayWindow: Breakaway panel for display controls.
ControlSpec - Class in de.sciss.jcollider.gui: Specification for a control input such as a synth control.
ControlSpec() - Constructor for class de.sciss.jcollider.gui.ControlSpec
ControlSpec(double, double) - Constructor for class de.sciss.jcollider.gui.ControlSpec
ControlSpec(double, double, Warp) - Constructor for class de.sciss.jcollider.gui.ControlSpec
ControlSpec(double, double, Warp, double) - Constructor for class de.sciss.jcollider.gui.ControlSpec
ControlSpec(double, double, Warp, double, double) - Constructor for class de.sciss.jcollider.gui.ControlSpec
ControlSpec(double, double, Warp, double, double, String) - Constructor for class de.sciss.jcollider.gui.ControlSpec
convertRGBStackToRGB(ImagePlus) - Static method in class loci.deepzoom.DeepZoom: Converts a 2 or 3 slice 8-bit stack to RGB.
COORDS - Static variable in class loci.visbio.overlays.OverlayBox: The names of the statistics this object reports.
COORDS - Static variable in class loci.visbio.overlays.OverlayLine: The names of the statistics this object reports.
COORDS - Static variable in class loci.visbio.overlays.OverlayMarker: The names of the statistics this object reports.
COORDS - Static variable in class loci.visbio.overlays.OverlayOval: The names of the statistics this object reports.
COORDS - Static variable in class loci.visbio.overlays.OverlayText: The names of the statistics this object reports.
copy - Variable in class loci.visbio.overlays.OverlayWidget: Button for copying selected overlays to the clipboard.
copy(boolean[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given boolean array.
copy(byte[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given byte array.
copy(char[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given char array.
copy(double[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given double array.
copy(float[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given float array.
copy(int[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given int array.
copy(long[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given long array.
copy(short[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given short array.
copy(Object[]) - Static method in class loci.visbio.util.ObjectUtil: Creates a copy of the given array of objects.
copy(Object, Object) - Static method in class loci.visbio.util.ObjectUtil: Copies source array into destination array, returning destination.
copyFrom(Server.Status) - Static method in class de.sciss.jcollider.Server.Status
copySelectedObjects() - Method in class loci.visbio.overlays.OverlayTransform: Copies selected overlay objects at the current dimensional position to the clipboard.
copySelectedObjects(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Copies selected overlay objects at the given dimensional position to the clipboard.
copySourceFiles() - Method in class loci.jar2lib.Jar2Lib: Copies any extra C++ source files into the project directory.
cos - Static variable in class de.sciss.jcollider.gui.Warp
count - Variable in class loci.visbio.data.ThumbnailHandler: Number of thumbnails that have been generated.
count - Variable in class loci.visbio.view.BioSlideWidget: Number of ticks this slider has.
COUNTS - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: create a status panel for server CPU usage and number of nodes.
COUNTS - Static variable in class de.sciss.jcollider.ServerEvent: returned by getID() : the server status has been updated
CppWrapMojo - Class in loci.maven.plugin.cppwrap: Goal which creates a C++ project wrapping a Maven Java project.
CppWrapMojo() - Constructor for class loci.maven.plugin.cppwrap.CppWrapMojo
create(int) - Method in interface de.sciss.jcollider.BlockAllocator.Factory: Creates a new block allocator instance of the given size.
create(int, int) - Method in interface de.sciss.jcollider.BlockAllocator.Factory: Creates a new block allocator instance of the given size, with Bus indices starting at a given index.
create(int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator.Factory
create(int, int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator.Factory
create(int) - Method in class de.sciss.jcollider.PowerOfTwoAllocator.Factory
create(int, int) - Method in class de.sciss.jcollider.PowerOfTwoAllocator.Factory
create(String) - Method in interface loci.deepzoom.workflow.IModuleFactory: Creates a module from XML.
create(String) - Method in class loci.deepzoom.workflow.ModuleFactory: Creates a component from XML.
create(String) - Method in class loci.deepzoom.workflow.PluginModuleFactory: Creates a plugin module from XML.
create(String) - Method in class loci.deepzoom.workflow.WorkFlowFactory: Creates a workflow from XML.
createChild(Element, String) - Static method in class loci.visbio.util.XMLUtil: Appends a child element with the given name to the specified DOM element.
createCMakeLists(String, String, File[], String, List<String>) - Method in class loci.jar2lib.VelocityAutogen
createContext() - Static method in class loci.jar2lib.VelocityTools
createDataset(String, String, BioTask) - Method in class loci.visbio.data.DataManager: Creates a dataset, updating the given task object as things progress.
createDebugTimeCheckPoint(String) - Static method in class loci.apps.flow.FlowCyto
createDebugTimeStartPoint(String) - Static method in class loci.apps.flow.FlowCyto
createDisplay(Component, boolean) - Method in class loci.visbio.view.DisplayManager: Pops up a dialog allowing the user to create a new display.
createDisplay(Component, String, boolean) - Method in class loci.visbio.view.DisplayManager: Pops up a dialog allowing the user to create a new display, with the given default name.
createDocument(String) - Static method in class loci.visbio.util.XMLUtil: Creates a new DOM.
createEngine() - Static method in class loci.jar2lib.VelocityTools
createHandlers() - Method in class loci.visbio.view.DisplayWindow: Constructs logic handlers.
createIntSpace(int, int) - Static method in class de.sciss.jcollider.gui.NumberSpace: Utility method for creating a generic integer space for a given minimum and maximum value.
createJaceHeader(String, String) - Method in class loci.jar2lib.VelocityAutogen
CreateOrphanBranchCommand - Class in loci.backup.github: Git command to create a new orphan branch (no parent commets, an empty branch).
CreateOrphanBranchCommand(Repository) - Constructor for class loci.backup.github.CreateOrphanBranchCommand
createOverlay(String, OverlayTransform) - Static method in class loci.visbio.overlays.OverlayIO: Instantiates an overlay object of the given class.
createOverlay(String, OverlayTransform, int) - Static method in class loci.visbio.overlays.OverlayIO: Instantiates an overlay object of the given class.
createRatioMask() - Method in class loci.apps.flow.Find_Particle_Areas: Creates a ratio mask stack for both brightfield and intensity images.
createTask(String) - Method in class loci.visbio.TaskManager: Creates a new task with the given name.
createText(Element, String) - Static method in class loci.visbio.util.XMLUtil: Appends a text node with the given information to the specified DOM element.
CreateThumbnail - Class in <Unnamed>: This file is used in the 'publish' cron job.
CreateThumbnail() - Constructor for class CreateThumbnail
Credentials - Class in loci.wiscscan.auth: Data structure for managing secure Kerberos logins.
Credentials() - Constructor for class loci.wiscscan.auth.Credentials
cross2D(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Computes the cross product of two 2D vectors.
cSet - Variable in class loci.slim.SlimTypes
CTR - Static variable in class loci.visbio.overlays.OverlayBox
CTR - Static variable in class loci.visbio.overlays.OverlayOval
cType - Variable in class loci.slim.SlimTypes
cueSoundFile(Server, String) - Static method in class de.sciss.jcollider.Buffer
cueSoundFile(Server, String, long) - Static method in class de.sciss.jcollider.Buffer
cueSoundFile(Server, String, long, int) - Static method in class de.sciss.jcollider.Buffer
cueSoundFile(Server, String, long, int, int) - Static method in class de.sciss.jcollider.Buffer
cueSoundFile(Server, String, long, int, int, Buffer.CompletionFunction) - Static method in class de.sciss.jcollider.Buffer
cueSoundFile(String) - Method in class de.sciss.jcollider.Buffer
cueSoundFile(String, long) - Method in class de.sciss.jcollider.Buffer
cueSoundFile(String, long, OSCMessage) - Method in class de.sciss.jcollider.Buffer
cueSoundFileMsg(String, long, OSCMessage) - Method in class de.sciss.jcollider.Buffer
current - Variable in class loci.visbio.view.BioSlideWidget: Label indicating current slider value.
currentCurves - Variable in class loci.slim.fit.BurnInRenderer
currentFont - Variable in class loci.visbio.overlays.OverlayWidget: Text field indicating current font.
currentIterations - Variable in class loci.slim.fit.CurveRenderer
currentRCSE - Variable in class loci.slim.fit.CurveFitter
currentSlice - Variable in class loci.visbio.view.StackLink: Data transform's current slice.
currentX - Variable in class loci.slim.fit.CurveRenderer
currentY - Variable in class loci.slim.fit.CurveRenderer
currProgress - Variable in class loci.slim.fit.CurveRenderer
cursor - Variable in class loci.visbio.view.TransformLink: Range values for current cursor location, to be displayed in bottom left corner.
cursorToDomain(DisplayImpl, double[]) - Static method in class loci.slim.TwoDPane: Converts the given cursor coordinates to domain coordinates.
cursorToDomain(DisplayImpl, RealType[], double[]) - Static method in class loci.slim.TwoDPane: Converts the given cursor coordinates to domain coordinates.
curve(double) - Static method in class de.sciss.jcollider.gui.Warp
curveChanged(CurveEvent) - Method in interface loci.slim.fit.CurveListener
curveChanged(CurveEvent) - Method in class loci.slim.SlimData: Handles curve collection computation progress.
CurveCollection - Class in loci.slim.fit: Data structure for managing a collection of curves.
CurveCollection(int[][][], Class, int, int, int) - Constructor for class loci.slim.fit.CurveCollection: Creates an object to manage a collection of curves for the given data.
CurveCollection(ICurveFitter[][]) - Constructor for class loci.slim.fit.CurveCollection: Creates an object to manage the given collection of curves.
curved - Variable in class loci.visbio.view.ColorPane: Opacity model options.
CURVED_ALPHA - Static variable in class loci.visbio.util.ColorUtil: Polynomial alpha curve transparency model.
curveData - Variable in class loci.slim.fit.CurveFitter
curveData(BufferedReader) - Static method in class loci.slim.fit.CurveFitterTester
curveData - Variable in class loci.slim.fit.CurveRenderer
curveEstimate - Variable in class loci.slim.fit.CurveFitter
CurveEvent - Class in loci.slim.fit: CurveEvent is an event for reporting the status of curve collection generation.
CurveEvent(Object, int, int, String) - Constructor for class loci.slim.fit.CurveEvent: Constructs a curve event.
CurveFitter - Class in loci.slim.fit: Base class for curve fitting algorithms.
CurveFitter() - Constructor for class loci.slim.fit.CurveFitter
curveFitterClass - Variable in class loci.slim.SlimData
CurveFitterTester - Class in loci.slim.fit: Test class for curve fitting algorithms.
CurveFitterTester() - Constructor for class loci.slim.fit.CurveFitterTester
curveFixed - Variable in class loci.slim.fit.CurveFitter
curveLength - Variable in class loci.visbio.overlays.OverlayNodedObject: Length of curve of a noded object.
CurveListener - Interface in loci.slim.fit: CurveListener is the interface for being notified of curve events.
curveListeners - Variable in class loci.slim.fit.CurveCollection
CurveRenderer - Class in loci.slim.fit: Base class for curve renderer implementations.
CurveRenderer(CurveCollection) - Constructor for class loci.slim.fit.CurveRenderer
CurveReporter - Interface in loci.slim.fit: CurveReporter is the interface for reporting curve events to listeners.
curves - Variable in class loci.slim.fit.CurveCollection: Curve fit data, dimensioned [maxDepth][numRows][numCols].
curves - Variable in class loci.slim.SlimData: Per-pixel curve estimates, dimensioned [channels].
CustomOption - Class in loci.visbio.state: CustomOption is an option in the VisBio Options dialog.
CustomOption(Component) - Constructor for class loci.visbio.state.CustomOption: Constructs a new option.
cutBins - Variable in class loci.slim.SlimData
CutTilesProcessor - Class in loci.chainableplugin.deepzoom: A processor that takes an image and chops it up into tiles.
CutTilesProcessor() - Constructor for class loci.chainableplugin.deepzoom.CutTilesProcessor: Default constructor.
CutTilesProcessor(int, int, int) - Constructor for class loci.chainableplugin.deepzoom.CutTilesProcessor: Constructor to specify width, height, and overlap of tiles.
CutTilesProcessor - Class in loci.multiinstanceplugin.deepzoom: A processor that takes an image and chops it up into tiles.
CutTilesProcessor() - Constructor for class loci.multiinstanceplugin.deepzoom.CutTilesProcessor: Default constructor.
CutTilesProcessor(int, int, int) - Constructor for class loci.multiinstanceplugin.deepzoom.CutTilesProcessor: Constructor to specify width, height, and overlap of tiles.
cVisible - Variable in class loci.slim.SlimData

D

data - Variable in class loci.slim.SlimData: Actual data values, dimensioned [channel][row][column][bin].
data - Variable in class loci.visbio.data.ThumbnailHandler: Data transform on which this thumbnail handler operates.
DATA_CHANGED - Static variable in class loci.visbio.data.TransformEvent: Transform event indicating transform's data has changed.
DATA_REMOVED - Static variable in class loci.visbio.data.TransformEvent: Transform event indicating transform is being deleted.
DataCache - Class in loci.visbio.data: Provides a simple caching mechanism for full-resolution data in memory.
DataCache() - Constructor for class loci.visbio.data.DataCache: Constructs a cache for managing full-resolution data in memory.
dataColors - Variable in class loci.visbio.view.TransformPanel: Button for editing colors for the selected data transform.
DataControls - Class in loci.visbio.data: DataControls is the control panel for managing data.
DataControls(LogicManager) - Constructor for class loci.visbio.data.DataControls: Constructs a tool panel for adjusting data parameters.
dataControls - Variable in class loci.visbio.data.DataManager: Datasets control panel.
dataControls - Variable in class loci.visbio.view.TransformPanel: Button for showing controls for the selected data transform.
DataManager - Class in loci.visbio.data: DataManager is the manager encapsulating VisBio's data transform logic.
DataManager(VisBioFrame) - Constructor for class loci.visbio.data.DataManager: Constructs a dataset manager.
DataSampling - Class in loci.visbio.data: DataSampling is a resampling of another transform.
DataSampling() - Constructor for class loci.visbio.data.DataSampling: Creates an uninitialized data sampling.
DataSampling(DataTransform, String, int[], int[], int[], int, int, boolean[]) - Constructor for class loci.visbio.data.DataSampling: Creates a data sampling from the given transform.
Dataset - Class in loci.visbio.data: A Dataset object encompasses a multidimensional biological image series.
Dataset() - Constructor for class loci.visbio.data.Dataset: Constructs an uninitialized multidimensional data object.
Dataset(String, String) - Constructor for class loci.visbio.data.Dataset: Constructs a multidimensional data object.
Dataset(String, String, StatusListener) - Constructor for class loci.visbio.data.Dataset: Constructs a new multidimensional data object from the given file pattern.
dataset - Variable in class loci.visbio.data.DatasetWidget: Associated dataset.
DatasetWidget - Class in loci.visbio.data: DatasetWidget is a set of GUI controls for a Dataset transform.
DatasetWidget(Dataset) - Constructor for class loci.visbio.data.DatasetWidget: Constructs widget for display of dataset's associated metadata.
DataTransform - Class in loci.visbio.data: DataTransform is the superclass of all data transform types.
DataTransform() - Constructor for class loci.visbio.data.DataTransform: Constructs an uninitialized data transform.
DataTransform(DataTransform, String) - Constructor for class loci.visbio.data.DataTransform: Creates a data transform with the given transform as its parent.
DataUtil - Class in loci.visbio.util: DataUtil contains useful VisAD data functions.
date - Variable in class loci.niche.MODSForm
DATE - Static variable in class loci.visbio.VisBio: Application build date.
de.sciss.jcollider - package de.sciss.jcollider
de.sciss.jcollider.gui - package de.sciss.jcollider.gui
debug() - Method in class de.sciss.jcollider.ContiguousBlockAllocator
debug(String) - Method in class loci.jvmlink.JVMLinkServer
DEBUG - Static variable in class loci.slim.fit.CurveFitter
DEBUG - Static variable in class loci.slim.SlimPlotter
debug(String) - Static method in class loci.slim.SlimPlotter
DEBUG - Static variable in class loci.visbio.data.DataCache: Debugging flag.
DEBUG - Static variable in class loci.visbio.VisBioFrame: Debugging flag for event logic.
decode(String, int, int) - Static method in class Binary
deepFree() - Method in class de.sciss.jcollider.Group
deepFreeMsg() - Method in class de.sciss.jcollider.Group
DeepZoom - Class in loci.deepzoom: TODO
DeepZoom() - Constructor for class loci.deepzoom.DeepZoom
DeepZoomExporter - Class in loci.chainableplugin.deepzoom: TODO
DeepZoomExporter(boolean, boolean, String, String, String, String, int, int) - Constructor for class loci.chainableplugin.deepzoom.DeepZoomExporter: Creates an object to export a particular image.
DeepZoomExporter - Class in loci.multiinstanceplugin.deepzoom: TODO
DeepZoomExporter(boolean, boolean, String, String, String, String, int, int) - Constructor for class loci.multiinstanceplugin.deepzoom.DeepZoomExporter: Creates an instance to export a particular image.
DeepZoomExporter.LevelProcessorX - Class in loci.multiinstanceplugin.deepzoom: Inner class at the top of the image chain.
DeepZoomExporter.TileProcessorX - Class in loci.multiinstanceplugin.deepzoom: Inner class that chains from the CutTileProcessor.
def - Variable in class de.sciss.jcollider.UGenInfo.Arg: Allowed range of its value and default value.
DEFAULT - Static variable in annotation type loci.deepzoom.plugin.annotations.Input
DEFAULT - Static variable in annotation type loci.deepzoom.plugin.annotations.Output
DEFAULT - Static variable in interface loci.multithreadedplugin.INode: Default input/output data name if none is specified.
DEFAULT_ANIMATION_RATE - Static variable in class loci.visbio.view.TransformHandler: Starting FPS for animation.
DEFAULT_BURN_DELAY - Static variable in class loci.visbio.view.TransformHandler: Starting burn-in delay in milliseconds.
DEFAULT_EYE_SEPARATION - Static variable in class loci.visbio.view.DisplayManager: Default eye separation distance for stereo displays.
DEFAULT_FONT - Static variable in class loci.visbio.util.FontChooserPane: Default font.
DEFAULT_PORT - Static variable in class de.sciss.jcollider.Server: We just use the same default scsynth server port (57110) here as assumed by sclang
DEFAULT_PREVIEW_TEXT - Static variable in class loci.visbio.util.FontChooserPane: Default text used in font preview pane.
DEFAULT_PRIORITY - Static variable in class loci.visbio.util.Docker: Default window docking priority.
DEFAULT_ROTATION - Static variable in class loci.visbio.view.ViewHandler: Default rotation factor for 3D displays.
DEFAULT_STACK_RESOLUTION - Static variable in class loci.visbio.view.DisplayManager: Default maximum resolution for images in a stack.
DEFAULT_THUMBNAIL_RESOLUTION - Static variable in class loci.visbio.data.DataManager: Default resolution for low-resolution thumbnails.
DEFAULT_VOLUME_RESOLUTION - Static variable in class loci.visbio.view.StackHandler: Default length of each volume rendered spatial axis.
DEFAULT_ZOOM_2D - Static variable in class loci.visbio.view.ViewHandler: Default zoom factor for 2D displays.
DEFAULT_ZOOM_3D - Static variable in class loci.visbio.view.ViewHandler: Default zoom factor for 3D displays.
defaultSpec - Static variable in class de.sciss.jcollider.gui.ControlSpec
DEGREES - Static variable in class loci.visbio.data.SliceWidget: Character representing degrees symbol.
delayTime - Variable in class loci.visbio.view.TransformPanel: Spinner for adjusting burn-in delay.
deleteBetween(int, int) - Method in class loci.visbio.overlays.OverlayNodedObject: Deletes a range of nodes from the node array.
deleteNode(int) - Method in class loci.visbio.overlays.OverlayNodedObject: Deletes a node from the node array.
depth - Variable in class loci.slim.fit.CurveCollection: Total number of samplings, counting full-resolution image.
descs - Variable in class de.sciss.jcollider.Control
deselectAll() - Method in class loci.visbio.overlays.OverlayTool: Deselect all selected overlays.
destroy() - Method in class loci.visbio.state.StateManager: Deletes VisBio state temp file.
destroy() - Method in class loci.visbio.view.TransformLink: Frees resources being consumed by this transform link.
destroy() - Method in class loci.visbio.VisBioFrame: Cleans up and releases resources before abandoning this instance of VisBio.
dialog - Variable in class loci.visbio.util.DialogPane: Currently visible dialog.
DialogPane - Class in loci.visbio.util: DialogPane provides an extensible interface for creating dialogs with Ok and Cancel buttons.
DialogPane(String) - Constructor for class loci.visbio.util.DialogPane: Creates a dialog pane.
DialogPane(String, boolean) - Constructor for class loci.visbio.util.DialogPane: Creates a dialog pane.
didWeBootTheServer() - Method in class de.sciss.jcollider.Server: Returns true if the server was locally booted by this client.
die(String) - Method in class loci.jar2lib.Jar2Lib
dims - Variable in class loci.visbio.data.DataTransform: A list of what each dimension in the multidimensional structure means.
disableButtons() - Method in class loci.visbio.util.WizardPane: Disables wizard's buttons.
discard() - Method in class loci.visbio.data.DataTransform: Called when this object is being discarded in favor of another object with a matching state.
discard() - Method in class loci.visbio.overlays.OverlayTransform: Called when this object is being discarded in favor of another object with a matching state.
discard() - Method in interface loci.visbio.state.Dynamic: Called when this object is being discarded in favor of another object with a matching state.
discard() - Method in class loci.visbio.view.DisplayPosition: Called when this object is being discarded in favor of another object with a matching state.
discard() - Method in class loci.visbio.view.DisplayWindow: Called when this object is being discarded in favor of another object with a matching state.
discard() - Method in class loci.visbio.view.TransformLink: Called when this object is being discarded in favor of another object with a matching state.
dispatchEvent() - Method in class de.sciss.jcollider.gui.EZSlider
display - Variable in class loci.slim.MouseBehaviorButtons
display - Variable in class loci.visbio.view.DisplayWindow: Associated VisAD display.
DISPLAY_DATA - Static variable in class loci.visbio.help.HelpManager: String for displaying new data.
displayChanged(DisplayEvent) - Method in class loci.slim.TwoDPane
displayChanged(DisplayEvent) - Method in class loci.visbio.data.DataTransform: Whenever a display to which this transform is linked changes, the DisplayEvent is passed to this method so that the transform can adjust itself (i.e., is interactive).
displayChanged(DisplayEvent) - Method in class loci.visbio.overlays.OverlayTransform: Responds to mouse gestures with appropriate overlay interaction.
displayChanged(DisplayEvent) - Method in class loci.visbio.view.DisplayWindow: Listens for keyboard presses within the display.
displayChanged(DisplayEvent) - Method in class loci.visbio.view.TransformLink: Handles VisAD display events.
DisplayControls - Class in loci.visbio.view: DisplayControls is the control panel for managing displays.
DisplayControls(LogicManager) - Constructor for class loci.visbio.view.DisplayControls: Constructs a tool panel for adjusting data parameters.
displayControls - Variable in class loci.visbio.view.DisplayManager: Displays control panel.
displayError(Component, Exception, String) - Static method in class de.sciss.jcollider.JCollider: Displays an error message dialog by examining a given Exception.
displayErrorMessage(String) - Method in class loci.visbio.overlays.OverlayWidget: Displays an error message.
displayHelp() - Static method in class loci.slim.data.MakeData
displayList - Variable in class loci.visbio.view.DisplayControls: List of displays.
DisplayManager - Class in loci.visbio.view: DisplayManager is the manager encapsulating VisBio's 2D and 3D displays.
DisplayManager(VisBioFrame) - Constructor for class loci.visbio.view.DisplayManager: Constructs a display manager.
DisplayPosition - Class in loci.visbio.view: DisplayPosition represents an orientation of VisAD display.
DisplayPosition() - Constructor for class loci.visbio.view.DisplayPosition: Constructs an uninitialized display position.
DisplayPosition(String, double[]) - Constructor for class loci.visbio.view.DisplayPosition: Constructs a display position.
DisplayUtil - Class in loci.visbio.util: DisplayUtil contains useful VisAD display functions.
DisplayWindow - Class in loci.visbio.view: DisplayWindow is a window containing a 2D or 3D VisAD display and associated controls.
DisplayWindow() - Constructor for class loci.visbio.view.DisplayWindow: Creates an uninitialized display object.
DisplayWindow(DisplayManager) - Constructor for class loci.visbio.view.DisplayWindow: Creates an uninitialized display object.
DisplayWindow(DisplayManager, String, boolean) - Constructor for class loci.visbio.view.DisplayWindow: Creates a new display object according to the given parameters.
dispose() - Method in class de.sciss.jcollider.gui.NodeTreeManager: Disposes all resources associated with the tree manager.
dispose() - Method in class de.sciss.jcollider.gui.NodeTreePanel: Frees resources when the component is not used any more.
dispose() - Method in class de.sciss.jcollider.gui.ServerPanel: Call this method if the server isn't used any more or the panel's parent window is disposed.
dispose() - Method in class de.sciss.jcollider.NodeWatcher: Disposes any resources allocated by this representation.
dispose() - Method in class de.sciss.jcollider.OSCMultiResponder
dispose() - Method in class de.sciss.jcollider.Server: Disposes any resources allocated by this representation.
disposeWindow(Window) - Method in class loci.visbio.WindowManager: Removes the window from the window manager and disposes of it.
disposeWindows() - Method in class loci.visbio.WindowManager: Disposes all windows, prior to program exit.
dist - Variable in class loci.visbio.overlays.FreeformTool.DistanceQuery: The distance to the freeform.
dist - Variable in class loci.visbio.overlays.OverlayWidget: Button for distributing an overlay across all positions between the copied position and the one selected.
DistanceQuery(double[], OverlayFreeform) - Constructor for class loci.visbio.overlays.FreeformTool.DistanceQuery: Constructs a DistanceQuery object.
distributed - Variable in class loci.visbio.WindowManager: Whether to distribute the menu bar across all registered frames.
distributeObjects() - Method in class loci.visbio.overlays.OverlayTransform: Distributes one object per dimensional position linearly between the position of the overlay currently on the clipboard, and the one selected at the current dimensional position.
distributeObjects(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Distributes one object per dimensional position linearly between the position of the overlay currently on the clipboard, and the one selected at the given dimensional position.
DO_STEREO - Static variable in class loci.visbio.view.DisplayManager: String for stereo displays option.
doAlphas() - Method in class loci.visbio.view.ColorPane: Updates image transparencies, when settings are adjusted.
doAnimationPanel() - Method in class loci.visbio.view.TransformPanel: Creates a panel with animation-related components.
doAppearancePanel() - Method in class loci.visbio.view.ViewPanel: Creates a panel with appearance-related components.
doAspect(double, double, double) - Method in class loci.visbio.view.ViewHandler: Adjusts the aspect ratio.
doAspect() - Method in class loci.visbio.view.ViewPanel: Updates aspect ratio based on text field values.
doAspectPanel() - Method in class loci.visbio.view.ViewPanel: Creates a panel with aspect ratio-related components.
doButtonLayout() - Method in class loci.visbio.util.DialogPane: Performs button layout.
doButtonLayout() - Method in class loci.visbio.util.WizardPane: Internal method for doing button layout.
docBuilder - Static variable in class loci.visbio.util.XMLUtil: Document builder for creating DOMs.
dock(Window, Window) - Method in class loci.visbio.util.Docker: Docks window A to window B.
docked - Variable in class loci.visbio.util.Docker: For each window, the set of windows docked to it.
Docker - Class in loci.visbio.util: This class is used to specify a group of windows able to be docked to one another.
Docker() - Constructor for class loci.visbio.util.Docker
docker - Variable in class loci.visbio.WindowManager: Object enabling docking between windows.
DOCKING - Static variable in class loci.visbio.WindowManager: String for window docking option.
docking - Variable in class loci.visbio.WindowManager: Whether window docking features are enabled.
doColorRanges() - Method in class loci.visbio.view.ColorPane: Updates image color ranges, when settings are adjusted.
doColorTables() - Method in class loci.visbio.view.ColorPane: Updates image color tables, when settings are adjusted.
documentUpdate(DocumentEvent) - Method in class loci.visbio.overlays.OverlayWidget: Handles text field changes.
doCustomMaps() - Method in class loci.visbio.view.StackHandler: Adds any required custom mappings to the display.
doCustomMaps() - Method in class loci.visbio.view.TransformHandler: Adds any required custom mappings to the display.
doDataInfo(DataTransform) - Method in class loci.visbio.data.DataControls: Updates data information panel, and toggles button availability.
doDataPanel() - Method in class loci.visbio.view.TransformPanel: Creates a panel with data transform-related components.
doDataProperties() - Method in class loci.visbio.view.StackPanel: Creates a panel for controls pertaining to the selected data object.
doDataProperties() - Method in class loci.visbio.view.TransformPanel: Creates a panel for controls pertaining to the selected data object.
doEvent(VisBioEvent) - Method in class loci.visbio.ConsoleManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.data.DataManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.ExitManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.ext.ExtManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.help.HelpManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.LogicManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.overlays.OverlayManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.PanelManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.state.OptionManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.state.StateManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.SystemManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.TaskManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.view.DisplayManager: Called to notify the logic manager of a VisBio event.
doEvent(VisBioEvent) - Method in class loci.visbio.WindowManager: Called to notify the logic manager of a VisBio event.
doGUI() - Method in class loci.visbio.overlays.OverlayManager: Adds overlay-related GUI components to VisBio.
doGUI() - Method in class loci.visbio.view.DisplayManager: Adds display-related GUI components to VisBio.
doGUI() - Method in class loci.visbio.WindowManager: Adds window-related GUI components to VisBio.
doit() - Method in class loci.apps.MultiLUT
doLinks(int, boolean) - Method in class loci.visbio.view.TransformHandler: Links in the transform links, starting at the given index.
doMain(String...) - Method in class loci.backup.github.GitHubBackup: Instanced main method entry point.
doMenuBars(JMenuBar) - Method in class loci.visbio.WindowManager: Propagates the given menu bar across all registered frames.
doNewDisplay(boolean) - Method in class loci.visbio.data.DataControls: Creates a new display and adds the selected data object to it.
doNewDisplayWithOverlays() - Method in class loci.visbio.data.DataControls: Do new display with overlays
doOrientationPanel() - Method in class loci.visbio.view.ViewPanel: Creates a panel with orientation-related components.
dot(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Computes the dot product of two N-D vectors.
doTransform() - Method in class loci.visbio.view.StackLink: Updates the currently displayed data for the given transform.
doTransform() - Method in class loci.visbio.view.TransformLink: Updates displayed data based on current dimensional position.
doTransform(long) - Method in class loci.visbio.view.TransformLink: Updates displayed data based on current dimensional position.
doTransform(long, boolean) - Method in class loci.visbio.view.TransformLink: Updates displayed data based on current dimensional position.
DOUBLE_TYPE - Static variable in class loci.jvmlink.ConnThread
DoubleSlider - Class in loci.visbio: A slider widget for selecting a double-precision value between certain bounds.
DoubleSlider(double, double, double, double) - Constructor for class loci.visbio.DoubleSlider
doWeightedMapping(FlatField, RealType[], double[][]) - Static method in class loci.visbio.data.SpectralTransform: Applies a spectral mapping to the given field based on the given weights and range types.
DownloadURL - Class in <Unnamed>: A poor, barebones impression of wget.
DownloadURL() - Constructor for class DownloadURL
downX - Variable in class loci.visbio.overlays.FreeformTool: Point at which mouseDown occurs.
downY - Variable in class loci.visbio.overlays.FreeformTool: Point at which mouseDown occurs.
dr(String, int) - Static method in class de.sciss.jcollider.UGen: "dr" stands for demand-rate
dr(String) - Static method in class de.sciss.jcollider.UGen
dr(String, int, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, int, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, int, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, int, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, int, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
dr(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
DRAW - Static variable in class loci.visbio.overlays.FreeformTool: Consant for "draw" mode.
DRAW_THRESH - Static variable in class loci.visbio.overlays.FreeformExtension: When drawing or editing, how far mouse must be dragged before new node is added.
DRAW_THRESH - Static variable in class loci.visbio.overlays.FreeformTool: When drawing or editing, how far mouse must be dragged before new node is added.
DRAW_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: When drawing or editing, how far mouse must be dragged before new node is added.
drawing - Variable in class loci.visbio.overlays.OverlayObject: Flag indicating this overlay is still being initially drawn.
drawText - Variable in class loci.visbio.overlays.OverlayTransform: Whether to draw text.
DST - Static variable in class loci.deepzoom.workflow.WorkFlow
DUMMY - Static variable in class loci.visbio.view.StackLink: Dummy data to avoid "Data is null" message for volume reference.
DUMP - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: create a button to turning OSC dumping on/off.
dump(DataTransform, int[], String) - Method in class loci.visbio.data.DataCache: Removes the data object at the specified dimensional position from the cache.
dump(DataTransform, String) - Method in class loci.visbio.data.DataCache: Removes from the cache data objects at all dimensional positions for the given data object.
dump(String) - Method in class loci.visbio.data.DataCache: Removes the data object at the specified key from the cache.
dumpAll() - Method in class loci.visbio.data.DataCache: Removes everything from the cache.
DumpClass - Class in <Unnamed>: Uses reflection to print a bunch of information about a class.
DumpClass() - Constructor for class DumpClass
dumpIncomingOSC(int) - Method in class de.sciss.jcollider.NodeWatcher: Changes the way incoming messages are dumped to the console.
dumpIncomingOSC(int) - Method in class de.sciss.jcollider.Server: Changes the way incoming messages are dumped to the console.
dumpName() - Method in class de.sciss.jcollider.Constant
dumpName() - Method in class de.sciss.jcollider.UGen: Returns a string representation of the UGen.
dumpName() - Method in class de.sciss.jcollider.UGenChannel
dumpName() - Method in interface de.sciss.jcollider.UGenInput
dumpOSC() - Method in class de.sciss.jcollider.Server: Sends a message to the server requesting OSC dump (text format).
dumpOSC(int) - Method in class de.sciss.jcollider.Server: Sends a message to the server requesting OSC dumping being turned on or off
dumpOSCMsg(int) - Method in class de.sciss.jcollider.Server: Creates the OSC message which will ask the server to turn on or off OSC dumping
dumpOutgoingOSC(int) - Method in class de.sciss.jcollider.Server: Changes the way outgoing messages are dumped to the console.
DumpStack - Class in loci.plugins: Provides a complete stack dump of all threads.
DumpStack() - Constructor for class loci.plugins.DumpStack
dumpTree(PrintStream, TreeNode) - Static method in class de.sciss.jcollider.gui.NodeTreeManager: Dumps a list of nodes to the given stream.
Dynamic - Interface in loci.visbio.state: The Dynamic interface provides methods for testing whether two objects have the same state, and for synchronizing states if they do not.

E

ECC - Static variable in class loci.visbio.overlays.OverlayOval
edge - Variable in class loci.visbio.util.BreakawayPanel: The edge upon which the breakaway panel lies.
edges - Variable in class loci.visbio.util.Docker: Whether to snap to the edges of the screen.
EDIT - Static variable in class loci.visbio.overlays.FreeformTool: Constant for "edit" mode.
EDIT_THRESH - Static variable in class loci.visbio.overlays.FreeformTool: Threshhold within which click must occur to invoke edit mode.
EDIT_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: Threshhold within which click must occur to invoke edit mode.
EditDistance - Class in <Unnamed>: Computes minimum edit distance between two strings.
EditDistance() - Constructor for class EditDistance
editRedo - Variable in class loci.visbio.state.StateManager: The Redo menu item from the Edit menu.
editRedo() - Method in class loci.visbio.state.StateManager: Redoes the last action undone.
editReset() - Method in class loci.visbio.state.StateManager: Resets the program to its initial state.
editUndo - Variable in class loci.visbio.state.StateManager: The Undo menu item from the Edit menu.
editUndo() - Method in class loci.visbio.state.StateManager: Undoes the last action taken.
enableButtons() - Method in class loci.visbio.util.WizardPane: Enables wizard's buttons.
enabled - Variable in class loci.visbio.util.Docker: Whether to perform docking operations at all.
enc_this - Variable in class de.sciss.jcollider.gui.NumberField
enc_this - Variable in class de.sciss.jcollider.gui.ServerPanel
enc_this - Variable in class de.sciss.jcollider.Server
END - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the node was destroyed
end - Variable in class loci.visbio.view.SliceToggler: Ending slice index.
equals(Object) - Method in class de.sciss.jcollider.Bus
equals(Object) - Method in class de.sciss.jcollider.Node: Two nodes are equal if they reside on the same server and have the same node ID.
ERASE - Static variable in class loci.visbio.overlays.FreeformTool: Constant for "erase" mode.
ERASE_THRESH - Static variable in class loci.visbio.overlays.FreeformTool: How close a mouseDrag event must be to a node in order to erase it.
ERASE_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: How close a mouseDrag event must be to a node in order to erase it.
eraseNearestNodeWithin(float, float, float) - Method in class loci.visbio.overlays.FreeformTool: Erases the nearest node of freeforms nearby.
estimate() - Method in class loci.slim.fit.CurveFitter: Initializes the curve fitter with a starting curve estimate.
estimate() - Method in interface loci.slim.fit.ICurveFitter: Initializes the curve fitter with a starting curve estimate.
estimate() - Method in class loci.slim.fit.LMCurveFitter
evaluate(FlatField, String[]) - Method in class loci.visbio.ext.ExternalFunction: Evaluates the function for the given input data and parameter values.
evaluate(FlatField, String[]) - Method in class loci.visbio.ext.ExternalProgram: Evaluates the function for the given input data and parameter values.
evaluate(FlatField, String[]) - Method in class loci.visbio.ext.MatlabFunction: Evaluates the function for the given input data and parameter values.
evaluate(String, FlatField, double[], RealType[]) - Static method in class loci.visbio.ext.MatlabUtil: Evaluates the given MATLAB function for the specified field, passing the given extra parameters to the function.
exec(ImagePlus, ImagePlus, float, int, int, int, int, int, float, float, float, int) - Method in class loci.apps.SlideScannerImport.SIFT_ExtractPointRoi: If unsure, just use default parameters by using exec(ImagePlus, ImagePlus, int) method, where only the model is specified.
exec(ImagePlus, ImagePlus, int) - Method in class loci.apps.SlideScannerImport.SIFT_ExtractPointRoi: Execute with default parameters, except the model.
exec(ImagePlus, ImagePlus) - Method in class loci.apps.SlideScannerImport.SIFT_ExtractPointRoi: Execute with default parameters (model is Rigid)
EXEC - Static variable in class loci.jvmlink.ConnThread
exec(String, FlatField, double[]) - Static method in class loci.visbio.ext.MatlabUtil: Executes the given MATLAB function, with the specified field and parameters as arguments.
execute() - Method in class loci.backup.github.GitHubBackupMojo
execute() - Method in class loci.backup.github.HelpMojo
execute() - Method in class loci.jar2lib.Jar2Lib: Generates a C++ wrapper project based on the current settings.
execute() - Method in class loci.maven.plugin.cppwrap.CppWrapMojo
EXIT - Static variable in class loci.jvmlink.ConnThread
ExitManager - Class in loci.visbio: ExitManager is the manager encapsulating VisBio's shutdown logic.
ExitManager(VisBioFrame) - Constructor for class loci.visbio.ExitManager: Constructs an exit manager.
exp - Static variable in class de.sciss.jcollider.gui.Warp
EXP_FUNCTIONS - Static variable in class loci.slim.fit.LMCurveFitter
EXP_WEIGHTS - Static variable in class loci.slim.fit.LMCurveFitter
EXP_X_VALS - Static variable in class loci.slim.fit.LMCurveFitter
expandTree(JTree, DefaultMutableTreeNode) - Static method in class loci.visbio.util.SwingUtil: Fully expands the given JTree from the specified node.
ExpFunction(int) - Constructor for class loci.slim.fit.LMCurveFitter.ExpFunction: Constructs a function with the given number of summed exponentials.
export() - Method in class loci.visbio.data.ExportPane: Exports the data according to the current input parameters.
export - Variable in class loci.visbio.overlays.OverlayWidget: Button for exporting overlays to .xls on disk.
ExportAsText - Class in loci.plugins: TODO
ExportAsText() - Constructor for class loci.plugins.ExportAsText
exportData() - Method in class loci.slim.SlimPlotter: Exports fit data to a user-specified file.
exportData(ImageTransform) - Method in class loci.visbio.data.DataControls: Exports a data object to disk.
exportData() - Method in class loci.visbio.data.DataManager: Exports the selected data object to disk.
exportData(ImageTransform) - Method in class loci.visbio.data.DataManager: Exports the given data object to disk.
exportOverlays(OverlayTransform) - Static method in class loci.visbio.overlays.OverlayIO: Saves overlays to a .xls workbook.
exportOverlays() - Method in class loci.visbio.overlays.OverlayTransform: Exports the overlays as .xls to the given output file.
ExportPane - Class in loci.visbio.data: ExportPane provides a full-featured set of options for exporting a multidimensional data series from VisBio to several different formats.
ExportPane(VisBioFrame) - Constructor for class loci.visbio.data.ExportPane: Creates a multidimensional data export dialog.
extend(float[]) - Method in class loci.visbio.overlays.FreeformExtension: Extends the tip of the freeform extension by "one" node.
EXTEND - Static variable in class loci.visbio.overlays.PolylineTool
EXTEND_ON_TAIL - Static variable in class loci.visbio.overlays.PolylineTool
extendOrReconnect(DisplayImpl, float, float, int, int, boolean) - Method in class loci.visbio.overlays.FreeformExtension: Extends the extension, reconnecting it with the curve proper if appropriate.
ExternalFunction - Class in loci.visbio.ext: ExternalFunction is an abstract transform that calls some form of external function.
ExternalFunction() - Constructor for class loci.visbio.ext.ExternalFunction: Creates an uninitialized external function transform.
ExternalFunction(DataTransform, String, String) - Constructor for class loci.visbio.ext.ExternalFunction: Creates an external function transform from the given transform.
ExternalProgram - Class in loci.visbio.ext: ExternalProgram is a transform that uses system calls to an external program to evaluate a function, using stdin and stdout for binary data transfer.
ExternalProgram() - Constructor for class loci.visbio.ext.ExternalProgram: Creates an uninitialized external program transform.
ExternalProgram(DataTransform, String, String) - Constructor for class loci.visbio.ext.ExternalProgram: Creates an external program transform from the given transform.
externalPut(String, ItemWrapper) - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Used to initiate a plugin chain.
externalPut(String, ItemWrapper) - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Initiates a plugin chain by feeding a named image to this launcher's plugin.
externalPut(ImageWrapper) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Used to put default image from outside the plugin.
externalPut(String, ImageWrapper) - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Used to put named image from outside the plugin.
externalPut(String, ImageWrapper) - Method in interface loci.multiinstanceplugin.IPluginLauncher: Used to initiate a plugin chain.
externalPut(ImageWrapper) - Method in class loci.multiinstanceplugin.LinkedPlugin: Used to put default image from outside the plugin.
externalPut(String, ImageWrapper) - Method in class loci.multiinstanceplugin.LinkedPlugin: Used to put named image from outside the plugin.
externalPut(String, ImageWrapper) - Method in class loci.multiinstanceplugin.PluginLauncher: Initiates a plugin chain by feeding a named image to this launcher's plugin.
externalPut(Object) - Method in class loci.multithreadedplugin.AbstractNode: Feeds an image to the default input of the subclass.
externalPut(String, Object) - Method in class loci.multithreadedplugin.AbstractNode: Feeds an image to a named input of the subclass.
externalPut(Object) - Method in interface loci.multithreadedplugin.INode: Used to put default data from outside the node.
externalPut(String, Object) - Method in interface loci.multithreadedplugin.INode: Used to put named data from outside the node.
ExtManager - Class in loci.visbio.ext: ExtManager is the manager encapsulating VisBio's support for external software interfaces (e.g., external programs or MATLAB).
ExtManager(VisBioFrame) - Constructor for class loci.visbio.ext.ExtManager: Constructs an external interface manager.
extractDimensionsFromBFReader() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
extractDimensionsFromBFReader(int) - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
extractDimensionsFromOMEXML() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
extractDimensionsFromOMEXML(int) - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
extractImage(FlatField) - Static method in class loci.visbio.util.ImageJUtil: Converts a VisAD FlatField of the form ((x, y) -> (r1, ..., rn)) to an ImageJ ImageProcessor object.
extractImage(FlatField, Component) - Static method in class loci.visbio.util.ImageJUtil: Converts a VisAD FlatField of the form ((x, y) -> (r1, ..., rn)) to an ImageJ ImageProcessor object.
extractXMLasDOM() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
extractXMLasString() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
EYE_DISTANCE - Static variable in class loci.visbio.view.DisplayManager: String for eye separation setting.
EZSlider - Class in de.sciss.jcollider.gui: Something similar to SClang's EZSlider: a combo of horizontal slider, number box and label.
EZSlider() - Constructor for class de.sciss.jcollider.gui.EZSlider

F

Factory() - Constructor for class de.sciss.jcollider.ContiguousBlockAllocator.Factory
Factory() - Constructor for class de.sciss.jcollider.PowerOfTwoAllocator.Factory
file - Variable in class loci.visbio.data.ThumbnailCache: File containing thumbnail cache data.
fileBox - Variable in class loci.visbio.view.ColorPane: LUT file chooser.
fileExit() - Method in class loci.visbio.ExitManager: Exits the application, allowing all logic managers to take appropriate actions before doing so.
FileOpsTest - Class in <Unnamed>: Tests performance of File.exists() vs File.listFiles().
FileOpsTest() - Constructor for class FileOpsTest
fileOptions() - Method in class loci.visbio.state.OptionManager: Brings up the options dialog box.
fileRestore() - Method in class loci.visbio.state.StateManager: Restores the current state from a text file specified by the user.
fileSave() - Method in class loci.visbio.state.StateManager: Saves the current state to a text file specified by the user.
fill(int, int, float) - Method in class de.sciss.jcollider.Buffer
fill(int[], int[], float[]) - Method in class de.sciss.jcollider.Buffer
fill(float) - Method in class de.sciss.jcollider.Bus
fill(int, int, float) - Method in class de.sciss.jcollider.Bus
fill(int[], float[]) - Method in class de.sciss.jcollider.Bus
fill(int[], int[], float[]) - Method in class de.sciss.jcollider.Bus
fill(String[], int[], float[]) - Method in class de.sciss.jcollider.Node: Sets ranges of the node's control parameters to new values.
fill(int[], int[], float[]) - Method in class de.sciss.jcollider.Node: Sets ranges of the node's control parameters to new values.
filled - Variable in class loci.visbio.overlays.OverlayObject: Flag indicating overlay is solid.
filled - Variable in class loci.visbio.overlays.OverlayWidget: Check box indicating whether overlay should be filled or hollow.
fillMsg(int, int, float) - Method in class de.sciss.jcollider.Buffer
fillMsg(int[], int[], float[]) - Method in class de.sciss.jcollider.Buffer
fillMsg(float) - Method in class de.sciss.jcollider.Bus
fillMsg(int, int, float) - Method in class de.sciss.jcollider.Bus
fillMsg(int[], float[]) - Method in class de.sciss.jcollider.Bus
fillMsg(int[], int[], float[]) - Method in class de.sciss.jcollider.Bus
fillMsg(String[], int[], float[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_fill message to adjust ranges of the node's control parameters to new values.
fillMsg(int[], int[], float[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_fill message to adjust ranges of the node's control parameters to new values.
fillTemplate(String, Module) - Method in class loci.niche.TemplateFiller: Populates the template specified by the given resource, using the input values from the given module instance.
filter(PrintStream) - Static method in class loci.slim.fit.LMCurveFitter
filterMatch(String, String[]) - Static method in class SysProps
finalize() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
finalize() - Method in interface loci.deepzoom.workflow.IWorkFlow: Leftover, un-wired module inputs and outputs become workflow inputs and outputs.
finalize() - Method in class loci.deepzoom.workflow.WorkFlow
Find_Particle_Areas - Class in loci.apps.flow: ImageJ plugin to isolate cell particles in images and image stacks.
Find_Particle_Areas() - Constructor for class loci.apps.flow.Find_Particle_Areas
Find_Particle_Areas(ImagePlus, ImagePlus, ImagePlus, String, double, double, int, boolean, boolean) - Constructor for class loci.apps.flow.Find_Particle_Areas
Find_Particle_Areas.MPFC_Ctrl - Interface in loci.apps.flow
findEnclosingJar(Class<?>) - Static method in class loci.jar2lib.Jar2Lib: Finds the JAR file (or file system path) from which the given class was loaded.
findNode(DataTransform) - Method in class loci.visbio.data.DataControls: Finds the tree node representing this data object.
findParticles(ImagePlus, boolean, boolean) - Method in class loci.apps.flow.Find_Particle_Areas
fireCurveEvent(CurveEvent) - Method in class loci.slim.fit.CurveCollection
fireCurveEvent(CurveEvent) - Method in interface loci.slim.fit.CurveReporter
fireNumberChanged() - Method in class de.sciss.jcollider.gui.NumberField
first - Variable in class loci.visbio.WindowInfo: True if the window has not yet been shown onscreen.
firstIndex - Variable in class loci.slim.fit.CurveFitter
firstName - Variable in class loci.niche.MODSForm
fitness - Variable in class loci.slim.fit.GACurveFitter
fitValue(double) - Method in class de.sciss.jcollider.gui.NumberSpace: Validates a value for this number space.
fitValue(double, double, double, double) - Static method in class de.sciss.jcollider.gui.NumberSpace: Validates a value for an ad-hoc number space.
fixConflicts() - Method in class loci.jar2lib.Jar2Lib: Post-processes the generated proxies to correct any conflicts identified in the specified conflicts file.
fixed - Variable in class loci.visbio.view.ColorHandler: Flags indicating color ranges should not be auto-scaled.
fixed - Variable in class loci.visbio.view.ColorPane: Option for fixed color scaling.
FixEOLSpaces - Class in <Unnamed>: Scans text files for end-of-line spaces or tabs, and multiple consecutive blank lines, and removes them.
FixEOLSpaces() - Constructor for class FixEOLSpaces
fixEscaped(String) - Static method in class loci.jar2lib.StringReplace
fixLibraryPaths() - Method in class loci.jar2lib.Jar2Lib: Converts "\\" to "/" in all library paths, making them platform safe for CMakeLists.txt files
FixProxies - Class in loci.jar2lib: FixProxies is a program to post-process Jace-generated proxies.
FixProxies(String) - Constructor for class loci.jar2lib.FixProxies
fixProxies(String) - Method in class loci.jar2lib.FixProxies
flatten(UGenInput[][]) - Static method in class de.sciss.jcollider.GraphElemArray
FLOAT_TYPE - Static variable in class loci.jvmlink.ConnThread
floatsToPixelDoubles(DisplayImpl, float[][]) - Static method in class loci.visbio.overlays.OverlayUtil: Casts and converts an array of floats in domain coordinates to doubles in pixel coordinates.
FlowCyto - Class in loci.apps.flow
FlowCyto() - Constructor for class loci.apps.flow.FlowCyto
fntBigName - Static variable in class de.sciss.jcollider.gui.ServerPanel: Font used for server name box.
fntConsole - Static variable in class de.sciss.jcollider.gui.ServerPanel: Font used for the text console.
fntGUI - Static variable in class de.sciss.jcollider.gui.ServerPanel: Font used for the GUI elements (buttons).
fntToolTip - Static variable in class de.sciss.jcollider.gui.SynthDefDiagram
fntUGen - Static variable in class de.sciss.jcollider.gui.SynthDefDiagram
font - Variable in class loci.visbio.data.DataTransform: Font used for this transform's text mappings.
FONT_CHANGED - Static variable in class loci.visbio.data.TransformEvent: Transform event indicating transform's font has changed.
fontBold - Variable in class loci.visbio.util.FontChooserPane: Checkbox for indicating font should be in bold face.
FontChooserPane - Class in loci.visbio.util: FontChooser is a dialog for graphical font selection.
FontChooserPane() - Constructor for class loci.visbio.util.FontChooserPane: Creates a new font chooser pane.
FontChooserPane(Font) - Constructor for class loci.visbio.util.FontChooserPane: Creates a new font chooser pane with the given initial font.
FontChooserPane(String) - Constructor for class loci.visbio.util.FontChooserPane: Creates a new font chooser pane with the given preview text.
FontChooserPane(Font, String) - Constructor for class loci.visbio.util.FontChooserPane: Creates a new font chooser apne with the given initial font and preview text.
fontItalic - Variable in class loci.visbio.util.FontChooserPane: Checkbox for indicating font should be in italics.
fontMetrics - Variable in class loci.visbio.overlays.OverlayTransform: Font metrics for the current font.
fontName - Variable in class loci.visbio.util.FontChooserPane: Dropdown combo box containing available font names.
fontSize - Variable in class loci.visbio.util.FontChooserPane: Spinner for selecting font size.
formatConst(float) - Static method in class de.sciss.jcollider.gui.SynthDefDiagram
FormsUtil - Class in loci.visbio.util: FormsUtil contains useful JGoodies Forms functions.
foundParticle(boolean, boolean, double, int, float, float, double) - Static method in class loci.apps.flow.FlowCyto
fps - Variable in class loci.visbio.view.CapturePanel: Output movie frames per second.
fps - Variable in class loci.visbio.view.TransformHandler: Animation rate.
fps - Variable in class loci.visbio.view.TransformPanel: Spinner for adjusting animation rate.
fracDigitsFromQuant(double) - Static method in class de.sciss.jcollider.gui.NumberSpace
free(int) - Method in interface de.sciss.jcollider.BlockAllocator: Frees a bus, that is makes it available again for new re-allocation.
free() - Method in class de.sciss.jcollider.Buffer
free(OSCMessage) - Method in class de.sciss.jcollider.Buffer
free() - Method in class de.sciss.jcollider.Bus
free(int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator
free() - Method in class de.sciss.jcollider.Node: Frees the node on the server.
free(int) - Method in class de.sciss.jcollider.PowerOfTwoAllocator
freeAll(Server) - Static method in class de.sciss.jcollider.Buffer: Frees all known buffers on a server.
freeAll() - Method in class de.sciss.jcollider.Group
freeAllMsg() - Method in class de.sciss.jcollider.Group
freeBuf(int) - Method in class de.sciss.jcollider.Server: For internal use by Buffer objects.
freeform - Variable in class loci.visbio.overlays.FreeformExtension: The freeform to which this extension is attached.
freeform - Variable in class loci.visbio.overlays.FreeformTool.DistanceQuery: The nearest freeform itself.
freeform - Variable in class loci.visbio.overlays.FreeformTool: Curve currently being drawn or modified.
FreeformExtension - Class in loci.visbio.overlays: The FreeformExtension class wraps information for the temporary section of a freeform, which appears like a tendril on screen, created during an edit of an existing freeform.
FreeformExtension(OverlayFreeform, int, int, boolean) - Constructor for class loci.visbio.overlays.FreeformExtension: Constructs a new freeform extension.
freeformExtension - Variable in class loci.visbio.overlays.FreeformTool: FreeformExtension wraps info about an edit to a curve.
FreeformTool - Class in loci.visbio.overlays: FreeformTool is the tool for creating freeform objects.
FreeformTool(OverlayTransform) - Constructor for class loci.visbio.overlays.FreeformTool: Constructs a freeform creation tool.
FreeformTool.DistanceQuery - Class in loci.visbio.overlays: Wraps information about the distance from a point to a freeform object.
freeMsg() - Method in class de.sciss.jcollider.Buffer
freeMsg(OSCMessage) - Method in class de.sciss.jcollider.Buffer
freeMsg() - Method in class de.sciss.jcollider.Node: Creates an OSC /n_free message for the node.
frmtZoom - Static variable in class de.sciss.jcollider.gui.SynthDefDiagram
fromOSCMessage(OSCMessage, Object, long, Node) - Static method in class de.sciss.jcollider.NodeEvent: Constructs a NodeEvent from a valid node notification OSC message.
fromOSCMessage(OSCMessage, Object, long) - Static method in class de.sciss.jcollider.NodeEvent
fromXML(String) - Method in interface loci.deepzoom.workflow.IModule: Restores module from XML string representation.
fromXML(String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Restores chained components from XML string representation.
fromXML(String) - Method in class loci.deepzoom.workflow.PluginModule: Restores component from XML string representation.
fromXML(String) - Method in class loci.deepzoom.workflow.WorkFlow
function - Variable in class loci.visbio.ext.ExternalFunction: The name of the external function to execute.
function - Variable in class loci.visbio.ext.FunctionWidget: Associated external function transform.
FunctionParam - Class in loci.visbio.ext: FunctionParam is a name/value pair for a function parameter.
FunctionParam(String, String) - Constructor for class loci.visbio.ext.FunctionParam: Constructs a new function parameter with the given name and default value.
FunctionWidget - Class in loci.visbio.ext: FunctionWidget is a set of GUI controls for an ExternalFunction transform.
FunctionWidget(ExternalFunction) - Constructor for class loci.visbio.ext.FunctionWidget

G

GACurveFitter - Class in loci.slim.fit: Genetic algorithm for exponential curve fitting.
GACurveFitter() - Constructor for class loci.slim.fit.GACurveFitter
GAP - Static variable in class loci.visbio.WindowInfo: Gap between cascading windows.
gap - Static variable in class loci.visbio.WindowInfo: Current gap from top left edge of screen.
garbageCollect() - Static method in class loci.apps.flow.FlowCyto
gc() - Static method in class loci.visbio.SystemManager: Does some garbage collection, to free up memory.
generateDeepZoom(String, String, String, int, int) - Static method in class loci.deepzoom.DeepZoom: Warning: this method is a hack upon a hack (upon a hack).
generateEvent(Object, String, boolean) - Method in class loci.visbio.VisBioFrame: Generates a state change event.
generateEvent(VisBioEvent) - Method in class loci.visbio.VisBioFrame: Generates an event and notifies all linked logic managers.
generateHeaders() - Method in class loci.jar2lib.Jar2Lib: Generates one header per input Java library.
generateProxies() - Method in class loci.jar2lib.Jar2Lib: Generates the C++ proxy classes enumerated in the C++ headers.
generateSkeleton() - Method in class loci.jar2lib.Jar2Lib: Copies static project resources into the project directory.
genericDoubleSpace - Static variable in class de.sciss.jcollider.gui.NumberSpace: Ready-made NumberField for double values, without boundaries.
genericIntSpace - Static variable in class de.sciss.jcollider.gui.NumberSpace: Ready-made NumberField for integer values, without boundaries.
geneticData - Variable in class loci.slim.fit.GACurveFitter
get(Bus.GetCompletionAction) - Method in class de.sciss.jcollider.Bus
get(int, Bus.GetCompletionAction) - Method in class de.sciss.jcollider.Bus
get(int[], Bus.GetCompletionAction) - Method in class de.sciss.jcollider.Bus
get(int) - Method in class de.sciss.jcollider.Synth: Queries the current value of a synth control.
get(int[]) - Method in class de.sciss.jcollider.Synth: Queries different current values of a synth control.
get(String) - Method in class de.sciss.jcollider.Synth: Queries the current value of a synth control.
get(String[]) - Method in class de.sciss.jcollider.Synth: Queries different current values of a synth control.
get(String) - Method in interface loci.chainableplugin.IPropertyCollection: Gets the value for a string
get(String) - Method in class loci.chainableplugin.PropertyCollection: Gets a value.
get() - Method in class loci.deepzoom.workflow.plugin.AbstractPlugin: Gets the default input image from previous in chain.
get(String) - Method in class loci.deepzoom.workflow.plugin.AbstractPlugin: Gets a named input image from previous in chain.
get() - Method in interface loci.deepzoom.workflow.plugin.IPlugin: Gets the default input image from previous in chain.
get(String) - Method in interface loci.deepzoom.workflow.plugin.IPlugin: Gets a named input image from previous in chain.
get(String) - Method in class loci.deepzoom.workflow.plugin.PluginScheduler: Gets image for fully-qualified name.
get() - Method in class loci.multiinstanceplugin.AbstractPlugin: Gets the default input image from previous in chain.
get(String) - Method in class loci.multiinstanceplugin.AbstractPlugin: Gets a named input image from previous in chain.
get() - Method in interface loci.multiinstanceplugin.IPlugin: Gets the default input image from previous in chain.
get(String) - Method in interface loci.multiinstanceplugin.IPlugin: Gets a named input image from previous in chain.
get(String) - Method in class loci.multiinstanceplugin.PluginScheduler: Gets image for fully-qualified name.
get() - Method in class loci.multithreadedplugin.AbstractNode: Gets the default input data from previous in chain.
get(String) - Method in class loci.multithreadedplugin.AbstractNode: Gets a named input image from previous in chain.
get() - Method in interface loci.multithreadedplugin.INode: Used within the run method.
get(String) - Method in interface loci.multithreadedplugin.INode: Used within the run method.
get(String) - Method in class loci.multithreadedplugin.NodeScheduler: Gets data for destination node + name.
get(String) - Static method in enum loci.plugins.stitching.StitchOmeTiff.FusionMethod
get(String) - Static method in enum loci.plugins.stitching.StitchPrairieTiff.FusionMethod
getActiveC() - Method in class loci.slim.TwoDPane
getActiveColor() - Method in class loci.visbio.overlays.OverlayWidget: Gets currently active overlay color.
getActiveDisplay() - Method in class loci.visbio.overlays.TransientSelectBox: Returns the display on which this TSB exists.
getActiveGroup() - Method in class loci.visbio.overlays.OverlayWidget: Gets currently active overlay group.
getActiveTool() - Method in class loci.visbio.overlays.OverlayWidget: Gets the currently selected overlay tool.
getAddr() - Method in class de.sciss.jcollider.Server: Returns the address which is assumed to be the one at which the server listens
getAddress() - Method in interface de.sciss.jcollider.BlockAllocator.Block: Queries the address or index of the block.
getAll() - Method in interface loci.chainableplugin.IPropertyCollection: Gets the map of all associations.
getAll() - Method in class loci.chainableplugin.PropertyCollection: Gets the entire string/object map.
getAllNodes() - Method in class de.sciss.jcollider.NodeWatcher: Queries a list of all registered nodes.
getAllocatedBlocks() - Method in interface de.sciss.jcollider.BlockAllocator: Queries a list of allocated blocks.
getAllocatedBlocks() - Method in class de.sciss.jcollider.ContiguousBlockAllocator
getAllocatedBlocks() - Method in class de.sciss.jcollider.PowerOfTwoAllocator
getAllowsChildren() - Method in class de.sciss.jcollider.Group
getAllowsChildren() - Method in class de.sciss.jcollider.Synth
getAngle() - Method in class loci.visbio.overlays.OverlayArrow: Computes the angle of this arrow.
getAnimationAxis() - Method in class loci.visbio.view.TransformHandler: Gets the currently assigned animation axis.
getAnimationRate() - Method in class loci.visbio.view.TransformHandler: Gets animation rate.
getArgNameForInput(UGen, int) - Method in class de.sciss.jcollider.UGenInfo: Returns the name for one of the ugens inputs.
getArguments() - Method in class loci.visbio.util.SpawnEvent: Gets the arguments passed from the spawned application instance.
getArrowLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes selection layer for OverlayArrow objects.
getAspectX() - Method in class loci.visbio.view.ViewHandler: Gets aspect ratio X component.
getAspectY() - Method in class loci.visbio.view.ViewHandler: Gets aspect ratio Y component.
getAspectZ() - Method in class loci.visbio.view.ViewHandler: Gets aspect ratio Z component.
getAudioBusAllocator() - Method in class de.sciss.jcollider.Server: Automatic audio bus allocator for package internal use only.
getAutoThumbGen() - Method in class loci.visbio.data.DataManager: Gets whether low-resolution thumbnails should be automatically generated from VisBio options.
getAvailableLookAndFeels() - Static method in class loci.visbio.util.LAFUtil: Gets list of available look and feels, taking some OS-specific look and feels into account.
getAxis() - Method in class loci.visbio.data.ArbitrarySlice: Gets the axis through which to slice.
getAxis(DataTransform, int) - Method in class loci.visbio.view.TransformHandler: Identifies the dimensional axis of the given transform to which the specified slider axis corresponds, or -1 if none.
getAxisCount() - Method in class loci.visbio.view.TransformPanel: Gets number of registered dimensional axes.
getBinaryOnlyXML(String, String) - Static method in class loci.wiscscan.OMEXMLhelper: Extracts only the OME-XML header and UUID for partial metadata block in OME-XML metadata population in images.
getBlockAllocFactory() - Method in class de.sciss.jcollider.ServerOptions
getBlockSize() - Method in class de.sciss.jcollider.ServerOptions
getBlue() - Method in class loci.visbio.view.ColorHandler: Gets RealType mapped to blue.
getBlue() - Method in class loci.visbio.view.ColorPane: Gets current blue RealType.
getBoxLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes selection layer for OverlayBox objects.
getBoxTip() - Static method in class loci.visbio.state.SpreadsheetOptionStrategy: Returns the checkbox tool tip for the spreadsheet option.
getBranchName() - Method in class loci.backup.github.CreateOrphanBranchCommand
getBrightness() - Method in class loci.visbio.view.ColorHandler: Gets brightness value.
getBrightness() - Method in class loci.visbio.view.ColorPane: Gets current brightness value.
getBufferAllocator() - Method in class de.sciss.jcollider.Server: Automatic buffer ID allocator for package internal use only.
getBufNum() - Method in class de.sciss.jcollider.Buffer: Queries the buffer's index.
getBurnDelay() - Method in class loci.visbio.view.TransformHandler: Gets the delay in milliseconds before full-resolution burn-in occurs.
getButtonTip() - Static method in class loci.visbio.state.SpreadsheetOptionStrategy: Returns the button tip for the spreadsheet option.
getCache() - Method in class loci.visbio.data.ThumbnailHandler: Gets the associated thumbnail disk cache object.
getCache() - Method in class loci.visbio.view.TransformHandler: Gets cache of full-resolution data in memory.
getCachedData(String) - Method in class loci.visbio.data.DataCache: Gets the data in the cache at the specified key.
getCacheFile() - Method in class loci.visbio.data.ThumbnailCache: Gets the disk cache file.
getCacheId(int[], boolean) - Method in class loci.visbio.data.ArbitrarySlice: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.CollapseTransform: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.DataSampling: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.Dataset: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.DataTransform: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.ProjectionTransform: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.data.SpectralTransform: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.ext.ExternalFunction: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCacheId(int[], boolean) - Method in class loci.visbio.overlays.OverlayTransform: Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
getCaptureHandler() - Method in class loci.visbio.view.DisplayWindow: Gets the capture handler.
getChannel(String) - Method in class de.sciss.jcollider.Control
getChannel(int) - Method in class de.sciss.jcollider.UGen
getChannel() - Method in class de.sciss.jcollider.UGenChannel: Returns the index in the array of outputs of the corresponding UGen (beginning at zero).
getChildAt(int) - Method in class de.sciss.jcollider.Group
getChildAt(int) - Method in class de.sciss.jcollider.Synth
getChildCount() - Method in class de.sciss.jcollider.Group
getChildCount() - Method in class de.sciss.jcollider.Synth
getChildren(Element, String) - Static method in class loci.visbio.util.XMLUtil: Retrieves the given DOM element's child elements with the specified name.
getChiSquaredError() - Method in class loci.slim.fit.CurveFitter: Returns the Chi Squared Error of the current curve estimate.
getChiSquaredError(double[][]) - Method in class loci.slim.fit.CurveFitter
getChiSquaredError() - Method in interface loci.slim.fit.ICurveFitter: Returns the Chi Squared Error of the current curve estimate.
getChiSquaredError(double[][]) - Method in interface loci.slim.fit.ICurveFitter
getClasspathJars() - Method in class loci.jar2lib.Jar2Lib
getClearAction() - Method in class de.sciss.jcollider.gui.LogTextArea
getClickCoordinates() - Method in class loci.apps.SlideScannerImport.MouseClickListener
getClientID() - Method in class de.sciss.jcollider.Server: Queries the client ID used for allocating node IDs.
getClipboardContents() - Method in class loci.slim.TextTransfer
getClipHi() - Method in class de.sciss.jcollider.gui.ControlSpec
getClipLo() - Method in class de.sciss.jcollider.gui.ControlSpec
getClosestFreeform(DisplayImpl, double, double, double) - Method in class loci.visbio.overlays.FreeformTool: Returns the closest (subject to a threshhold) OverlayFreeform object to the given point.
getColor() - Method in class loci.visbio.overlays.OverlayObject: Gets color of this overlay.
getColorHandler() - Method in class loci.visbio.view.TransformLink: Gets the link's color handler.
getColorMode() - Method in class loci.visbio.view.ColorPane: Gets current color model.
getColorModel() - Method in class loci.visbio.view.ColorHandler: Gets color model (RGB_MODEL, HSV_MODEL or COMPOSITE_MODEL).
getColorPane() - Method in class loci.visbio.view.ColorHandler: Gets GUI control pane for this color handler.
getCommand(int) - Static method in class loci.jvmlink.ConnThread
getCommandName() - Method in class de.sciss.jcollider.OSCResponderNode: Queries the name which is used as the message filter
getComponent() - Method in class loci.visbio.state.BioOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.BooleanOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.CustomOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.ListOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.NumericOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.ResolutionOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.ResolutionToggleOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.SpreadsheetLaunchOption: Gets a GUI component representing this option.
getComponent() - Method in class loci.visbio.state.StringOption: Gets a GUI component representing this option.
getComponentCount() - Method in class loci.slim.fit.CurveFitter: Returns the number of exponentials to be fitted.
getComponentCount() - Method in interface loci.slim.fit.ICurveFitter: Returns the number of exponentials to be fitted.
getConflicts() - Method in class loci.backup.github.CreateOrphanBranchCommand
getConflictsPath() - Method in class loci.jar2lib.Jar2Lib
getContent() - Method in class loci.deepzoom.util.xmllight.XMLTag: Gets the content of the tag.
getContentPane() - Method in class loci.visbio.util.BreakawayPanel: Gets pane to which GUI components can be added.
getContrast() - Method in class loci.visbio.view.ColorHandler: Gets contrast value.
getContrast() - Method in class loci.visbio.view.ColorPane: Gets current contrast value.
getControlBusAllocator() - Method in class de.sciss.jcollider.Server: Automatic control bus allocator for package internal use only.
getControls() - Method in class loci.visbio.data.ArbitrarySlice: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.CollapseTransform: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.DataManager: Gets associated control panel.
getControls() - Method in class loci.visbio.data.DataSampling: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.Dataset: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.DataTransform: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.ProjectionTransform: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.data.SpectralTransform: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.ext.ExternalFunction: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.overlays.OverlayTransform: Gets associated GUI controls for this transform.
getControls() - Method in class loci.visbio.SystemManager: Gets associated control panel.
getControls() - Method in class loci.visbio.TaskManager: Gets associated control panel.
getControls() - Method in class loci.visbio.view.DisplayManager: Gets associated control panel.
getControls() - Method in class loci.visbio.view.DisplayWindow: Gets associated breakaway control panel.
getCopyrightString() - Static method in class de.sciss.jcollider.JCollider: Returns a copyright information string about the library
getCorePath() - Method in class loci.jar2lib.Jar2Lib
getCornersDomain() - Method in class loci.visbio.overlays.TransientSelectBox: Gets domain coordinates of box corners Corners are returned as a double[4][2].
getCreditsString() - Static method in class de.sciss.jcollider.JCollider: Returns a license and website information string about the library
getCurrentIterations() - Method in class loci.slim.fit.CurveRenderer
getCurrentIterations() - Method in interface loci.slim.fit.ICurveRenderer
getCurrentIterations() - Method in class loci.slim.fit.RendererSwitcher
getCurrentProgress() - Method in class loci.slim.fit.CurveRenderer
getCurrentProgress() - Method in interface loci.slim.fit.ICurveRenderer
getCurrentProgress() - Method in class loci.slim.fit.RendererSwitcher
getCurrentSlice() - Method in class loci.visbio.view.StackLink: Gets the current slice index, assuming the currently assigned stack axis.
getCurrentX() - Method in class loci.slim.fit.CurveRenderer
getCurrentX() - Method in interface loci.slim.fit.ICurveRenderer
getCurrentX() - Method in class loci.slim.fit.RendererSwitcher
getCurrentY() - Method in class loci.slim.fit.CurveRenderer
getCurrentY() - Method in interface loci.slim.fit.ICurveRenderer
getCurrentY() - Method in class loci.slim.fit.RendererSwitcher
getCurve() - Method in class loci.slim.fit.CurveFitter: Returns the current curve estimate.
getCurve() - Method in interface loci.slim.fit.ICurveFitter: Returns the current curve estimate.
getCurveCollection() - Method in class loci.slim.fit.CurveRenderer
getCurveCollection() - Method in interface loci.slim.fit.ICurveRenderer
getCurveCollection() - Method in class loci.slim.fit.RendererSwitcher
getCurveCollections() - Method in class loci.slim.fit.RendererSwitcher
getCurveFitters() - Method in class loci.slim.TwoDPane: Gets the curve fitter for each spectral channel at the current ROI coordinates.
getCurveLength() - Method in class loci.visbio.overlays.OverlayNodedObject: Gets length of curve.
getCurveRenderers() - Method in class loci.slim.fit.RendererSwitcher
getCurves() - Method in class loci.slim.fit.CurveCollection: Gets the collection of curves at full resolution.
getCurves(int) - Method in class loci.slim.fit.CurveCollection: Gets the collection of curves subsampled at the given depth.
getData() - Method in class loci.slim.fit.CurveFitter: Gets the data to be used to generate curve estimates.
getData() - Method in interface loci.slim.fit.ICurveFitter: Gets the data to be used to generate curve estimates.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.ArbitrarySlice: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.CollapseTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(DataTransform, int[], String, int) - Method in class loci.visbio.data.DataCache: Gets the data object from the cache, computing it if the cache misses.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.DataTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.ImageTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.ProjectionTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.data.SpectralTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.ext.ExternalFunction: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData() - Method in class loci.visbio.overlays.OverlayArrow: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayBox: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayLine: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayMarker: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayNodedObject: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayObject: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayOval: Gets VisAD data object representing this overlay.
getData() - Method in class loci.visbio.overlays.OverlayText: Gets VisAD data object representing this overlay.
getData(TransformLink, int[], int, DataCache) - Method in class loci.visbio.overlays.OverlayTransform: Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
getData() - Method in class loci.visbio.overlays.TransientSelectBox: Returns a VisAD data object representing this box.
getDataById(int) - Method in class loci.visbio.data.DataManager: Gets the data transform with the associated ID.
getDataList() - Method in class loci.visbio.data.DataManager: Gets a list of data transforms present in the tree.
getDataRoot() - Method in class loci.visbio.data.DataControls: Gets the root node of the data object tree.
getDataRoot() - Method in class loci.visbio.data.DataManager: Gets the root node of the data object tree.
getDebug() - Method in class loci.jvmlink.JVMLinkServer
getDefaultApplicationPath() - Static method in class loci.visbio.overlays.SpreadsheetLauncher: Returns the default spreadsheet application path for the current OS.
getDefaultGroup() - Method in class de.sciss.jcollider.Server: Returns the "default" group of the server.
getDefaultTokens() - Method in class loci.checks.BlankLinesCheck
getDefaultVal() - Method in class de.sciss.jcollider.gui.ControlSpec
getDefaultValue() - Method in class de.sciss.jcollider.ControlDesc
getDefaultWidth() - Method in class loci.visbio.overlays.OverlayMarker: Returns the defualt width of this marker.
getDefName() - Method in class de.sciss.jcollider.Synth
getDesc(int) - Method in class de.sciss.jcollider.Control
getDevice() - Method in class de.sciss.jcollider.ServerOptions
getDimensions(String, int, int, int, double[]) - Static method in class loci.visbio.ext.MatlabUtil: Gets output pixel dimensions for the given input dimensions and parameter values.
getDimTypes() - Method in class loci.visbio.data.DataTransform: Gets string descriptors for each dimensional axis type.
getDisplay() - Method in class loci.visbio.OrthoStack
getDisplay() - Method in class loci.visbio.view.DisplayWindow: Gets the associated VisAD display.
getDisplayName(UGen) - Method in class de.sciss.jcollider.UGenInfo: Returns a string ready to display to the user.
getDisplays() - Method in class loci.visbio.view.DisplayControls: Gets the current list of displays.
getDisplays() - Method in class loci.visbio.view.DisplayManager: Gets the current list of displays.
getDisplayWindow(DisplayImpl) - Static method in class loci.visbio.view.DisplayWindow: Figures out which DisplayWindow contains the given display, if any.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayArrow: Computes the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayBox: Computes the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayLine: Computes the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayMarker: Computes the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayNodedObject: Compute the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayObject: Computes the shortest distance from this overlay to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayOval: Computes the shortest distance from this object to the given point.
getDistance(double, double) - Method in class loci.visbio.overlays.OverlayText: Computes the shortest distance from this object to the given point.
getDistance(double[], double[], double[]) - Static method in class loci.visbio.util.MathUtil: Gets the distance between the points p and q, using the given conversion values between pixels and microns.
getDistance(double[], double[], double[], boolean) - Static method in class loci.visbio.util.MathUtil: Computes the minimum distance between the point v and the line a-b.
getDistance(double[], double[]) - Static method in class loci.visbio.util.MathUtil: Computes the minimum distance between the point p and the point v.
getDistance(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Computes the minimum distance between the point p and the point v in double precision.
getDistanceToBoundingBox(double, double) - Method in class loci.visbio.overlays.OverlayNodedObject: Computes the shortest distance from this object's bounding box to the given point.
getDistanceToSection(float[][], DisplayImpl, double, double) - Method in class loci.visbio.overlays.FreeformExtension: Computes distance between a point and a section of the freeform.
getDistSegWt(double[][], double, double) - Static method in class loci.visbio.util.MathUtil: Gets distance to a curve of points connected by straight line segments.
getDistSegWt(float[][], float, float) - Static method in class loci.visbio.util.MathUtil: Gets distance to a curve of points connected by straight line segments.
getDockSet(int) - Method in class loci.visbio.util.Docker: Gets the set of docked windows for the window at the specified index.
getDockSet(Window) - Method in class loci.visbio.util.Docker: Gets the set of docked windows for the given window.
getDomainType() - Method in class loci.visbio.overlays.OverlayTransform: Gets domain type (XY).
getDoubleValue() - Method in class loci.visbio.DoubleSlider
getDrawThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the drawing threshold.
getDumpMode() - Method in class de.sciss.jcollider.Server: Queries the current OSC dumping mode.
getDuration() - Method in class de.sciss.jcollider.Buffer: Queries the buffer's duration in seconds.
getEdge() - Method in class loci.visbio.util.BreakawayPanel: Gets the edge upon which the breakaway panel lies.
getEditDistance(String, String) - Static method in class EditDistance
getEditThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the editing threshold.
getElement(int) - Method in class de.sciss.jcollider.GraphElemArray
getEraseThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the erasing threshold.
getEstimates(double[][]) - Method in class loci.slim.fit.CurveFitter
getEstimates(double[][]) - Method in interface loci.slim.fit.ICurveFitter
getEventType() - Method in class loci.visbio.VisBioEvent: Gets the type of this event.
getException() - Method in exception loci.visbio.state.SaveException: Gets the exception upon which this save exception is based.
getExtrasPath() - Method in class loci.jar2lib.Jar2Lib
getFileFormat() - Method in class loci.visbio.data.Dataset: Gets a description of the source files' file format.
getFilenames() - Method in class loci.visbio.data.Dataset: Gets filenames of all files in dataset.
getFireAllNodes() - Method in class de.sciss.jcollider.NodeWatcher: Queries the event dispatching mode.
getFirst() - Method in class loci.slim.fit.CurveFitter
getFirst() - Method in interface loci.slim.fit.ICurveFitter
getFirstCalibration(IMetadata) - Static method in class loci.plugins.stitching.TileUtils: Creates a Calibration object using the first valid physical sizes X, Y and Z across all series in the provided Metadata.
getFirstChild(Element, String) - Static method in class loci.visbio.util.XMLUtil: Retrieves the given DOM element's first child element with the specified name.
getFirstPrivateBus() - Method in class de.sciss.jcollider.ServerOptions: Utility method to return the audio bus offset for the first bus which is not connected to audio hardware interface channels.
getFixed() - Method in class loci.slim.fit.CurveCollection: Gets which parameters should be fixed, versus allowed to converge.
getFixed() - Method in class loci.slim.fit.CurveFitter
getFixed() - Method in class loci.slim.fit.CurveRenderer
getFixed() - Method in interface loci.slim.fit.ICurveFitter: For each parameter, gets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.
getFixed() - Method in interface loci.slim.fit.ICurveRenderer
getFixed() - Method in class loci.slim.fit.RendererSwitcher
getFixed() - Method in class loci.visbio.view.ColorHandler: Gets whether each color mapping has a fixed range.
getFixed() - Method in class loci.visbio.view.ColorPane: Gets whether each color table has a fixed color range.
getFlags() - Method in class de.sciss.jcollider.gui.NumberField
getFloatingValue() - Method in class loci.visbio.state.NumericOption: Gets this option's current setting as a double-precision floating point value.
getFont() - Method in class loci.visbio.data.DataTransform: Gets the font used for this transform's text mappings.
getFontMetrics() - Method in class loci.visbio.overlays.OverlayTransform: Gets font metrics for the current font.
getFPS() - Method in class loci.visbio.view.CaptureHandler: Gets movie frames per second.
getFPS() - Method in class loci.visbio.view.CapturePanel: Gets movie frames per second.
getFreeforms(boolean) - Method in class loci.visbio.overlays.FreeformTool: Compiles a list of other freeforms at the current dimensional position.
getFullSlideImage() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getFullSlideImage() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getGreen() - Method in class loci.visbio.view.ColorHandler: Gets RealType mapped to green.
getGreen() - Method in class loci.visbio.view.ColorPane: Gets current green RealType.
getGroup() - Method in class de.sciss.jcollider.Node: Queries the group in which the node resides.
getGroup() - Method in class loci.visbio.overlays.OverlayObject: Gets group to which this overlay belongs.
getHandler() - Method in class loci.visbio.view.TransformLink: Gets the link's transform handler.
getHardwareBufferSize() - Method in class de.sciss.jcollider.ServerOptions
getHeaderPath() - Method in class loci.jar2lib.Jar2Lib
getHeadNode() - Method in class de.sciss.jcollider.Group
getHeadNodeID() - Method in class de.sciss.jcollider.NodeEvent
getHeight() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the height of the image.
getHeight() - Method in class loci.visbio.WindowState: Gets window height.
getHi() - Method in class loci.visbio.view.ColorHandler: Gets color mapping maximums.
getHi() - Method in class loci.visbio.view.ColorPane: Gets color table range maximums.
getHighlightedNodeIndex() - Method in class loci.visbio.overlays.OverlayNodedObject: Returns index of highlighted node.
getHTMLDescription() - Method in class loci.visbio.data.DataSampling: Gets a description of this transform, with HTML markup.
getHTMLDescription() - Method in class loci.visbio.data.Dataset: Gets a description of this dataset, with HTML markup.
getHTMLDescription() - Method in class loci.visbio.data.DataTransform: Gets a description of this transform, with HTML markup.
getHTMLDescription() - Method in class loci.visbio.data.ImageTransform: Gets a description of this transform, with HTML markup.
getIcon() - Method in class loci.visbio.overlays.OverlayTool: Gets path to icon file.
getIcon() - Method in class loci.visbio.VisBioFrame: Gets VisBio program icon.
getId() - Method in class loci.visbio.data.TransformEvent: Gets the type of transform event.
getIDFromOSCMessage(OSCMessage) - Static method in class de.sciss.jcollider.NodeEvent: Queries the event ID which would be used if the event was generated from a provided OSC message.
getImage() - Method in class loci.slim.fit.BurnInRenderer
getImage() - Method in class loci.slim.fit.CurveRenderer
getImage() - Method in interface loci.slim.fit.ICurveRenderer
getImage() - Method in class loci.slim.fit.RendererSwitcher
getImage(int[]) - Method in class loci.visbio.data.DataSampling: Obtains an image from the source(s) at the given dimensional position.
getImage(int[]) - Method in class loci.visbio.data.Dataset: Obtains an image from the source(s) at the given dimensional position.
getImage(int[]) - Method in class loci.visbio.data.ImageTransform: Obtains an image from the source(s) at the given dimensional position.
getImageData(int[]) - Method in class loci.visbio.view.StackLink: Gets 2D data from the specified data transform.
getImageData(int[]) - Method in class loci.visbio.view.TransformLink: Gets the transform's data at the given dimensional position.
getImageHeight() - Method in class loci.visbio.data.CollapseTransform: Gets height of each image.
getImageHeight() - Method in class loci.visbio.data.DataSampling: Gets height of each image.
getImageHeight() - Method in class loci.visbio.data.Dataset: Gets height of each image.
getImageHeight() - Method in class loci.visbio.data.ImageTransform: Gets the height in pixels of each image.
getImageHeight() - Method in class loci.visbio.data.ProjectionTransform: Gets height of each image.
getImageHeight() - Method in class loci.visbio.data.SpectralTransform: Gets height of each image.
getImageHeight() - Method in class loci.visbio.ext.ExternalFunction: Gets height of each image.
getImagePixels(FlatField) - Static method in class loci.visbio.ext.MatlabUtil: Gets pixel values from the given field, converting the result to a 3D array of double-precision floating point values.
getImagePlus() - Method in class loci.visbio.OrthoStack
getImageProcessor() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the underlying ImageJ ImageProcessor.
getImageUnits() - Method in class loci.visbio.data.ImageTransform: Gets X and Y units for use with image domain sets, computed from micron information.
getImageWidth() - Method in class loci.visbio.data.CollapseTransform: Gets width of each image.
getImageWidth() - Method in class loci.visbio.data.DataSampling: Gets width of each image.
getImageWidth() - Method in class loci.visbio.data.Dataset: Gets width of each image.
getImageWidth() - Method in class loci.visbio.data.ImageTransform: Gets the width in pixels of each image.
getImageWidth() - Method in class loci.visbio.data.ProjectionTransform: Gets width of each image.
getImageWidth() - Method in class loci.visbio.data.SpectralTransform: Gets width of each image.
getImageWidth() - Method in class loci.visbio.ext.ExternalFunction: Gets width of each image.
getImageX() - Method in class loci.slim.fit.BurnInRenderer
getImageX() - Method in class loci.slim.fit.CurveRenderer
getImageX() - Method in interface loci.slim.fit.ICurveRenderer
getImageX() - Method in class loci.slim.fit.RendererSwitcher
getImageY() - Method in class loci.slim.fit.BurnInRenderer
getImageY() - Method in class loci.slim.fit.CurveRenderer
getImageY() - Method in interface loci.slim.fit.ICurveRenderer
getImageY() - Method in class loci.slim.fit.RendererSwitcher
getIndex() - Method in class de.sciss.jcollider.Bus
getIndex(TreeNode) - Method in class de.sciss.jcollider.Group
getIndex(TreeNode) - Method in class de.sciss.jcollider.Synth
getIndex(Window) - Method in class loci.visbio.util.Docker: Gets the given window's index.
getIndices() - Method in class loci.visbio.view.BioSlideWidget: Gets indices into transforms affected by this slider.
getInput(int) - Method in class de.sciss.jcollider.UGen: Returns the UGen's input at the given index.
getInputNames() - Method in interface loci.deepzoom.workflow.IModule: Gets input image names.
getInputNames() - Method in class loci.deepzoom.workflow.plugin.PluginAnnotations: Gets the set of annotated input names.
getInputNames() - Method in class loci.deepzoom.workflow.PluginModule: Gets input image names.
getInputNames() - Method in class loci.deepzoom.workflow.WorkFlow
getInputNames() - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Gets the set of annotated input names.
getInputNames() - Method in class loci.multiinstanceplugin.LinkedPlugin: Gets the set of annotated input names.
getInputNames() - Method in class loci.multiinstanceplugin.PluginAnnotations: Gets the set of annotated input names.
getInputNames() - Method in class loci.multithreadedplugin.AbstractNode: Gets the set of annotated input names.
getInputs() - Method in class de.sciss.jcollider.UGen: Returns an array of the UGen's inputs.
getInputStreamsEnabled() - Method in class de.sciss.jcollider.ServerOptions
getInstance() - Static method in class loci.deepzoom.workflow.ModuleFactory: Gets singleton instance.
getInstance() - Static method in class loci.deepzoom.workflow.plugin.PluginScheduler: Gets the singleton.
getInstance() - Static method in class loci.deepzoom.workflow.PluginModuleFactory
getInstance() - Static method in class loci.deepzoom.workflow.WorkFlowFactory
getInstance() - Static method in class loci.multiinstanceplugin.PluginScheduler: Gets the singleton.
getInstance() - Static method in class loci.multithreadedplugin.NodeScheduler: Gets the singleton.
getIntegerValue() - Method in class loci.visbio.state.NumericOption: Gets this option's current setting as an integer value.
getItem() - Method in class loci.deepzoom.workflow.plugin.ItemWrapper: Gets the underlying ImageJ ImageProcessor.
getIterations() - Method in class loci.slim.fit.CurveFitter: Returns the number of iterations so far.
getIterations() - Method in class loci.slim.fit.GACurveFitter
getIterations() - Method in interface loci.slim.fit.ICurveFitter: Returns the number of iterations so far.
getIterations() - Method in class loci.slim.fit.LMCurveFitter
getKey(DataTransform, int[], String) - Method in class loci.visbio.data.DataCache: Gets a key string suitable for hashing for the given transform at the specified position.
getLabel() - Method in class de.sciss.jcollider.gui.EZSlider
getLabel() - Static method in class loci.visbio.state.SpreadsheetOptionStrategy: Returns the label for the spreadsheet option.
getLabels() - Method in class loci.visbio.data.DataTransform: Gets label for each dimensional position.
getLag() - Method in class de.sciss.jcollider.ControlDesc
getLast() - Method in class loci.slim.fit.CurveFitter
getLast() - Method in interface loci.slim.fit.ICurveFitter
getLastNodeX() - Method in class loci.visbio.overlays.OverlayNodedObject: Gets most recent x-coordinate in node array.
getLastNodeY() - Method in class loci.visbio.overlays.OverlayNodedObject: Gets most recent y-coordinate in node array.
getLastSegmentLength() - Method in class loci.visbio.overlays.OverlayNodedObject: Determines length of last line segment in this curve.
getLauncher() - Method in interface loci.deepzoom.workflow.IModule: Gets associated launcher
getLauncher() - Method in class loci.deepzoom.workflow.PluginModule
getLauncher() - Method in class loci.deepzoom.workflow.WorkFlow: Gets launcher.
getLauncher() - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Gets the plugin launcher for this linked plugin.
getLauncher() - Method in class loci.multiinstanceplugin.LinkedPlugin: Gets the plugin launcher for this linked plugin.
getLeftRightAxis() - Method in class loci.visbio.view.TransformPanel: Gets axis mapped to left/right arrow keys.
getLength() - Method in class loci.visbio.overlays.OverlayArrow: Computes the length of this arrow.
getLengths() - Method in class loci.visbio.data.DataTransform: Gets length of each dimensional axis.
getLibraryJars() - Method in class loci.jar2lib.Jar2Lib
getLineLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Returns a selection layer for OverlayLine objects.
getLink() - Method in class loci.visbio.view.ColorHandler: Gets associated transform link.
getLink(DataTransform) - Method in class loci.visbio.view.TransformHandler: Gets the transform link object for the given data transform.
getLinkIndex(DataTransform) - Method in class loci.visbio.view.TransformHandler: Gets the transform link index for the given data transform.
getLo() - Method in class loci.visbio.view.ColorHandler: Gets color mapping minimums.
getLo() - Method in class loci.visbio.view.ColorPane: Gets color table range minimums.
getLoadDefs() - Method in class de.sciss.jcollider.ServerOptions
getLocation() - Method in class loci.visbio.data.ArbitrarySlice: Gets the location for the arbitrary slice.
getLocation(int) - Method in class loci.visbio.util.Docker: Gets the last recorded location of the window at the specified index.
getLocation(Window) - Method in class loci.visbio.util.Docker: Gets the given window's last recorded location.
getLogStream() - Method in class de.sciss.jcollider.gui.LogTextArea
getLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Gets the name and class of the current look and feel.
getLowResScanImage() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getLowResScanImage() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getM_password() - Method in class loci.wiscscan.auth.Credentials
getM_username() - Method in class loci.wiscscan.auth.Credentials
getManager() - Method in class de.sciss.jcollider.gui.NodeTreePanel
getManager() - Method in class loci.visbio.ControlPanel: Gets control panel's logic manager.
getManager() - Method in class loci.visbio.view.DisplayWindow: Gets associated display manager.
getManager(Class<?>) - Method in class loci.visbio.VisBioFrame: Gets the logic manager of the given class.
getManagers() - Method in class loci.visbio.VisBioFrame: Gets all logic managers.
getMaps(DisplayImpl, RealType[]) - Static method in class loci.visbio.util.DataUtil: Gets an array of ScalarMaps from the given display, corresponding to the specified RealTypes.
getMaps(DisplayImpl, ScalarType[], DisplayRealType[]) - Static method in class loci.visbio.util.DisplayUtil: Gets an array of ScalarMaps from the given display, matching the specified RealTypes and/or DisplayRealTypes.
getMaps() - Method in class loci.visbio.view.ColorHandler: Gets color mappings for this color handler's transform link.
getMarkerLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Returns a selection layer for OverlayMarker objects.
getMask() - Method in class loci.slim.fit.BurnInRenderer
getMask() - Method in class loci.slim.fit.CurveRenderer
getMask() - Method in interface loci.slim.fit.ICurveRenderer
getMask() - Method in class loci.slim.fit.RendererSwitcher
getMatlabVersion() - Static method in class loci.visbio.ext.MatlabUtil: Gets the version of MATLAB available, or null if none.
getMatrix() - Method in class loci.visbio.view.DisplayPosition: Gets the position's description.
getMatrix() - Method in class loci.visbio.view.ViewHandler: Gets the display's current matrix transform.
getMax() - Method in class loci.visbio.data.DataSampling: Gets maximum dimensional index values.
getMax() - Method in class loci.visbio.DoubleSlider
getMaximum() - Method in class loci.slim.fit.CurveEvent: Gets the progress maximum for the event.
getMaximumMemory() - Method in class loci.visbio.SystemManager: Gets maximum amount of memory available to VisBio in megabytes.
getMaximumSize() - Method in class loci.visbio.BioTask
getMaxIterations() - Method in class loci.slim.fit.CurveRenderer
getMaxIterations() - Method in interface loci.slim.fit.ICurveRenderer
getMaxIterations() - Method in class loci.slim.fit.RendererSwitcher
getMaxNodes() - Method in class de.sciss.jcollider.ServerOptions
getMaxNodes() - Method in class loci.visbio.overlays.OverlayNodedObject: Returns total number of nodes in array.
getMaxProgress() - Method in class loci.slim.fit.CurveRenderer
getMaxProgress() - Method in interface loci.slim.fit.ICurveRenderer
getMaxProgress() - Method in class loci.slim.fit.RendererSwitcher
getMaxRCSE() - Method in class loci.slim.fit.CurveRenderer
getMaxRCSE() - Method in interface loci.slim.fit.ICurveRenderer
getMaxRCSE() - Method in class loci.slim.fit.RendererSwitcher
getMaxSynthDefs() - Method in class de.sciss.jcollider.ServerOptions
getMaxVal() - Method in class de.sciss.jcollider.gui.ControlSpec
getMemoryUsage() - Method in class loci.visbio.SystemManager: Gets a string detailing current memory usage.
getMemSize() - Method in class de.sciss.jcollider.ServerOptions
getMessage() - Method in class loci.slim.fit.CurveEvent: Gets the message describing the event.
getMessage() - Method in class loci.visbio.VisBioEvent: Gets the message for this event.
getMetadata() - Method in class loci.visbio.data.Dataset: Gets metadata associated with the dataset.
getMicronHeight() - Method in class loci.visbio.data.ImageTransform: Gets physical image height in microns.
getMicronStep(int) - Method in class loci.visbio.data.DataSampling: Gets the physical distance between image planes in microns for the given axis.
getMicronStep() - Method in class loci.visbio.data.ImageTransform: Gets physical distance between image slices in microns.
getMicronStep(int) - Method in class loci.visbio.data.ImageTransform: Gets physical distance between image slices in microns for the given axis.
getMicronWidth() - Method in class loci.visbio.data.ImageTransform: Gets physical image width in microns.
getMin() - Method in class loci.visbio.data.DataSampling: Gets minimum dimensional index values.
getMin() - Method in class loci.visbio.DoubleSlider
getMinVal() - Method in class de.sciss.jcollider.gui.ControlSpec
getModel() - Method in class de.sciss.jcollider.gui.NodeTreeManager: Returns a TreeModel suitable to creating a JTree gadget.
getModel() - Method in class loci.visbio.view.BioColorWidget: Gets the widget's color model (RGB, HSV or COMPOSITE).
getMouseClicked() - Method in class loci.apps.SlideScannerImport.MouseClickListener
getMsg() - Method in class de.sciss.jcollider.Bus
getMsg(int[]) - Method in class de.sciss.jcollider.Bus
getMsg(int) - Method in class de.sciss.jcollider.Synth
getMsg(int[]) - Method in class de.sciss.jcollider.Synth
getMsg(String) - Method in class de.sciss.jcollider.Synth
getMsg(String[]) - Method in class de.sciss.jcollider.Synth
getMultiplier(TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Returns a multiplier suitable for scaling distances to pixel coordinates.
getMultiplier(DisplayImpl) - Static method in class loci.visbio.overlays.OverlayUtil: Returns a multiplier suitable for scaling distances to pixel coordinates.
getMultiResponder() - Method in class de.sciss.jcollider.Server
getn(int[], int[], Bus.GetCompletionAction) - Method in class de.sciss.jcollider.Bus
getn(int, int) - Method in class de.sciss.jcollider.Synth: Queries a range of current values of the synth's controls.
getn(String, int) - Method in class de.sciss.jcollider.Synth: Queries a range of current values of the synth's controls.
getn(int[], int[]) - Method in class de.sciss.jcollider.Synth: Queries different ranges of current values of the synth's controls.
getn(String[], int[]) - Method in class de.sciss.jcollider.Synth: Queries different ranges of current values of the synth's controls.
getName() - Method in class de.sciss.jcollider.ControlDesc
getName() - Method in class de.sciss.jcollider.Node: Queries the custom name of the node.
getName() - Method in class de.sciss.jcollider.Server: Queries the server representation's name
getName() - Method in class de.sciss.jcollider.SynthDef: Returns the name of the synth definition
getName() - Method in class de.sciss.jcollider.UGen: Returns the class name of the UGen.
getName() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the name of the image.
getName() - Method in class loci.deepzoom.util.xmllight.XMLTag: Get the name of the tag.
getName() - Method in interface loci.deepzoom.workflow.IModule: Gets name of module.
getName() - Method in class loci.deepzoom.workflow.PluginModule: Gets name of component.
getName() - Method in class loci.deepzoom.workflow.WorkFlow
getName() - Method in class loci.visbio.ControlPanel: Gets the name of this control panel.
getName() - Method in class loci.visbio.data.DataTransform: Gets the name of this transform.
getName() - Method in class loci.visbio.ext.FunctionParam: Gets the name of this parameter.
getName() - Method in class loci.visbio.help.HelpTopic: Gets the name associated with this help topic.
getName() - Method in class loci.visbio.overlays.OverlayTool: Gets tool name.
getName() - Method in class loci.visbio.view.BioSlideWidget: Gets slider name.
getName() - Method in class loci.visbio.view.DisplayPosition: Gets the positions's name.
getName() - Method in class loci.visbio.view.DisplayWindow: Gets the name of this display.
getName() - Method in class loci.visbio.WindowState: Gets window name.
getNearest(double, int, int, int) - Static method in class loci.visbio.util.MathUtil: Rounds the value to nearest value along the given progression.
getNearestNode(float, float) - Method in class loci.visbio.overlays.OverlayNodedObject: Gets the nearest node to the given point.
getNeededImageIndexes() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getNextTag(String) - Method in class loci.deepzoom.util.xmllight.XMLParser: Parses the XML string and returns the XMLTag data structure for the first tag it encounters.
getnMsg() - Method in class de.sciss.jcollider.Bus
getnMsg(int) - Method in class de.sciss.jcollider.Bus
getnMsg(int, int) - Method in class de.sciss.jcollider.Bus
getnMsg(int[], int[]) - Method in class de.sciss.jcollider.Bus
getnMsg(int, int) - Method in class de.sciss.jcollider.Synth
getnMsg(int[], int[]) - Method in class de.sciss.jcollider.Synth
getnMsg(String, int) - Method in class de.sciss.jcollider.Synth
getnMsg(String[], int[]) - Method in class de.sciss.jcollider.Synth
getNode() - Method in class de.sciss.jcollider.NodeEvent
getNodeCoords(int) - Method in class loci.visbio.overlays.OverlayNodedObject: Returns coordinates of node at given index in the node array.
getNodedLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes selection layer for OverlayNodedObject objects.
getNodeID() - Method in class de.sciss.jcollider.Node: Queries the node's identifier.
getNodeID() - Method in class de.sciss.jcollider.NodeEvent
getNodes() - Method in class loci.visbio.overlays.OverlayNodedObject: Returns a copy of the node array.
getNodeType() - Method in class de.sciss.jcollider.NodeEvent
getNotes() - Method in class loci.visbio.overlays.OverlayObject: Gets notes for this overlay.
getNotes() - Method in class loci.visbio.overlays.OverlayWidget: Gets notes for current overlay.
getNumAudioBusChannels() - Method in class de.sciss.jcollider.ServerOptions
getNumber() - Method in class de.sciss.jcollider.gui.NumberEvent: Queries the new number
getNumber() - Method in class de.sciss.jcollider.gui.NumberField: Return the number currently displayed
getNumBuffers() - Method in class de.sciss.jcollider.ServerOptions
getNumChannels() - Method in class de.sciss.jcollider.Buffer: Queries the buffer's number of channels.
getNumChannels() - Method in class de.sciss.jcollider.Bus
getNumCols() - Method in class loci.slim.fit.CurveCollection: Gets the full X resolution.
getNumControlBusChannels() - Method in class de.sciss.jcollider.ServerOptions
getNumDescs() - Method in class de.sciss.jcollider.Control
getNumElements() - Method in class de.sciss.jcollider.GraphElemArray
getNumFrames() - Method in class de.sciss.jcollider.Buffer: Queries the buffer data's number of frames (samples per channel).
getNumInputBusChannels() - Method in class de.sciss.jcollider.ServerOptions
getNumInputs() - Method in class de.sciss.jcollider.UGen: Returns the number of input arguments.
getNumNodes() - Method in class loci.visbio.overlays.OverlayNodedObject: Returns the number of real nodes in the array.
getNumOutputBusChannels() - Method in class de.sciss.jcollider.ServerOptions
getNumOutputs() - Method in class de.sciss.jcollider.Constant
getNumOutputs() - Method in interface de.sciss.jcollider.GraphElem
getNumOutputs() - Method in class de.sciss.jcollider.GraphElemArray
getNumOutputs() - Method in class de.sciss.jcollider.UGen
getNumOutputs() - Method in class de.sciss.jcollider.UGenChannel: Returns 1 naturally
getNumOutputs(int, int) - Method in class de.sciss.jcollider.UGenInfo: Given the number of instantiating arguments, returns the number of output channels the ugen will have.
getNumRGens() - Method in class de.sciss.jcollider.ServerOptions
getNumRows() - Method in class loci.slim.fit.CurveCollection: Gets the full Y resolution.
getNumWireBufs() - Method in class de.sciss.jcollider.ServerOptions
getObjects() - Method in class loci.visbio.overlays.OverlayTransform: Gets the overlay objects at the current dimensional position.
getObjects(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Gets the overlay objects at the given dimensional position.
getOffset(String) - Method in class loci.visbio.data.ThumbnailCache: Gets the offset corresponding to the given id string.
getOldParentGroupID() - Method in class de.sciss.jcollider.NodeEvent
getOldPredNodeID() - Method in class de.sciss.jcollider.NodeEvent
getOldSuccNodeID() - Method in class de.sciss.jcollider.NodeEvent
getOMEXML() - Method in class loci.visbio.data.Dataset: Gets an OME-XML string for the dataset.
getOMEXMLRoot() - Method in class loci.visbio.data.Dataset: Gets an OME-XML root for the dataset.
getOpacityModel() - Method in class loci.visbio.view.ColorHandler: Gets opacity model (CONSTANT_ALPHA or CURVED_ALPHA).
getOpacityModel() - Method in class loci.visbio.view.ColorPane: Gets current opacity model.
getOpacityValue() - Method in class loci.visbio.view.ColorHandler: Gets opacity value.
getOpacityValue() - Method in class loci.visbio.view.ColorPane: Gets current opacity value.
getOption(String) - Method in class loci.visbio.state.OptionManager: Gets the VisBio option with the given text.
getOptions() - Method in class de.sciss.jcollider.Server: Queries the options for booting the server.
getOptions() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
getOutlineLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes a standard outline layer for an OverlayObject.
getOutput(int) - Method in class de.sciss.jcollider.Constant
getOutput(int) - Method in interface de.sciss.jcollider.GraphElem
getOutput(int) - Method in class de.sciss.jcollider.GraphElemArray
getOutput(int) - Method in class de.sciss.jcollider.UGen
getOutput(int) - Method in class de.sciss.jcollider.UGenChannel: Returns this naturally
getOutputNames() - Method in interface loci.deepzoom.workflow.IModule: Gets output names.
getOutputNames() - Method in class loci.deepzoom.workflow.plugin.PluginAnnotations: Gets the set of annotated output names.
getOutputNames() - Method in class loci.deepzoom.workflow.PluginModule: Gets output names.
getOutputNames() - Method in class loci.deepzoom.workflow.WorkFlow
getOutputNames() - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Gets the set of annotated output names.
getOutputNames() - Method in class loci.multiinstanceplugin.LinkedPlugin: Gets the set of annotated output names.
getOutputNames() - Method in class loci.multiinstanceplugin.PluginAnnotations: Gets the set of annotated output names.
getOutputNames() - Method in class loci.multithreadedplugin.AbstractNode: Gets the set of annotated output names.
getOutputPath() - Method in class loci.jar2lib.Jar2Lib
getOutputRate(int) - Method in class de.sciss.jcollider.UGen: Returns the rate of one of the UGens output channels.
getOutputRates() - Method in class de.sciss.jcollider.UGen: Returns an array of the rates at which the individual output channels run.
getOutputStreamsEnabled() - Method in class de.sciss.jcollider.ServerOptions
getOvalLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes a selection layer for OverlayOval objects.
getOverlayTypes() - Static method in class loci.visbio.overlays.OverlayUtil: Get list of all OverlayObject subclasses.
getPanel(String) - Method in class loci.visbio.PanelManager: Gets the control panel with the given name.
getPanel() - Method in class loci.visbio.view.CaptureHandler: Gets GUI controls for this capture handler.
getPanel() - Method in class loci.visbio.view.TransformHandler: Gets GUI controls for this transform handler.
getPanel() - Method in class loci.visbio.view.ViewHandler: Gets GUI controls for this view handler.
getParameterDefaults() - Method in class loci.visbio.ext.ExternalFunction: Gets the default parameter values for this external function transform.
getParameterNames() - Method in class loci.visbio.ext.ExternalFunction: Gets the name of each parameter for this external function transform.
getParameters() - Method in class loci.visbio.ext.ExternalFunction: Gets the current parameter values for this external function transform.
getParameters(String) - Static method in class loci.visbio.ext.MatlabUtil: Gets the list of parameters for the given MATLAB function.
getParent() - Method in class de.sciss.jcollider.Node
getParent() - Method in class loci.visbio.data.DataTransform: Gets the parent of this transform.
getParentGroupID() - Method in class de.sciss.jcollider.NodeEvent
getPartialDerivate(double, double[], int) - Method in class loci.slim.fit.LMCurveFitter.ExpFunction
getPath() - Method in class de.sciss.jcollider.Buffer: Queries the buffer's sound file path.
getPattern() - Method in class loci.visbio.data.Dataset: Gets the string pattern describing this dataset.
getPitch() - Method in class loci.visbio.data.ArbitrarySlice: Gets the pitch for the slicing line.
getPixels() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the pixel array.
getPolylineThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the polyline threshold.
getPos() - Method in class loci.visbio.overlays.OverlayTransform: Gets transform's current dimensional position.
getPos(DataTransform) - Method in class loci.visbio.view.TransformHandler: Gets the dimensional position specified by the given transform's slider widgets.
getPositions() - Method in class loci.visbio.view.CaptureHandler: Gets positions on the list.
getPositions() - Method in class loci.visbio.view.CapturePanel: Gets positions on the list.
getPPMofLowResImage() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getPPMofLowResImage() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getPredNode() - Method in class de.sciss.jcollider.Node: Queries the node's predecessor in the graph tree.
getPredNodeID() - Method in class de.sciss.jcollider.NodeEvent
getPreferredSize() - Method in class loci.visbio.util.BioComboBox: Gets a slightly wider preferred size than normal, to work around a bug in the Windows and GTK Look and Feels where combo boxes are slightly too narrow.
getPreferredTaskWidth() - Method in class loci.visbio.TaskControls: Gets the preferred width of tasks.
getPrintStream() - Static method in class de.sciss.jcollider.Server: Queries the currently used print stream for outputting messages
getPriority(int) - Method in class loci.visbio.util.Docker: Gets the docking priority for the window at the specified index.
getPriority(Window) - Method in class loci.visbio.util.Docker: Gets the docking priority for the given window.
getProcess() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
getProgram() - Static method in class de.sciss.jcollider.Server: Queries the application path to scsynth.
getProjectId() - Method in class loci.jar2lib.Jar2Lib
getProjection(double[], double[], double[], boolean) - Static method in class loci.visbio.util.MathUtil: Computes the projection of the point v onto the line segment a-b.
getProjectName() - Method in class loci.jar2lib.Jar2Lib
getProperties() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the properties associated with this image.
getProperties() - Method in class loci.deepzoom.workflow.plugin.ItemWrapper: Gets the properties associated with this image.
getProtocol() - Method in class de.sciss.jcollider.ServerOptions
getPtA() - Method in class loci.visbio.util.Segment2D
getPtB() - Method in class loci.visbio.util.Segment2D
getRange() - Method in class de.sciss.jcollider.gui.ControlSpec
getRange() - Method in class loci.visbio.data.DataSampling: Gets included range components.
getRangeCount() - Method in class loci.visbio.data.CollapseTransform: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.data.DataSampling: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.data.Dataset: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.data.ImageTransform: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.data.ProjectionTransform: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.data.SpectralTransform: Gets number of range components at each pixel.
getRangeCount() - Method in class loci.visbio.ext.ExternalFunction: Gets number of range components at each pixel.
getRangeType() - Method in class loci.visbio.overlays.OverlayTransform: Gets range type (RGB).
getRangeTypes() - Method in class loci.visbio.data.ImageTransform: Gets the RealTypes used for the range components.
getRate() - Method in class de.sciss.jcollider.Bus
getRate() - Method in class de.sciss.jcollider.Constant
getRate() - Method in class de.sciss.jcollider.ControlDesc
getRate() - Method in class de.sciss.jcollider.UGen: Returns the rate at which this UGen is running
getRate() - Method in class de.sciss.jcollider.UGenChannel
getRate() - Method in interface de.sciss.jcollider.UGenInput: A UGen input is naturally single-channelled.
getRatio() - Method in class de.sciss.jcollider.gui.ControlSpec
getRatioBoolean(boolean, double, int, float, float, double, boolean) - Static method in class loci.apps.flow.FlowCyto
getReader() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
getRealType(String) - Static method in class loci.visbio.util.DataUtil: Gets a RealType with the given name, converting invalid characters within the name to underscores.
getRealType(String, Unit) - Static method in class loci.visbio.util.DataUtil: Gets a RealType with the given name and unit, converting invalid characters within the name to underscores.
getReconnectThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the reconnect threshold.
getRed() - Method in class loci.visbio.view.ColorHandler: Gets RealType mapped to red.
getRed() - Method in class loci.visbio.view.ColorPane: Gets current red RealType.
getReducedChiSquaredError() - Method in class loci.slim.fit.CurveFitter: Returns the Reduced Chi Squared Error of the current curve estimate This is based on the number of dataPoints in data and the number of exponentials in setComponentCount.
getReducedChiSquaredError(double[][]) - Method in class loci.slim.fit.CurveFitter
getReducedChiSquaredError() - Method in interface loci.slim.fit.ICurveFitter: Returns the Reduced Chi Squared Error of the current curve estimate This is based on the number of datapoints in data and the number of exponentials in setComponentCount.
getReducedChiSquaredError(double[][]) - Method in interface loci.slim.fit.ICurveFitter
getReference() - Method in class loci.visbio.view.TransformLink: Gets the link's reference.
getReferences() - Method in class loci.visbio.view.StackLink: Gets references corresponding to each plane in the image stack.
getRegisteredDataLabels() - Method in class loci.visbio.data.DataManager: Gets list of regitered data transform labels.
getRegisteredDataTypes() - Method in class loci.visbio.data.DataManager: Gets list of registered data transform types.
getRemainder() - Method in class loci.deepzoom.util.xmllight.XMLTag: Gets the remainder of the XML string after the tag.
getRenderer() - Method in class loci.visbio.view.TransformLink: Gets the link's renderer.
getRenderers() - Method in class loci.visbio.view.StackLink: Gets renderers corresponding to each plane in the image stack.
getRendezvous() - Method in class de.sciss.jcollider.ServerOptions
getRepackSize(Window) - Static method in class loci.visbio.util.SwingUtil: Gets the dimension of this window were it to be repacked.
getResolution() - Method in class loci.visbio.data.ArbitrarySlice: Gets the resolution for the slicing line.
getResourceString(String) - Static method in class de.sciss.jcollider.JCollider
getResumeThreshold() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the resume threshold.
getRightBisectorVector2D(float[], float[], float[]) - Static method in class loci.visbio.util.MathUtil: Gets a unit vector which bisects (p1 - p2) and (p3 - p2).
getRightPerpendicularVector2D(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Gets a vector perpendicular to the vector p2-p1, pointing to the right with respect to the direction of p2-p1.
getROICount() - Method in class loci.slim.TwoDPane
getROIMask() - Method in class loci.slim.TwoDPane
getROIPercent() - Method in class loci.slim.TwoDPane
getROIsList() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getROIsList() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getROIX() - Method in class loci.slim.TwoDPane
getROIY() - Method in class loci.slim.TwoDPane
getSampleRate() - Method in class de.sciss.jcollider.Buffer: Queries the buffer data's sample rate.
getSampleRate() - Method in class de.sciss.jcollider.Server: Queries the server's (audio) sampling rate.
getSampleRate() - Method in class de.sciss.jcollider.ServerOptions
getScalingValue() - Method in class loci.visbio.overlays.OverlayTransform: Gets a scaling value suitable for computing an overlay size or picking threshold.
getScalingValueX() - Method in class loci.visbio.overlays.OverlayTransform: Gets a scaling value along the X axis, suitable for computing an overlay width or picking threshold.
getScalingValueY() - Method in class loci.visbio.overlays.OverlayTransform: Gets a scaling value along the Y axis, suitable for computing an overlay height or picking threshold.
getSelected() - Method in class loci.visbio.state.SpreadsheetLaunchOption: Gets whether the checkbox is selected.
getSelectedData() - Method in class loci.visbio.data.DataControls: Gets the currently selected data object.
getSelectedData() - Method in class loci.visbio.data.DataManager: Gets the currently selected data object.
getSelectedFont() - Method in class loci.visbio.util.FontChooserPane: Gets the font indicated by the font chooser.
getSelectedItem() - Method in class loci.visbio.view.BioColorWidget: Gets the currently selected RealType, or null if none.
getSelectionLayer(OverlayObject, TransformLink, boolean) - Static method in class loci.visbio.overlays.OverlayUtil: Computes a type-specific selection layer for the given OverlayObject.
getServer() - Method in class de.sciss.jcollider.Buffer: Queries the server at which the buffer resides
getServer() - Method in class de.sciss.jcollider.Bus
getServer() - Method in class de.sciss.jcollider.Node: Queries the server at which the node resides
getServer() - Method in class de.sciss.jcollider.ServerEvent
getSize() - Method in interface de.sciss.jcollider.BlockAllocator.Block: Queries the number of channels in the block.
getSize(int) - Static method in class loci.jvmlink.ConnThread
getSliceCount() - Method in class loci.visbio.view.StackLink: Gets the number of slices, assuming the currently assigned stack axis.
getSlider() - Method in class loci.visbio.view.BioSlideWidget: Gets the slider component.
getSlider(int) - Method in class loci.visbio.view.TransformHandler: Gets the slider at the given index, or null if no such slider exists.
getSliderPanel() - Method in class loci.visbio.view.TransformHandler: Gets a panel containing sliders widgets for linked transforms.
getSmoothingFactor() - Static method in class loci.visbio.overlays.OverlayNumericStrategy: Returns the single exponential smoothing factor.
getSnapshot() - Method in class loci.visbio.view.CaptureHandler: Gets a snapshot of the display.
getSource() - Method in class loci.visbio.help.HelpTopic: Gets the content source for this help topic.
getSourcePath() - Method in class loci.jar2lib.Jar2Lib
getSpace() - Method in class de.sciss.jcollider.gui.NumberField: Returns the used number space.
getSpecialIndex() - Method in class de.sciss.jcollider.UGen: Returns the so-called special index of the UGen.
getSpeed() - Method in class loci.visbio.view.CaptureHandler: Gets movie speed.
getSpeed() - Method in class loci.visbio.view.CapturePanel: Gets movie speed.
getStackAxis() - Method in class loci.visbio.view.StackLink: Gets the currently assigned stack axis.
getStackResolution() - Method in class loci.visbio.view.DisplayManager: Gets maximum resolution of stacked images from VisBio options.
getStallCount() - Method in class loci.slim.fit.BurnInRenderer
getStartPoint() - Method in class loci.backup.github.CreateOrphanBranchCommand
getStat(String) - Method in class loci.visbio.overlays.OverlayArrow: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayBox: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayLine: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayMarker: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayNodedObject: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayObject: Gets a specific overlay statistic.
getStat(String) - Method in class loci.visbio.overlays.OverlayOval: Returns a specific statistic of this object.
getStat(String) - Method in class loci.visbio.overlays.OverlayText: Returns a specific statistic of this object.
getStatistics() - Method in class loci.visbio.overlays.OverlayArrow: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayBox: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayLine: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayMarker: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayNodedObject: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayObject: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayOval: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayText: Retrieves useful statistics about this overlay.
getStatistics() - Method in class loci.visbio.overlays.OverlayWidget: Gets statistics for current overlay.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayArrow: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayBox: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayLine: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayMarker: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayNodedObject: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayOval: Returns the names of the statistics this object reports.
getStatTypes() - Static method in class loci.visbio.overlays.OverlayText: Returns the names of the statistics this object reports.
getStatTypes(String) - Static method in class loci.visbio.overlays.OverlayUtil: Returns statistic names for a particular class.
getStatus() - Method in class de.sciss.jcollider.Server: Queries the latest reported server status.
getStep() - Method in class de.sciss.jcollider.gui.ControlSpec
getStep() - Method in class loci.visbio.data.DataSampling: Gets dimensional index step values.
getStep() - Method in class loci.visbio.DoubleSlider
getStereoConfiguration() - Static method in class loci.visbio.util.DisplayUtil: Gets a graphics configuration for use with stereo displays.
getSubsampleLevel() - Method in class loci.slim.fit.CurveRenderer
getSubsampleLevel() - Method in interface loci.slim.fit.ICurveRenderer
getSubsampleLevel() - Method in class loci.slim.fit.RendererSwitcher
getSubsamplingDepth() - Method in class loci.slim.fit.CurveCollection: Gets the maximum subsampling depth of the curve collection.
getSuccNode() - Method in class de.sciss.jcollider.Node: Queries the node's successor in the graph tree.
getSuccNodeID() - Method in class de.sciss.jcollider.NodeEvent
getSuggestedMaps() - Method in class loci.visbio.data.ArbitrarySlice: Retrieves a set of mappings for displaying this transform effectively.
getSuggestedMaps() - Method in class loci.visbio.data.DataTransform: Retrieves a set of mappings for displaying this transform effectively.
getSuggestedMaps() - Method in class loci.visbio.data.ImageTransform: Retrieves a set of mappings for displaying this transform effectively.
getSuggestedMaps() - Method in class loci.visbio.overlays.OverlayTransform: Retrieves a set of mappings for displaying this transform effectively.
getSync() - Method in class de.sciss.jcollider.OSCMultiResponder
getTab(String) - Method in class loci.visbio.state.OptionPane: Gets the tab with the given name, initializing it if necessary.
getTables() - Method in class loci.visbio.view.ColorHandler: Gets current color tables.
getTables() - Method in class loci.visbio.view.ColorPane: Gets color table values.
getTailNode() - Method in class de.sciss.jcollider.Group
getTailNodeID() - Method in class de.sciss.jcollider.NodeEvent
getTask() - Method in class loci.visbio.util.SplashScreen: Gets current task number.
getTaskCount() - Method in class loci.visbio.util.SplashScreen: Gets number of tasks for splash screen progress bar.
getTasks() - Method in class loci.visbio.ConsoleManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.data.DataManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.ExitManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.ext.ExtManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.help.HelpManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.LogicManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.overlays.OverlayManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.PanelManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.state.OptionManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.state.StateManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.SystemManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.TaskManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.view.DisplayManager: Gets the number of tasks required to initialize this logic manager.
getTasks() - Method in class loci.visbio.WindowManager: Gets the number of tasks required to initialize this logic manager.
getText() - Method in class loci.visbio.overlays.OverlayObject: Gets text to render.
getText() - Method in class loci.visbio.overlays.OverlayWidget: Gets text string for current overlay.
getText() - Method in class loci.visbio.state.BioOption: Gets text identifying this option.
getText() - Static method in class loci.visbio.state.SpreadsheetOptionStrategy: Returns the text for the spreadsheet option.
getText(Element) - Static method in class loci.visbio.util.XMLUtil: Gets the text information associated with the given DOM element.
getTextArea() - Method in class loci.visbio.util.OutputConsole
getTextLayer(OverlayObject, TransformLink) - Static method in class loci.visbio.overlays.OverlayUtil: Computes a selection layer for OverlayText objects.
getTextRangeType() - Method in class loci.visbio.overlays.OverlayTransform: Gets range type for text overlays (R, G, B, text).
getTextRangeValue(String, float, float, float, float) - Method in class loci.visbio.overlays.OverlayTransform: Constructs a range value with the given component values.
getTextTip() - Static method in class loci.visbio.state.SpreadsheetOptionStrategy: Returns the text tooltip for the spreadsheet option.
getThumb(int[]) - Method in class loci.visbio.data.ThumbnailHandler: Gets the thumbnail at the given dimensional position.
getThumbCount() - Method in class loci.visbio.data.ThumbnailCache: Gets the number of thumbnails in the disk cache.
getThumbHandler() - Method in class loci.visbio.data.DataTransform: Gets thumbnail handler for thumbnail-related operations.
getThumbnailResolution() - Method in class loci.visbio.data.DataManager: Gets resolution of low-resolution thumbnails from VisBio options.
getTiffInfo() - Method in class loci.apps.SlideScannerImport.MiniBioformatsTool
getTip() - Method in class loci.visbio.ControlPanel: Gets the tip for this control panel.
getTip() - Method in class loci.visbio.overlays.OverlayTool: Gets tool tip text.
getTipCoords() - Method in class loci.visbio.overlays.FreeformExtension: Returns the coordinates of the extension's tip or start node.
getToBeDeleted() - Method in class loci.backup.github.CreateOrphanBranchCommand
getTotalIterations() - Method in class loci.slim.fit.CurveRenderer
getTotalIterations() - Method in interface loci.slim.fit.ICurveRenderer
getTotalIterations() - Method in class loci.slim.fit.RendererSwitcher
getTotalRCSE() - Method in class loci.slim.fit.BurnInRenderer
getTotalRCSE() - Method in class loci.slim.fit.CurveRenderer
getTotalRCSE() - Method in interface loci.slim.fit.ICurveRenderer
getTotalRCSE() - Method in class loci.slim.fit.RendererSwitcher
getTransform() - Method in class loci.visbio.overlays.OverlayTool: Gets associated overlay transform.
getTransform() - Method in class loci.visbio.view.TransformLink: Gets the link's data transform.
getTransformCount() - Method in class loci.visbio.view.TransformHandler: Gets number of data transforms linked to the display.
getTransformHandler() - Method in class loci.visbio.view.DisplayWindow: Gets the transform handler.
getTransformId() - Method in class loci.visbio.data.DataTransform: Gets the data transform ID.
getTransforms() - Method in class loci.visbio.view.BioSlideWidget: Gets transforms affected by this slider.
getTransforms() - Method in class loci.visbio.view.TransformHandler: Gets data transforms linked to the display.
getType(int) - Static method in class loci.jvmlink.ConnThread
getType() - Method in class loci.visbio.data.ImageTransform: Gets MathType of images generated by this image transform.
getUGen() - Method in class de.sciss.jcollider.UGenChannel: Returns the UGen whose output this object represents
getUGens() - Method in class de.sciss.jcollider.SynthDef: Return a list of all UGens in the graph (in the depth-first sorted topological order).
getUnitDescription(String, int) - Static method in class loci.visbio.data.DataTransform: Gets the unit description for a dimensional type.
getUnits() - Method in class de.sciss.jcollider.gui.ControlSpec
getUnmappedValue() - Method in class de.sciss.jcollider.gui.EZSlider
getUpDownAxis() - Method in class loci.visbio.view.TransformPanel: Gets axis mapped to up/down arrow keys.
getUsage() - Method in class loci.visbio.data.ThumbnailCache: Gets thumbnail cache disk usage in bytes.
getUserMax() - Static method in class de.sciss.jcollider.NodeIDAllocator
getUserSelectedZero() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getUserSelectedZero() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getValidOSCCommands() - Static method in class de.sciss.jcollider.NodeEvent: Returns a list of strings describing all known OSC command names that form valid node notification messages, that is "/n_go", "/n_end" etc.
getValue() - Method in class de.sciss.jcollider.Constant
getValue() - Method in class de.sciss.jcollider.gui.EZSlider
getValue(Object) - Static method in class loci.jvmlink.ConnThread
getValue() - Method in class loci.slim.fit.CurveEvent: Gets the progress value for the event.
getValue() - Method in class loci.visbio.ext.FunctionParam: Gets the default value of this parameter.
getValue() - Method in class loci.visbio.state.BooleanOption: Gets this option's current setting.
getValue() - Method in class loci.visbio.state.ListOption: Gets this option's current setting.
getValue() - Method in class loci.visbio.state.ResolutionToggleOption: Gets whether resolution toggle is on.
getValue() - Method in class loci.visbio.state.SpreadsheetLaunchOption: Gets this option's current setting.
getValue() - Method in class loci.visbio.state.StringOption: Gets this option's current setting.
getValue() - Method in class loci.visbio.view.BioSlideWidget: Gets the current slider value.
getValueWithUnit(BigInteger, int) - Static method in class loci.visbio.util.MathUtil: Returns the given number as a string complete with unit (e.g., kilo, mega, etc.), to the specififed number of decimal places.
getValueX() - Method in class loci.visbio.state.ResolutionOption: Gets this option's current X resolution.
getValueX() - Method in class loci.visbio.state.ResolutionToggleOption: Gets this option's current X resolution.
getValueY() - Method in class loci.visbio.state.ResolutionOption: Gets this option's current Y resolution.
getValueY() - Method in class loci.visbio.state.ResolutionToggleOption: Gets this option's current Y resolution.
GETVAR - Static variable in class loci.jvmlink.ConnThread
getVerbosity() - Method in class de.sciss.jcollider.ServerOptions
getVersion() - Static method in class de.sciss.jcollider.JCollider: Returns the library's version.
getViewHandler() - Method in class loci.visbio.view.DisplayWindow: Gets the view handler.
getVisBio() - Method in class loci.visbio.LogicManager: Gets the VisBio frame for this logic manager.
getVisBio() - Method in class loci.visbio.view.DisplayWindow: Gets associated VisBio frame.
getVisBio() - Static method in class loci.visbio.VisBioFrame: Gets the running instance of VisBio.
getVisBioFileChooser() - Static method in class loci.visbio.util.SwingUtil: Constructs a JFileChooser that recognizes accepted VisBio file types.
getVisible() - Method in class loci.visbio.WindowState: Gets window visibility.
getVolumeResolution() - Method in class loci.visbio.view.StackLink: Gets maximum resolution per axis of rendered volumes.
getWarp() - Method in class de.sciss.jcollider.gui.ControlSpec
getWeights() - Method in class loci.visbio.data.SpectralTransform: Gets spectral channel weights.
getWidth() - Method in class loci.deepzoom.plugin.ImageWrapper: Gets the width of the image.
getWidth() - Method in class loci.visbio.overlays.OverlayMarker: Returns the width of this marker.
getWidth() - Method in class loci.visbio.WindowState: Gets window width.
getWindow() - Method in class loci.visbio.util.BreakawayPanel: Gets floating window used when panel breaks away from its parent.
getWindow(int) - Method in class loci.visbio.util.Docker: Gets the window at the specified index.
getWindow() - Method in class loci.visbio.util.OutputConsole
getWindow(Component) - Static method in class loci.visbio.util.SwingUtil: Gets the containing window for the given component.
getWindow() - Method in class loci.visbio.view.CaptureHandler: Gets associated display window.
getWindow() - Method in class loci.visbio.view.ColorHandler: Gets the VisBio display window affected by this color handler.
getWindow() - Method in class loci.visbio.view.TransformHandler: Gets associated display window.
getWindow() - Method in class loci.visbio.view.ViewHandler: Gets associated display window.
getWindow() - Method in class loci.visbio.WindowInfo: Gets the associated window.
getWindowByTitle(String) - Method in class loci.visbio.WindowManager: Gets window information about the first window matching the specified window title.
getWindows() - Method in class loci.visbio.WindowManager: Gets a list of windows being handled by the window manager.
getWindowTitle(Window) - Static method in class loci.visbio.util.SwingUtil: Gets the title of the given window.
getWires() - Method in interface loci.deepzoom.workflow.IWorkFlow: Gets the current chains.
getWires() - Method in class loci.deepzoom.workflow.WorkFlow
getWorstRCSE() - Method in class loci.slim.fit.BurnInRenderer
getWorstRCSE() - Method in class loci.slim.fit.CurveRenderer
getWorstRCSE() - Method in interface loci.slim.fit.ICurveRenderer
getWorstRCSE() - Method in class loci.slim.fit.RendererSwitcher
getX() - Method in class loci.visbio.overlays.OverlayObject: Gets X coordinate of the overlay's first endpoint.
getX() - Method in class loci.visbio.WindowState: Gets window X coordinate.
getX1() - Method in class loci.visbio.overlays.OverlayWidget: Gets X1 coordinate value for current overlay.
getX1() - Method in class loci.visbio.overlays.TransientSelectBox: Gets X coordinate of the first endpoint.
getX2() - Method in class loci.visbio.overlays.OverlayObject: Gets X coordinate of the overlay's second endpoint.
getX2() - Method in class loci.visbio.overlays.OverlayWidget: Gets X2 coordinate value for current overlay.
getX2() - Method in class loci.visbio.overlays.TransientSelectBox: Gets X coordinate of the second endpoint.
getXType() - Method in class loci.visbio.data.ImageTransform: Gets the RealType used for the X-axis.
getY(double, double[]) - Method in class loci.slim.fit.LMCurveFitter.ExpFunction
getY() - Method in class loci.visbio.overlays.OverlayObject: Gets Y coordinate of the overlay's first endpoint.
getY() - Method in class loci.visbio.WindowState: Gets window Y coordinate.
getY1() - Method in class loci.visbio.overlays.OverlayWidget: Gets Y1 coordinate value for current overlay.
getY1() - Method in class loci.visbio.overlays.TransientSelectBox: Gets Y coordinate of the first endpoint.
getY2() - Method in class loci.visbio.overlays.OverlayObject: Gets Y coordinate of the overlay's second endpoint.
getY2() - Method in class loci.visbio.overlays.OverlayWidget: Gets Y2 coordinate value for current overlay.
getY2() - Method in class loci.visbio.overlays.TransientSelectBox: Gets Y coordinate of the second endpoint.
getYaw() - Method in class loci.visbio.data.ArbitrarySlice: Gets the yaw for the slicing line.
getYType() - Method in class loci.visbio.data.ImageTransform: Gets the RealType used for the Y-axis.
getZoomRatioXY() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
getZoomRatioXY() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
getZType() - Method in class loci.visbio.data.ImageTransform: Gets the RealType used for the Z-axis.
getZUnit(int) - Method in class loci.visbio.data.ImageTransform: Gets Z unit for use with image stack domain sets, computed from micron information.
ggNumber - Variable in class de.sciss.jcollider.gui.EZSlider
ggSlider - Variable in class de.sciss.jcollider.gui.EZSlider
GitHubBackup - Class in loci.backup.github: Backs up GitHub information to a branch in a local git repository.
GitHubBackup() - Constructor for class loci.backup.github.GitHubBackup
GitHubBackupGUI - Class in loci.backup.github: Swing-based GUI entry point for GitHubBackup.
GitHubBackupGUI() - Constructor for class loci.backup.github.GitHubBackupGUI
GitHubBackupMojo - Class in loci.backup.github: Maven mojo for running GitHubBackup on git projects that are also maven-ized.
GitHubBackupMojo() - Constructor for class loci.backup.github.GitHubBackupMojo
global - Variable in class loci.visbio.data.ThumbnailHandler: Flag indicating cache string ids are for use in default, global cache.
GLOW_ALPHA - Static variable in class loci.visbio.overlays.OverlayObject
GLOW_ALPHA - Static variable in class loci.visbio.overlays.OverlayUtil: Alpha of the selection layer.
GLOW_COLOR - Static variable in class loci.visbio.overlays.OverlayObject
GLOW_COLOR - Static variable in class loci.visbio.overlays.OverlayUtil: Color of the selection layer.
GLOW_WIDTH - Static variable in class loci.visbio.overlays.OverlayObject
GLOW_WIDTH - Static variable in class loci.visbio.overlays.OverlayUtil: Width of the selection layer beyond the object's boundaries.
GO - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the node was created
go(String[]) - Method in class loci.apps.MultiLUT
grabbed - Variable in class loci.visbio.overlays.PointerTool: Vector of "grabbed" objects.
grabX - Variable in class loci.visbio.overlays.PointerTool: Location where an object was first "grabbed" with a mouse press.
grabY - Variable in class loci.visbio.overlays.PointerTool: Location where an object was first "grabbed" with a mouse press.
grain(String, Node) - Static method in class de.sciss.jcollider.Synth
grain(String, String[], float[], Node) - Static method in class de.sciss.jcollider.Synth
grain(String, String[], float[], Node, int) - Static method in class de.sciss.jcollider.Synth
GraphElem - Interface in de.sciss.jcollider: This interface does the dirty job of putting all kinds of different elements under one brand which can be used in UGen graph generation.
GraphElemArray - Class in de.sciss.jcollider: This interface does the dirty job of putting all kinds of different elements under one brand which can be used in UGen graph generation.
GraphElemArray(GraphElem[]) - Constructor for class de.sciss.jcollider.GraphElemArray
green - Variable in class loci.visbio.view.ColorHandler: Red, green and blue components of images.
green - Variable in class loci.visbio.view.ColorPane: Color map widgets.
GREEN_TYPE - Static variable in class loci.visbio.overlays.OverlayTransform: MathType for green color mappings.
Group - Class in de.sciss.jcollider: Mimics SCLang's Group class, that is, it's a client side representation of a group in the synthesis graph
Group(Group) - Constructor for class de.sciss.jcollider.Group
Group(Node, int) - Constructor for class de.sciss.jcollider.Group
GROUP - Static variable in class de.sciss.jcollider.NodeEvent: returned by getType() : the node is a group
group - Variable in class loci.visbio.overlays.OverlayObject: Group to which this overlay belongs.
groupList - Variable in class loci.visbio.overlays.OverlayWidget: Combo box for selecting an overlay group.
guessAspect() - Method in class loci.visbio.view.ViewHandler: Guesses aspect ratio based on first linked data transform.
guessType(RealType[]) - Method in class loci.visbio.view.BioColorWidget: Chooses most desirable range type for this widget's color.
guessTypes() - Method in class loci.visbio.view.ColorPane: Guesses reasonable mappings from range RealTypes to color components.

H

h - Variable in class loci.plugins.stitching.Pt
handle(Callback[]) - Method in class loci.wiscscan.auth.AutoLoginHandler
handleAbout(ApplicationEvent) - Method in class loci.visbio.MacAdapter: Handles the About menu item.
handlePreferences(ApplicationEvent) - Method in class loci.visbio.MacAdapter: Handles the Preferences menu item.
handleQuit(ApplicationEvent) - Method in class loci.visbio.MacAdapter: Handles the Quit menu item.
handler - Variable in class loci.visbio.view.CapturePanel: Capture handler for this capture window.
handler - Variable in class loci.visbio.view.ColorPane: Color handler for this color pane.
handler - Variable in class loci.visbio.view.SliceToggler: Stack handler for this slice toggler.
handler - Variable in class loci.visbio.view.TransformLink: Associated transform handler.
handler - Variable in class loci.visbio.view.TransformPanel: Transform handler upon which GUI controls operate.
handler - Variable in class loci.visbio.view.ViewPanel: View handler upon which GUI controls operate.
hasBegun() - Method in class loci.visbio.overlays.FreeformExtension: Whether this extension has begun or remains in the initial state.
hasData(DataTransform, int[], String) - Method in class loci.visbio.data.DataCache: Gets whether the cache has data for the given transform at the specified dimensional position.
hasData() - Method in class loci.visbio.overlays.OverlayArrow: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayBox: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayLine: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayMarker: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayNodedObject: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayObject: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayOval: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasData() - Method in class loci.visbio.overlays.OverlayText: Returns whether this object is drawable, i.e., is of nonzero size, area, length, etc.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayArrow: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayBox: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayLine: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayMarker: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayNodedObject: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayObject: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayOval: True iff this overlay has an endpoint coordinate pair.
hasEndpoint() - Method in class loci.visbio.overlays.OverlayText: True iff this overlay has an endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayArrow: True iff this overlay has a second endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayBox: True iff this overlay has a second endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayLine: True iff this overlay has a second endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayNodedObject: True iff this overlay has a second endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayObject: True iff this overlay has a second endpoint coordinate pair.
hasEndpoint2() - Method in class loci.visbio.overlays.OverlayOval: True iff this overlay has a second endpoint coordinate pair.
hash - Variable in class loci.visbio.data.DataCache: Hashtable backing this cache of full-resolution data.
hashCode() - Method in class de.sciss.jcollider.Bus
hashCode() - Method in class de.sciss.jcollider.Node
hasPosition() - Method in class loci.visbio.WindowState: Whether the window has a specified position.
hasSize() - Method in class loci.visbio.WindowState: Whether the window has a specified size.
hasText() - Method in class loci.visbio.overlays.OverlayObject: True iff this overlay returns text to render.
hasText() - Method in class loci.visbio.overlays.OverlayText: True iff this overlay object returns text to render.
hasToolChanged() - Method in class loci.visbio.overlays.OverlayTransform: Gets whether the current tool has changed since last mouse gesture.
hasTransform(DataTransform) - Method in class loci.visbio.view.DisplayWindow: Gets whether the given transform is currently linked to the display.
hasTransform(DataTransform) - Method in class loci.visbio.view.TransformHandler: Gets whether the given transform is currently linked to the display.
hasTransform(DataTransform) - Method in class loci.visbio.view.TransformPanel: Gets whether the given transform is currently linked to the display.
head(Group) - Static method in class de.sciss.jcollider.Group
head(Group, String) - Static method in class de.sciss.jcollider.Synth
head(Node, String, String[], float[]) - Static method in class de.sciss.jcollider.Synth
header(String) - Static method in class loci.jar2lib.ClassList: Gets the C++ header name corresponding to the given class name.
height - Variable in class loci.slim.SlimData
height - Variable in class loci.visbio.WindowState: Dimensions of the window.
heightField - Variable in class loci.visbio.data.SamplingWidget: Text field for image height.
helpAbout() - Method in class loci.visbio.help.HelpManager: Brings up VisBio's about dialog.
helpHelp() - Method in class loci.visbio.help.HelpManager: Brings up a window detailing basic program usage.
HelpManager - Class in loci.visbio.help: HelpManager is the manager encapsulating VisBio's help window logic.
HelpManager(VisBioFrame) - Constructor for class loci.visbio.help.HelpManager: Constructs an exit manager.
HelpMojo - Class in loci.backup.github: Display help information on github-backup.
Call mvn github-backup:help -Ddetail=true -Dgoal=<goal-name> to display parameter details.
HelpMojo() - Constructor for class loci.backup.github.HelpMojo
HelpTopic - Class in loci.visbio.help: HelpTopic is a tree node representing a help topic.
HelpTopic(String, String) - Constructor for class loci.visbio.help.HelpTopic: Creates a VisBio help topic.
helpWindow - Variable in class loci.visbio.help.HelpManager: Help dialog for detailing basic program usage.
HelpWindow - Class in loci.visbio.help: HelpWindow details basic VisBio program usage.
HelpWindow() - Constructor for class loci.visbio.help.HelpWindow: Creates a VisBio help window.
hexToColor(String) - Static method in class loci.visbio.util.ColorUtil: Gets the corresponding Color object for this hexidecimal string.
HHMMSS - Static variable in class de.sciss.jcollider.gui.NumberField: Constructor flag : Format the values as minutes:seconds
hi - Variable in class loci.visbio.view.ColorHandler: Minimum and maximum color range values.
hidden - Variable in class loci.visbio.view.SliceToggler: Option for hiding selected slices.
HIDE_ALL - Static variable in class loci.visbio.WindowManager: String for global minimization option.
hideAll - Variable in class loci.visbio.WindowManager: Whether minimizing main VisBio window hides all other windows.
hideControls(DataTransform) - Method in class loci.visbio.data.DataControls: Hides frame containing controls for the given data object.
hideWindows() - Method in class loci.visbio.WindowManager: Hides all windows.
HIGH_PRIORITY - Static variable in class loci.visbio.util.Docker: A docking priority higher than the default.
highlight - Variable in class loci.visbio.view.StackPanel: Checkbox for choosing whether current slice is highlighted.
highlightIndex - Variable in class loci.visbio.overlays.OverlayNodedObject: Index of the highlighted node.
highlightNode - Variable in class loci.visbio.overlays.OverlayNodedObject: Whether there is a higlighted node.
history - Variable in class loci.multithreadedplugin.Image
hiVal - Variable in class loci.visbio.view.ColorPane: Text field for high color scale value.
HLT_ALPHA - Static variable in class loci.visbio.overlays.OverlayNodedObject: Alpha value for highlighting.
HLT_ALPHA - Static variable in class loci.visbio.overlays.OverlayUtil: Alpha of the highlight layer for noded object.
HLT_COLOR - Static variable in class loci.visbio.overlays.OverlayUtil: Color of the highlight layer for noded objects.
horizGridCount - Variable in class loci.visbio.overlays.OverlayObject: Number of horizontal and vertical dividing lines for selection grid.
hsv - Variable in class loci.visbio.view.ColorPane: Color model options.
HSV_MODEL - Static variable in class loci.visbio.util.ColorUtil: HSV color space model.
HT - Static variable in class loci.visbio.overlays.OverlayBox
hyperlinkUpdate(HyperlinkEvent) - Method in class loci.visbio.help.HelpWindow: Handles hyperlinks.

I

i - Variable in class loci.plugins.stitching.Pt
icon - Variable in class loci.visbio.overlays.OverlayTool: Filename of icon.
icon - Variable in class loci.visbio.VisBioFrame: VisBio program icon.
ICurveFitter - Interface in loci.slim.fit: Interface for curve fitting algorithms.
ICurveRenderer - Interface in loci.slim.fit: Interface defining methods common to all curve renderers.
id - Variable in class loci.visbio.data.TransformEvent: The type of transform event.
ids - Variable in class loci.visbio.data.ThumbnailCache: Thumbnail id strings.
IGNORE - Static variable in class loci.visbio.overlays.OverlayIO
ignore - Variable in class loci.visbio.view.ColorPane: Should changes to the color components be ignored?
ignoreEvents - Variable in class loci.visbio.overlays.OverlayWidget: Flag indicating AWT/Swing events should be ignored, used for programmatic update of GUI components.
ILinkedPlugin - Interface in loci.multiinstanceplugin: Provides an interface to chain plugins together.
Image - Class in loci.multithreadedplugin: TODO
Image() - Constructor for class loci.multithreadedplugin.Image
image - Variable in class loci.slim.fit.BurnInRenderer
imageBox - Variable in class loci.visbio.view.CaptureHandler: File chooser for snapshot output.
ImageJUtil - Class in loci.visbio.util: ImageJUtil contains useful ImageJ functions.
ImageTransform - Class in loci.visbio.data: ImageTransform is a DataTransform superclass that provides image data.
ImageTransform() - Constructor for class loci.visbio.data.ImageTransform: Constructs an uninitialized image transform.
ImageTransform(DataTransform, String) - Constructor for class loci.visbio.data.ImageTransform: Creates an image transform with the given transform as its parent.
ImageTransform(DataTransform, String, double, double, double) - Constructor for class loci.visbio.data.ImageTransform: Creates an image transform with the given transform as its parent, that is dimensioned according to the specified values in microns.
ImageWrapper - Class in loci.deepzoom.plugin: Wrapper for an image.
ImageWrapper(ImageProcessor) - Constructor for class loci.deepzoom.plugin.ImageWrapper: Creates an ImageWrapper based on an ImageJ ImageProcessor.
ImageWrapper(ImageWrapper) - Constructor for class loci.deepzoom.plugin.ImageWrapper: Creates an ImageWrapper based on another ImageWrapper.
ImageWrapper(ImageWrapper, String, int, int) - Constructor for class loci.deepzoom.plugin.ImageWrapper: Creates an ImageWrapper for a new image based on another ImageWrapper.
Img - Annotation Type in loci.deepzoom.plugin.annotations: TODO
IModule - Interface in loci.deepzoom.workflow: TODO
IModuleFactory - Interface in loci.deepzoom.workflow: TODO
Import_Slide_Scanner_ROIs - Class in loci.apps.SlideScannerImport
Import_Slide_Scanner_ROIs() - Constructor for class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
importData(JComponent, Transferable) - Method in class loci.visbio.BioDropHandler: Performs a drop operation with the given transferable component.
importData() - Method in class loci.visbio.data.DataManager: Imports a dataset.
importData(Component) - Method in class loci.visbio.data.DataManager: Imports a dataset, using the given parent component for user dialogs.
incorporate(BasicEvent) - Method in class de.sciss.jcollider.gui.NumberEvent
incorporate(BasicEvent) - Method in class de.sciss.jcollider.NodeEvent: Used by the EventManager to fuse successive events together when they queue.
incorporate(BasicEvent) - Method in class de.sciss.jcollider.ServerEvent: Used by the EventManager to fuse successive events together when they queue.
incrementAll() - Method in class loci.visbio.overlays.FreeformExtension: Simultaneously increments all extension pointers into node array, to adjust for the insertion of a node before the base of the extension.
indices - Variable in class loci.visbio.view.BioSlideWidget: Indices into affected transforms.
INFO - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the event was created by a /n_query command
inform(String) - Static method in class de.sciss.jcollider.Server
infos - Static variable in class de.sciss.jcollider.UGenInfo: This field contains a read-only map which maps String (ugen class names and alias names such as the unary/binary operator names) to UGenInfo elements).
init(String, int, int, double) - Static method in class loci.apps.flow.FlowCyto
INIT - Static variable in class loci.visbio.overlays.FreeformTool: Constant for "init" mode.
INIT - Static variable in class loci.visbio.overlays.OverlayIO
initColors(boolean) - Method in class loci.visbio.view.ColorHandler: Applies color settings to the latest linked data object.
initialEdge - Variable in class loci.visbio.view.DisplayWindow: Initial edge of breakaway panel.
initialize() - Method in class loci.slim.fit.GACurveFitter
initialize() - Method in class loci.sonification.Sonification
initializeReader(File) - Static method in class loci.plugins.stitching.TileUtils
initLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Initializes some look and feel parameters.
initState(Dynamic) - Method in class loci.visbio.data.ArbitrarySlice: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.CollapseTransform: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.DataSampling: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.Dataset: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.DataTransform: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.ProjectionTransform: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.data.SpectralTransform: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.ext.ExternalFunction: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.overlays.OverlayTransform: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in interface loci.visbio.state.Dynamic: Modifies this object's state to match that of the given object.
initState(CaptureHandler) - Method in class loci.visbio.view.CaptureHandler: Modifies this object's state to match that of the given object.
initState(ColorHandler) - Method in class loci.visbio.view.ColorHandler: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.view.DisplayPosition: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.view.DisplayWindow: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.view.StackLink: Modifies this object's state to match that of the given object.
initState(TransformHandler) - Method in class loci.visbio.view.TransformHandler: Modifies this object's state to match that of the given object.
initState(Dynamic) - Method in class loci.visbio.view.TransformLink: Modifies this object's state to match that of the given object.
initState(ViewHandler) - Method in class loci.visbio.view.ViewHandler: Modifies this object's state to match that of the given object.
initTree() - Method in class de.sciss.jcollider.Server: After the server has been contacted, calling this method will create the default group.
INode - Interface in loci.multithreadedplugin: Defines call that are made externally to an INode.
Input - Annotation Type in loci.deepzoom.plugin.annotations: TODO
input(ItemWrapper) - Method in interface loci.deepzoom.workflow.IModule: Furnish default input image
input(ItemWrapper, String) - Method in interface loci.deepzoom.workflow.IModule: Furnish named input image
input(ItemWrapper) - Method in class loci.deepzoom.workflow.PluginModule: Furnish input image.
input(ItemWrapper, String) - Method in class loci.deepzoom.workflow.PluginModule: Furnish input image
INPUT - Static variable in class loci.deepzoom.workflow.WorkFlow
input(ItemWrapper) - Method in class loci.deepzoom.workflow.WorkFlow
input(ItemWrapper, String) - Method in class loci.deepzoom.workflow.WorkFlow
INPUTS - Static variable in class loci.deepzoom.workflow.WorkFlow
insertNode(int, float, float, boolean) - Method in class loci.visbio.overlays.OverlayNodedObject: Inserts a node at coordinates provided before the node at the index provided.
insertUpdate(DocumentEvent) - Method in class loci.slim.ColorWidget
insertUpdate(DocumentEvent) - Method in class loci.slim.SlimPlotter
insertUpdate(DocumentEvent) - Method in class loci.slim.TwoDPane
insertUpdate(DocumentEvent) - Method in class loci.visbio.overlays.OverlayWidget
insertUpdate(DocumentEvent) - Method in class loci.visbio.view.ColorPane: Handles text field additions.
insertUpdate(DocumentEvent) - Method in class loci.visbio.view.ViewPanel: Handles text insertions into a text field.
inside(float[], float[], float[]) - Static method in class loci.visbio.util.MathUtil: Whether the point a is inside the N-D box implied by points b2 and b2 (i.e., in 2D, whether a is inside the box with diagonal b1-b2; in 3D, whether a is inside the cube with diagonal b1-b2).
INSTANCE_PORT - Static variable in class loci.visbio.VisBio: Port to use for communicating between application instances.
InstanceServer - Class in loci.visbio.util: The InstanceServer provides a mechanism for managing the instances of an application running concurrently.
InstanceServer(int) - Constructor for class loci.visbio.util.InstanceServer: Creates a new instance server on the given port.
instanceServer - Variable in class loci.visbio.VisBioFrame: Instance server for this instance of VisBio.
instanceSpawned(SpawnEvent) - Method in interface loci.visbio.util.SpawnListener: Used to notify listeners when a new application instance is spawned.
instanceSpawned(SpawnEvent) - Method in class loci.visbio.VisBioFrame: Responds when new instances of VisBio are spawned.
INT_TYPE - Static variable in class loci.jvmlink.ConnThread
interpretROISfromVentana(String) - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
interpretROISfromXML() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
interpretROISfromXML(String) - Static method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
interpretROISfromXML() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
interpretROISfromXML(String) - Static method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
intersects(Segment2D) - Method in class loci.visbio.util.Segment2D: Whether another segment intersects this one.
IOutputListener - Interface in loci.deepzoom.workflow: TODO
IPipelineProcessor - Interface in loci.chainableplugin: Interface for a pipelined processor.
IPlugin - Interface in loci.deepzoom.workflow.plugin: Interface for a Plugin.
IPlugin - Interface in loci.multiinstanceplugin: Interface for a Plugin.
IPluginInternal - Interface in loci.deepzoom.workflow.plugin: Defines an internal interface that is used to launch a plugin.
IPluginInternal - Interface in loci.multiinstanceplugin: Defines an internal interface that is used to launch a plugin.
IPluginLauncher - Interface in loci.deepzoom.workflow.plugin: Interface to the plugin launcher.
IPluginLauncher - Interface in loci.multiinstanceplugin: Interface to the plugin launcher.
IProcessor - Interface in loci.chainableplugin: Interface for a processor.
IPropertyCollection - Interface in loci.chainableplugin
ir(String) - Static method in class de.sciss.jcollider.Control
ir(String, float) - Static method in class de.sciss.jcollider.Control
ir(String[], float[]) - Static method in class de.sciss.jcollider.Control
ir(String, float[]) - Static method in class de.sciss.jcollider.Control
ir(float) - Static method in class de.sciss.jcollider.UGen: A shorthand method for creating a constant in the ugen graph.
ir(String, int) - Static method in class de.sciss.jcollider.UGen
ir(String) - Static method in class de.sciss.jcollider.UGen
ir(String, int, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, int, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, int, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, int, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, int, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
ir(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
is3D() - Method in class loci.visbio.view.DisplayWindow: Gets whether this view handler's display is 3D.
is3DTextured() - Method in class loci.visbio.view.DisplayManager: Gets whether to use 3D texturing from VisBio options.
isAdjusting() - Method in class de.sciss.jcollider.gui.NumberEvent
isAlwaysDisplayed() - Method in class loci.visbio.util.MessagePane: Gets whether this warning pane should always be displayed.
isAnimating() - Method in class loci.visbio.view.TransformHandler: Gets whether display is currently animating.
isAnnotatedName(PluginAnnotations.InputOutput, String) - Method in class loci.deepzoom.workflow.plugin.PluginAnnotations: Checks whether a given name appears in the annotations for input or output images.
isAnnotatedName(PluginAnnotations.InputOutput, String) - Method in class loci.multiinstanceplugin.PluginAnnotations: Checks whether a given name appears in the annotations for input or output images.
isArray - Variable in class de.sciss.jcollider.UGenInfo.Arg: If true, this argument requires an array of values.
isAudioOut() - Method in class de.sciss.jcollider.Bus: Queries whether this bus is playing audio onto the hardware audio interface channels.
isAutoPopup() - Method in class loci.visbio.ConsoleManager: Gets whether consoles are automatically shown when output occurs.
isAutoSize() - Method in class loci.visbio.util.BreakawayPanel: Gets whether changing the edge intelligently resizes the owner window.
isBooting() - Method in class de.sciss.jcollider.Server: Queries the booting state
isBoundingBox() - Method in class loci.visbio.view.ViewHandler: Gets visibility of the display's bounding box.
isBoundingBoxVisible() - Method in class loci.visbio.view.StackLink: Gets visibility of the given data transform's yellow bounding box.
IScheduledNode - Interface in loci.multithreadedplugin: Methods used by the NodeScheduler and AbstractBaseNode as well as those available to use within the INode implementation.
isCompatible(Dynamic) - Method in class loci.visbio.data.ArbitrarySlice: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.CollapseTransform: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.DataSampling: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.Dataset: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.DataTransform: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.ProjectionTransform: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.data.SpectralTransform: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.ext.ExternalFunction: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.overlays.OverlayTransform: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in interface loci.visbio.state.Dynamic: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.view.DisplayPosition: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.view.DisplayWindow: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.view.StackLink: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isCompatible(Dynamic) - Method in class loci.visbio.view.TransformLink: Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
isDebug() - Method in class loci.visbio.ConsoleManager: Gets whether debugging mode is enabled.
isDefault() - Method in class loci.visbio.data.ThumbnailCache: Gets whether the default cache file was used because the one supplied to the constructor was unavailable.
isDefFile(File) - Static method in class de.sciss.jcollider.SynthDef: Checks to see if a given file is a synth definition file.
isDisplay3D(DisplayImpl) - Static method in class loci.visbio.util.DisplayUtil: Determines whether the given display is 3D.
isDrawing() - Method in class loci.visbio.overlays.OverlayObject: Gets whether this overlay is still being initially drawn.
isFilled() - Method in class loci.visbio.overlays.OverlayObject: Gets whether overlay is solid.
isFilled() - Method in class loci.visbio.overlays.OverlayWidget: Gets whether current overlay is filled.
isGTKLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Gets whether the current look and feel is GTK+.
isHighlightNode() - Method in class loci.visbio.overlays.OverlayNodedObject: True iff there is a highlighted node.
isImmediate() - Method in class loci.visbio.data.ArbitrarySlice: Arbitrary slices are rendered immediately, due to frequent user interaction.
isImmediate() - Method in class loci.visbio.data.DataTransform: Gets whether this transform should be drawn immediately, or "burned in" at full resolution after the usual delay by a separate thread.
isImmediate() - Method in class loci.visbio.data.ImageTransform: Most image transforms are not rendered immediately.
isImmediate() - Method in class loci.visbio.overlays.OverlayTransform: Overlay transforms are rendered immediately, due to frequent user interaction.
isInteger() - Method in class de.sciss.jcollider.gui.NumberSpace: States if the NumberSpace's quant is integer (and not zero).
isJNLP() - Method in class loci.visbio.SystemManager: Detects whether VisBio was launched with Java Web Start.
isLeaf() - Method in class de.sciss.jcollider.Group
isLeaf() - Method in class de.sciss.jcollider.Synth
isLineVisible() - Method in class loci.visbio.data.ArbitrarySlice: Gets whether slicing line is shown.
isLinux() - Static method in class loci.visbio.overlays.SpreadsheetLauncher: Whether OS is Linux.
isListening() - Method in class de.sciss.jcollider.OSCResponderNode: Queries the node's state.
isLocal() - Method in class de.sciss.jcollider.Server: Returns true if the server has an address on the same machine as the client.
isMac() - Static method in class loci.visbio.overlays.SpreadsheetLauncher: Whether the OS is mac.
isMacLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Gets whether the current look and feel is Mac OS X native.
isMacOS - Static variable in class de.sciss.jcollider.JCollider: true if we're running on Mac OS X.
isNearEndNode() - Method in class loci.visbio.overlays.FreeformTool.DistanceQuery: Whether the nearest node is an end node.
isNewPackage(String, String) - Static method in class loci.jar2lib.ClassList: Returns true iff the two classes are from different packages.
isNiceTransparency() - Method in class loci.visbio.view.DisplayManager: Gets whether to use nicest transparency mode from VisBio options.
isNotified() - Method in class de.sciss.jcollider.Server: Queries the server notification status.
isParallel() - Method in class loci.visbio.view.ViewHandler: Gets whether 3D display uses a parallel projection.
isParentRequired() - Static method in class loci.visbio.data.ArbitrarySlice: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.data.CollapseTransform: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.data.DataSampling: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.data.Dataset: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.data.ProjectionTransform: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.data.SpectralTransform: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.ext.ExternalProgram: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.ext.MatlabFunction: Indicates whether this transform type requires a parent transform.
isParentRequired() - Static method in class loci.visbio.overlays.OverlayTransform: Indicates whether this transform type requires a parent transform.
isPlasticLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Gets whether the current look and feel is one of the JGoodies Plastic series.
isPlaying() - Method in class de.sciss.jcollider.Node: Queries whether the node exists on the server and is playing (not paused).
isProbe() - Method in class loci.slim.MouseBehaviorButtons
isRegion() - Method in class loci.slim.MouseBehaviorButtons
isRestoring() - Method in class loci.visbio.state.StateManager: Gets whether state is currently being restored.
isRunning() - Method in class de.sciss.jcollider.Node: Queries whether the node exists on the server.
isRunning() - Method in class de.sciss.jcollider.Server: Queries the running state.
isScalable() - Method in class loci.visbio.overlays.OverlayMarker: OverlayMarker's are scalable--returns true.
isScalable() - Method in class loci.visbio.overlays.OverlayObject: Gets whether overlay is scalable.
isScale() - Method in class loci.visbio.view.ViewHandler: Gets visibility of scale.
isSelected() - Method in class loci.visbio.overlays.OverlayObject: Gets whether this overlay is currently selected.
isShowable(DisplayWindow) - Method in class loci.visbio.view.DisplayControls: Gets whether the given display should be allowed to be shown onscreen.
isSliceComputed() - Method in class loci.visbio.data.ArbitrarySlice: Gets whether arbitary slice is computed.
isSliceVisible(int) - Method in class loci.visbio.view.StackLink: Gets visibility at the specified slice index.
isSmooth() - Method in class loci.visbio.view.CaptureHandler: Gets whether transitions use a smoothing sine function.
isSmooth() - Method in class loci.visbio.view.CapturePanel: Gets whether transitions use a smoothing sine function.
isStopped() - Method in class loci.visbio.BioTask: Gets whether the task has been stopped.
issueComments(boolean) - Static method in class loci.backup.github.ResumePoint
issueComments(boolean, int) - Static method in class loci.backup.github.ResumePoint
isTextDrawn() - Method in class loci.visbio.overlays.OverlayTransform: Gets whether text is drawn.
isTextureMapped() - Method in class loci.visbio.view.DisplayManager
isUndoable() - Method in class loci.visbio.VisBioEvent: Gets whether the event is undoable.
isValidDimension(int) - Method in class loci.visbio.data.ArbitrarySlice: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.CollapseTransform: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.DataSampling: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.Dataset: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.DataTransform: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.ProjectionTransform: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.data.SpectralTransform: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.ext.ExternalFunction: Gets whether this transform provides data of the given dimensionality.
isValidDimension(int) - Method in class loci.visbio.overlays.OverlayTransform: Gets whether this transform provides data of the given dimensionality.
isValidParent(DataTransform) - Static method in class loci.visbio.data.ArbitrarySlice: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.data.CollapseTransform: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.data.DataSampling: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.data.Dataset: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.data.ProjectionTransform: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.data.SpectralTransform: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.ext.ExternalProgram: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.ext.MatlabFunction: Indicates whether this transform type would accept the given transform as its parent transform.
isValidParent(DataTransform) - Static method in class loci.visbio.overlays.OverlayTransform: Indicates whether this transform type would accept the given transform as its parent transform.
isVisible() - Method in class loci.visbio.view.StackLink: Gets visibility of the transform.
isVisible() - Method in class loci.visbio.view.TransformLink: Gets visibility of the transform.
isVolumeRendered() - Method in class loci.visbio.view.StackLink: Gets status of volume rendering.
isWatching() - Method in class de.sciss.jcollider.NodeWatcher: Queries the watching state
isWindows - Static variable in class de.sciss.jcollider.JCollider: true if we're running on a Windows system
isWindows() - Static method in class loci.visbio.overlays.SpreadsheetLauncher: Whether the OS is windows.
isWindowsLookAndFeel() - Static method in class loci.visbio.util.LAFUtil: Gets whether the current look and feel is Windows native.
itemStateChanged(ItemEvent) - Method in class loci.slim.SlimPlotter
itemStateChanged(ItemEvent) - Method in class loci.visbio.data.SliceWidget: Handles combo box updates.
itemStateChanged(ItemEvent) - Method in class loci.visbio.view.CapturePanel: Called when check box is toggled.
itemStateChanged(ItemEvent) - Method in class loci.visbio.view.ColorPane: ItemListener method for handling color mapping changes.
ItemWrapper - Class in loci.deepzoom.workflow.plugin: Wrapper for wired data item.
ItemWrapper(Object) - Constructor for class loci.deepzoom.workflow.plugin.ItemWrapper: Creates an ItemWrapper based on an ImageJ ImageProcessor.
ItemWrapper(ItemWrapper) - Constructor for class loci.deepzoom.workflow.plugin.ItemWrapper: Creates an ItemWrapper based on another ItemWrapper.
iterate() - Method in class loci.slim.fit.CurveFitter: iterate() runs through one iteration of whatever curve fitting technique this curve fitter uses.
iterate() - Method in class loci.slim.fit.GACurveFitter: iterate() runs through one iteration of whatever curve fitting technique this curve fitter uses.
iterate() - Method in interface loci.slim.fit.ICurveFitter: iterate() runs through one iteration of whatever curve fitting technique this curve fitter uses.
iterate() - Method in class loci.slim.fit.LMCurveFitter
iterCount - Variable in class loci.slim.fit.LMCurveFitter
IWorkFlow - Interface in loci.deepzoom.workflow: An interface to build a workflow based on components that are chained together.

J

Jar2Lib - Class in loci.jar2lib: Generates a C++ project for C++ proxies corresponding to a list of Java JAR files.
Jar2Lib() - Constructor for class loci.jar2lib.Jar2Lib
JCollider - Class in de.sciss.jcollider: This is a helper class containing utility static functions
JCollider() - Constructor for class de.sciss.jcollider.JCollider
JVMLinkServer - Class in loci.jvmlink: Java server for JVMLink.
JVMLinkServer(int) - Constructor for class loci.jvmlink.JVMLinkServer

K

kAddAfter - Static variable in interface de.sciss.jcollider.Constants
kAddBefore - Static variable in interface de.sciss.jcollider.Constants
kAddReplace - Static variable in interface de.sciss.jcollider.Constants
kAddToHead - Static variable in interface de.sciss.jcollider.Constants
kAddToTail - Static variable in interface de.sciss.jcollider.Constants
kAudioRate - Static variable in interface de.sciss.jcollider.Constants
kControlRate - Static variable in interface de.sciss.jcollider.Constants
kDemandRate - Static variable in interface de.sciss.jcollider.Constants
kDoneFree - Static variable in interface de.sciss.jcollider.Constants: done action: free the enclosing synth
kDoneFreeAll - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and all other nodes in this group (before and after)
kDoneFreeAllPred - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and all preceding nodes in this group
kDoneFreeAllSucc - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and all following nodes in this group
kDoneFreeGroup - Static variable in interface de.sciss.jcollider.Constants: done action: free the enclosing group and all nodes within it (including this synth)
kDoneFreePausePred - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and pause the preceding node
kDoneFreePauseSucc - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and pause the following node
kDoneFreePred - Static variable in interface de.sciss.jcollider.Constants: done action: free both this synth and the preceding node
kDoneFreePredGroup - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth; if the preceding node is a group then do g_freeAll on it, else free it
kDoneFreePredGroupDeep - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and if the preceding node is a group then do g_deepFree on it, else free it
kDoneFreeSucc - Static variable in interface de.sciss.jcollider.Constants: done action: free both this synth and the following node
kDoneFreeSuccGroup - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth; if the following node is a group then do g_freeAll on it, else free it
kDoneFreeSuccGroupDeep - Static variable in interface de.sciss.jcollider.Constants: done action: free this synth and if the following node is a group then do g_deepFree on it, else free it
kDoneNothing - Static variable in interface de.sciss.jcollider.Constants: done action: do nothing when the UGen is finished
kDonePause - Static variable in interface de.sciss.jcollider.Constants: done action: pause the enclosing synth, but do not free it
kDumpBoth - Static variable in interface de.sciss.jcollider.Constants
kDumpHex - Static variable in interface de.sciss.jcollider.Constants
kDumpOff - Static variable in interface de.sciss.jcollider.Constants
kDumpText - Static variable in interface de.sciss.jcollider.Constants
KerberosAuth - Class in loci.wiscscan.auth: Code to manage kerberos user authentication in WiscScan.
KerberosAuth() - Constructor for class loci.wiscscan.auth.KerberosAuth
keyPressed(int, int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to a key press.
keyPressed(KeyEvent) - Method in class loci.visbio.view.DisplayWindow: Handles key presses.
keyReleased(int, int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to a key release.
keyReleased(KeyEvent) - Method in class loci.visbio.view.DisplayWindow: Handles key releases.
keys - Variable in class loci.visbio.data.DatasetWidget: Metadata hashtable's sorted key lists.
keyTyped(KeyEvent) - Method in class loci.visbio.view.DisplayWindow: Handles key strokes.
kHeaderAIFF - Static variable in interface de.sciss.jcollider.Constants: header format used for /b_write: AIFF
kHeaderIRCAM - Static variable in interface de.sciss.jcollider.Constants: header format used for /b_write: IRCAM
kHeaderNeXT - Static variable in interface de.sciss.jcollider.Constants: header format used for /b_write: NeXT / AU
kHeaderRaw - Static variable in interface de.sciss.jcollider.Constants: header format used for /b_write: Raw (headerless)
kHeaderWAVE - Static variable in interface de.sciss.jcollider.Constants: header format used for /b_write: WAVE
kr(String) - Static method in class de.sciss.jcollider.Control
kr(String, float) - Static method in class de.sciss.jcollider.Control
kr(String[], float[]) - Static method in class de.sciss.jcollider.Control
kr(String, float[]) - Static method in class de.sciss.jcollider.Control
kr(String, float, float) - Static method in class de.sciss.jcollider.LagControl
kr(String[], float[], float[]) - Static method in class de.sciss.jcollider.LagControl
kr(String) - Static method in class de.sciss.jcollider.TrigControl
kr(String, float) - Static method in class de.sciss.jcollider.TrigControl
kr(String[], float[]) - Static method in class de.sciss.jcollider.TrigControl
kr(String, int) - Static method in class de.sciss.jcollider.UGen
kr(String) - Static method in class de.sciss.jcollider.UGen
kr(String, int, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, int, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, int, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, int, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, int, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kr(String, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem, GraphElem) - Static method in class de.sciss.jcollider.UGen
kSampleALaw - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 8-bit a-law noise
kSampleDouble - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: double precision floating point
kSampleFloat - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: single precision floating point
kSampleInt16 - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 16-bit integer
kSampleInt24 - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 24-bit integer
kSampleInt32 - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 32-bit integer
kSampleInt8 - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 8-bit integer
kSampleMuLaw - Static variable in interface de.sciss.jcollider.Constants: sample encoding used for /b_write: 8-bit mu-law noise
kScalarRate - Static variable in interface de.sciss.jcollider.Constants
kw1 - Variable in class loci.niche.MODSForm
kw2 - Variable in class loci.niche.MODSForm
kw3 - Variable in class loci.niche.MODSForm

L

labels() - Static method in enum loci.plugins.stitching.StitchOmeTiff.FusionMethod
labels() - Static method in enum loci.plugins.stitching.StitchPrairieTiff.FusionMethod
labels - Variable in class loci.visbio.data.DataTransform: Label for each value at each dimensional axis.
labels - Variable in class loci.visbio.data.SpectralWidget: Labels indicating current slider values.
LAFUtil - Class in loci.visbio.util: LAFUtil contains useful functions relating to Look and Feel.
LagControl - Class in de.sciss.jcollider: Class for the LagControl UGen.
last - Variable in class loci.visbio.data.ThumbnailCache: Last retrieved thumbnail index.
lastIndex - Variable in class loci.slim.fit.CurveFitter
lastName - Variable in class loci.niche.MODSForm
lastPos - Variable in class loci.visbio.view.StackLink: Last known dimensional position of the link.
lastToolType - Variable in class loci.visbio.overlays.OverlayTransform: Type of last tool used.
launch(String[]) - Static method in class loci.visbio.VisBio: Launches VisBio, returning the newly constructed VisBioFrame object.
launchSpreadsheet(File) - Method in class loci.visbio.overlays.OverlayWidget: Launches the spreadsheet.
launchSpreadsheet(File) - Method in class loci.visbio.overlays.SpreadsheetLauncher: Tries to launch the appropriate spreadsheet application.
launchSpreadsheet(File, String) - Method in class loci.visbio.overlays.SpreadsheetLauncher: Tries to launch the appropriate spreadsheet application.
left - Variable in class loci.visbio.util.BreakawayPanel: Arrow buttons.
leftRightBox - Variable in class loci.visbio.view.TransformPanel: List of axes for left/right arrow mapping.
LENGTH - Static variable in class loci.visbio.overlays.OverlayArrow
LENGTH - Static variable in class loci.visbio.overlays.OverlayLine
LENGTH - Static variable in class loci.visbio.overlays.OverlayNodedObject
lengths - Variable in class loci.visbio.data.DataTransform: Length of each dimension in the multidimensional structure.
LevelProcessor - Class in loci.multiinstanceplugin.deepzoom: Class at the top of the image chain.
LevelProcessor() - Constructor for class loci.multiinstanceplugin.deepzoom.LevelProcessor
LevelProcessorX() - Constructor for class loci.multiinstanceplugin.deepzoom.DeepZoomExporter.LevelProcessorX
lin - Static variable in class de.sciss.jcollider.gui.Warp
LIN_PATH - Static variable in class loci.visbio.overlays.SpreadsheetLauncher: Default path to spreadsheet (OpenOffice) on Linux computers.
line - Variable in class loci.visbio.overlays.LineTool: Line currently being drawn.
line - Variable in class loci.visbio.overlays.PolylineTool: Curve currently being drawn or modified.
LINEAR - Static variable in class loci.visbio.util.ColorUtil: Linear color table component used in several presets.
LineLength - Class in <Unnamed>: Scans text files for lines longer than a specified length.
LineLength(String) - Constructor for class LineLength
LineTool - Class in loci.visbio.overlays: LineTool is the tool for creating measurement lines.
LineTool(OverlayTransform) - Constructor for class loci.visbio.overlays.LineTool: Constructs a measurement line creation tool.
link(VisBioFrame) - Static method in class loci.visbio.MacAdapter: Associates the VisBio frame with a Mac OS X adapter.
link - Variable in class loci.visbio.view.ColorHandler: Associated link between data object and display.
link() - Method in class loci.visbio.view.StackLink: Links this stack into the display.
link() - Method in class loci.visbio.view.TransformLink: Links this transform into the display.
LinkedPlugin - Class in loci.multiinstanceplugin: The LinkedPlugin represents a given plugin class in a given stage of a pipeline.
LinkedPlugin(Class<?>) - Constructor for class loci.multiinstanceplugin.LinkedPlugin: Create an instance for a given class.
linkMenuItem(JMenuItem, JMenuItem) - Static method in class loci.visbio.util.SwingUtil: Forces slave menu item to reflect master menu item using a property change listener.
links - Variable in class loci.visbio.view.TransformHandler: Data transform links.
listen() - Method in class loci.jvmlink.JVMLinkServer: Orders the server to begin listening for incoming connections.
listener - Variable in class loci.visbio.data.Dataset: Optional listener for constructor progress.
listeners - Variable in class loci.visbio.data.DataTransform: List of transform listeners.
listeners - Variable in class loci.visbio.util.InstanceServer: List of application instance spawn listeners.
listModel - Variable in class loci.visbio.view.DisplayControls: Display list model.
ListOption - Class in loci.visbio.state: ListOption is an option from a list in the VisBio Options dialog.
ListOption(String, String, String[]) - Constructor for class loci.visbio.state.ListOption: Constructs a new option.
lm - Variable in class loci.visbio.ControlPanel: Associated logic manager.
lma - Variable in class loci.slim.fit.LMCurveFitter
LMCurveFitter - Class in loci.slim.fit: Levenberg-Marquardt curve fitter that uses L-M Fit package.
LMCurveFitter() - Constructor for class loci.slim.fit.LMCurveFitter
LMCurveFitter.ConsoleStream - Class in loci.slim.fit: HACK - OutputStream extension for filtering out hardcoded RuntimeException.printStackTrace() exceptions within LMA library.
LMCurveFitter.ExpFunction - Class in loci.slim.fit: A summed exponential function of the form: y(t) = a1*e^(-b1*t) + ...
lo - Variable in class loci.visbio.view.ColorHandler: Minimum and maximum color range values.
load(Server) - Method in class de.sciss.jcollider.SynthDef: Stores the def in a temp file and sends a corresponding OSC /d_load message to the server.
load(Server, OSCMessage) - Method in class de.sciss.jcollider.SynthDef: Stores the def in a temp file and sends a corresponding OSC /d_load message to the server.
load(Server, OSCMessage, File) - Method in class de.sciss.jcollider.SynthDef: Stores the def in a file and sends a corresponding OSC /d_load message to the server.
load(long) - Method in class loci.visbio.data.ThumbnailCache: Loads the data object at the given byte offset of the cache file.
load - Variable in class loci.visbio.overlays.OverlayWidget: Button for loading overlays from disk.
loadColorTable(File) - Static method in class loci.visbio.util.ColorUtil: Loads the color table from the given file.
loader - Variable in class loci.visbio.data.ThumbnailHandler: Background thumbnail generation thread.
loadOverlays(BufferedReader, OverlayTransform) - Static method in class loci.visbio.overlays.OverlayIO: Reads the overlays from the given reader.
loadOverlays(BufferedReader) - Method in class loci.visbio.overlays.OverlayTransform: Reads the overlays from the given reader.
loadSettings() - Method in class loci.visbio.overlays.StatsOptionsPane: Loads current pane selections from OptionManager.
loadThumb(int) - Method in class loci.visbio.data.ThumbnailHandler: Computes the ith thumbnail.
loc - Variable in class loci.visbio.data.ArbitrarySlice: Arbitrary slice's location along slicing line.
location - Variable in class loci.visbio.data.SliceWidget: Slider for adjusting location.
locations - Variable in class loci.visbio.util.Docker: List of window locations.
locationValue - Variable in class loci.visbio.data.SliceWidget: Label for current location value.
loci.apps - package loci.apps
loci.apps.flow - package loci.apps.flow
loci.apps.prairie - package loci.apps.prairie
loci.apps.SlideScannerImport - package loci.apps.SlideScannerImport
loci.backup.github - package loci.backup.github
loci.chainableplugin - package loci.chainableplugin
loci.chainableplugin.deepzoom - package loci.chainableplugin.deepzoom
loci.checks - package loci.checks
loci.deepzoom - package loci.deepzoom
loci.deepzoom.plugin - package loci.deepzoom.plugin
loci.deepzoom.plugin.annotations - package loci.deepzoom.plugin.annotations
loci.deepzoom.util.xmllight - package loci.deepzoom.util.xmllight
loci.deepzoom.workflow - package loci.deepzoom.workflow
loci.deepzoom.workflow.plugin - package loci.deepzoom.workflow.plugin
loci.jar2lib - package loci.jar2lib
loci.jvmlink - package loci.jvmlink
loci.maven.plugin.cppwrap - package loci.maven.plugin.cppwrap
loci.multiinstanceplugin - package loci.multiinstanceplugin
loci.multiinstanceplugin.deepzoom - package loci.multiinstanceplugin.deepzoom
loci.multithreadedplugin - package loci.multithreadedplugin
loci.niche - package loci.niche
loci.plugins - package loci.plugins
loci.plugins.stitching - package loci.plugins.stitching
loci.slim - package loci.slim
loci.slim.data - package loci.slim.data
loci.slim.fit - package loci.slim.fit
loci.sonification - package loci.sonification
loci.visbio - package loci.visbio
loci.visbio.data - package loci.visbio.data
loci.visbio.ext - package loci.visbio.ext
loci.visbio.help - package loci.visbio.help
loci.visbio.overlays - package loci.visbio.overlays
loci.visbio.state - package loci.visbio.state
loci.visbio.util - package loci.visbio.util
loci.visbio.view - package loci.visbio.view
loci.wiscscan - package loci.wiscscan
loci.wiscscan.auth - package loci.wiscscan.auth
log(String) - Method in class loci.jar2lib.Jar2Lib
log(String) - Static method in class loci.slim.SlimPlotter: Logs the given output to the appropriate location.
logFile - Variable in class de.sciss.jcollider.gui.LogTextArea
logFileWriter - Variable in class de.sciss.jcollider.gui.LogTextArea
LOGIC_ADDED - Static variable in class loci.visbio.VisBioEvent: Indicates a new logic manager has been integrated into VisBio.
LogicManager - Class in loci.visbio: LogicManager is the superclass of all VisBio logic handlers.
LogicManager(VisBioFrame) - Constructor for class loci.visbio.LogicManager: Constructs a logic manager.
logInImageJ(String) - Static method in class loci.apps.flow.FlowCyto
LogTextArea - Class in de.sciss.jcollider.gui: A JTextArea encompassing a PrintWriter that can be used as an alternative to the standard System.out or System.err objects.
LogTextArea(int, int, boolean, File) - Constructor for class de.sciss.jcollider.gui.LogTextArea: Constructs a new text area for logging messages.
LogTextArea() - Constructor for class de.sciss.jcollider.gui.LogTextArea
LONG_TYPE - Static variable in class loci.jvmlink.ConnThread
lostOwnership(Clipboard, Transferable) - Method in class loci.slim.TextTransfer
loVal - Variable in class loci.visbio.view.ColorPane: Text field for low color scale value.
LOW_PRIORITY - Static variable in class loci.visbio.util.Docker: A docking priority lower than the default.
LUT_BLUE - Static variable in class loci.visbio.util.ColorUtil: Blue color look-up table.
LUT_CYAN - Static variable in class loci.visbio.util.ColorUtil: Cyan color look-up table.
LUT_FIRE - Static variable in class loci.visbio.util.ColorUtil: Fire color look-up table.
LUT_GRAY - Static variable in class loci.visbio.util.ColorUtil: Grayscale color look-up table.
LUT_GREEN - Static variable in class loci.visbio.util.ColorUtil: Green color look-up table.
LUT_HSV - Static variable in class loci.visbio.util.ColorUtil: HSV color look-up table.
LUT_ICE - Static variable in class loci.visbio.util.ColorUtil: Ice color look-up table.
LUT_LEN - Static variable in class loci.visbio.util.ColorUtil: Color table file length.
LUT_MAGENTA - Static variable in class loci.visbio.util.ColorUtil: Magenta color look-up table.
LUT_NAMES - Static variable in class loci.slim.ColorWidget: Names for preset color look-up table.
LUT_NAMES - Static variable in class loci.visbio.view.ColorPane: Names for preset color look-up table.
LUT_RED - Static variable in class loci.visbio.util.ColorUtil: Red color look-up table.
LUT_RGB - Static variable in class loci.visbio.util.ColorUtil: RGB (pseudocolor) color look-up table.
LUT_YELLOW - Static variable in class loci.visbio.util.ColorUtil: Yellow color look-up table.
lutLoad - Variable in class loci.visbio.view.ColorPane: Button for loading color look-up table.
lutPresets - Variable in class loci.visbio.view.ColorPane: Button for selecting a color look-up table from a list of presets.
LUTS - Static variable in class loci.slim.ColorWidget: Preset color look-up tables.
LUTS - Static variable in class loci.visbio.view.ColorPane: Preset color look-up tables.
lutSave - Variable in class loci.visbio.view.ColorPane: Button for saving color look-up table.
lutsMenu - Variable in class loci.visbio.view.ColorPane: Popup menu for selecting a preset color look-up table.

M

m_password - Variable in class loci.wiscscan.auth.Credentials
m_username - Variable in class loci.wiscscan.auth.Credentials
MAC_PATH - Static variable in class loci.visbio.overlays.SpreadsheetLauncher: Default path to spreadsheet (Excel) on Macintosh computers.
MacAdapter - Class in loci.visbio: An adapter for handling the Mac OS X application menu items.
MacAdapter(VisBioFrame) - Constructor for class loci.visbio.MacAdapter: Constructs a Mac OS X adapter.
mag(float[]) - Static method in class loci.visbio.util.MathUtil: Computes the magnitude of an N-D vector.
main(String[]) - Static method in class Ascii
main(String[]) - Static method in class Binary
main(String[]) - Static method in class BinaryDiff
main(String[]) - Static method in class CompareTrees
main(String[]) - Static method in class CreateThumbnail
main(String[]) - Static method in class de.sciss.jcollider.JCollider: This method gets called when one tries to start the .jar file directly.
main(String[]) - Static method in class DownloadURL
main(String[]) - Static method in class DumpClass
main(String[]) - Static method in class EditDistance
main(String[]) - Static method in class FileOpsTest
main(String[]) - Static method in class FixEOLSpaces
main(String[]) - Static method in class LineLength
main(String[]) - Static method in class loci.apps.flow.Find_Particle_Areas
main(String[]) - Static method in class loci.apps.flow.FlowCyto
main(String[]) - Static method in class loci.apps.MultiLUT: Run with 'java -mx256m MultiLUT' in directory with SPB1.PIC, SPB2.PIC, ..., SPB17.PIC.
main(String[]) - Static method in class loci.apps.prairie.PrairieInjector
main(String[]) - Static method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
main(String...) - Static method in class loci.backup.github.GitHubBackup: Main method for running from the command line.
main(String[]) - Static method in class loci.backup.github.GitHubBackupGUI
main(String[]) - Static method in class loci.checks.About
main(String[]) - Static method in class loci.deepzoom.DeepZoom: Main method used for testing only.
main(String[]) - Static method in class loci.jar2lib.FixProxies
main(String[]) - Static method in class loci.jar2lib.Jar2Lib
main(String[]) - Static method in class loci.jar2lib.StringReplace
main(String[]) - Static method in class loci.jvmlink.JVMLinkServer
main(String...) - Static method in class loci.plugins.stitching.VisualizeTiles
main(String[]) - Static method in class loci.slim.data.MakeData
main(String[]) - Static method in class loci.slim.fit.CurveFitterTester
main(String[]) - Static method in class loci.slim.SlimPlotter
main(String[]) - Static method in class loci.sonification.Sonification
main(String[]) - Static method in class loci.sonification.SonificationTool
main(String[]) - Static method in class loci.visbio.util.Docker: Tests the Docker class.
main(String[]) - Static method in class loci.visbio.VisBio: Launches the VisBio GUI.
Main - Class in ome.xml.version: Main entry point into the OME-XML injector.
Main() - Constructor for class ome.xml.version.Main
main(String[]) - Static method in class ome.xml.version.Main
main(String[]) - Static method in class RandomPass
main(String[]) - Static method in class SortList
main(String[]) - Static method in class SysProps
main(String[]) - Static method in class TestMem
main(String[]) - Static method in class UniqueTraces
main(String[]) - Static method in class UnusedImports
MAJ - Static variable in class loci.visbio.overlays.OverlayOval
makeArgs(String, String, String, String, String, String, boolean) - Static method in class loci.backup.github.BackupTools
makeButton(Object, String, String, int, int) - Static method in class loci.visbio.util.SwingUtil: Constructs a JButton with an icon from the given file id.
makeButton(String, String, String, String) - Method in class loci.visbio.view.ViewPanel: Creates a button with a graphical icon.
makeButtons(boolean) - Method in class loci.visbio.util.DialogPane: Internal method for creating dialog buttons.
makeButtons(boolean) - Method in class loci.visbio.util.WizardPane: Internal method for creating dialog buttons.
makeCantIdentifyOSMessage() - Static method in class loci.visbio.overlays.SpreadsheetLauncher: Returns an error message indicating the OS could not be identified.
makeColumn(Object, Object) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeColumn(Object, Object, Object) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeColumn(Object[]) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeColumn(Object[], boolean[]) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeColumn(Object[], String, boolean) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeColumn(Object[], boolean[], String, boolean) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one column.
makeCommandErrorMessage(String) - Method in class loci.visbio.overlays.SpreadsheetLauncher: Makes an error message from the given command.
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim.SpringUtilities: Aligns the first rows * cols components of parent in a grid.
makeCube(FlatField, int) - Static method in class loci.visbio.util.DataUtil: Resamples a volume of the form ((x, y, z) -> (v1, ..., vn)) to the given resolution along each of its three spatial axes.
makeCurveFitters(int[][][], Class, int, int, int) - Static method in class loci.slim.fit.CurveCollection: Creates a list of curve fitters using the given data as a source.
MakeData - Class in loci.slim.data: Utility for synthesizing test data for use with curve fitting algorithms.
MakeData() - Constructor for class loci.slim.data.MakeData
makeDefaultMatrix() - Method in class loci.visbio.view.ViewHandler: Creates a matrix at the default orientation for the display.
makeDisplay(String, boolean) - Static method in class loci.visbio.util.DisplayUtil: Creates a VisAD display according to the given parameters.
makeDisplay(String, boolean, GraphicsConfiguration) - Static method in class loci.visbio.util.DisplayUtil: Creates a VisAD display according to the given parameters.
makeField(FlatField[], RealType) - Static method in class loci.visbio.util.DataUtil: Creates a field of the form (z -> type) from the given list of fields, where type is the MathType of each component field.
makeField(FlatField[], RealType, Unit) - Static method in class loci.visbio.util.DataUtil: Creates a field of the form (z -> type) from the given list of fields, where type is the MathType of each component field.
makeField(FlatField[], RealType, double, double) - Static method in class loci.visbio.util.DataUtil: Creates a field of the form (z -> type) from the given list of fields, where type is the MathType of each component field.
makeField(FlatField[], RealType, double, double, Unit) - Static method in class loci.visbio.util.DataUtil: Creates a field of the form (z -> type) from the given list of fields, where type is the MathType of each component field.
makeField(FlatField[], RealType, SampledSet) - Static method in class loci.visbio.util.DataUtil: Creates a field of the form (z -> type) from the given list of fields, where type is the MathType of each component field.
makeFileDoesNotExistMessage(File) - Method in class loci.visbio.overlays.SpreadsheetLauncher: Makes an error message from the given file.
makeGrid(Container, int, int, int, int, int, int) - Static method in class loci.slim.SpringUtilities: Aligns the first rows * cols components of parent in a grid.
makeGridded2DSets(RealTupleType, float[][], float[][], float[][], float) - Static method in class loci.visbio.overlays.OverlayUtil: Makes valid Gridded2DSets from the arrays supplied.
makeLabels() - Method in class loci.visbio.data.DataSampling: Creates labels based on data transform parameters.
makeLabels() - Method in class loci.visbio.data.DataTransform: Creates labels based on data transform parameters.
makeMappingsPanel() - Method in class loci.visbio.view.ColorPane: Constructs panel containing color mapping combo boxes.
makeModelPanel() - Method in class loci.visbio.view.ColorPane: Constructs panel containing color model radio buttons.
makePanel() - Method in class loci.visbio.view.StackHandler: Constructs GUI controls for the stack handler.
makePanel() - Method in class loci.visbio.view.TransformHandler: Constructs GUI controls for the transform handler.
makeRangeTuple() - Static method in class loci.visbio.overlays.OverlayTransform: Constructs the overlay range type for most overlays.
makeRow(Object, Object) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeRow(Object, Object, Object) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeRow(Object[]) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeRow(Object[], boolean[]) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeRow(Object[], String, boolean) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeRow(Object[], boolean[], String, boolean) - Static method in class loci.visbio.util.FormsUtil: Creates a panel with the given components in one row.
makeSliderPanel() - Method in class loci.visbio.view.ColorPane: Constructs panel with brightness, contrast and transparency sliders.
makeSystemOutput() - Method in class de.sciss.jcollider.gui.LogTextArea
makeTablesPanel() - Method in class loci.visbio.view.ColorPane: Constructs panel containing color table components.
makeThumb(Data) - Method in class loci.visbio.data.ThumbnailHandler: Creates an image thumbnail from the given data.
makeToggleButton(Object, String, String, int, int) - Static method in class loci.visbio.util.SwingUtil: Constructs a JToggleButton with an icon from the given file id.
makeTransform(DataManager) - Static method in class loci.visbio.data.ArbitrarySlice: Creates a new set of overlays, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.data.CollapseTransform: Creates a new dimensional collapse, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.data.DataSampling: Creates a new data sampling, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.data.Dataset: Creates a new dataset, with user interaction.
makeTransform(DataManager, File, Component) - Static method in class loci.visbio.data.Dataset: Creates a new dataset, with user interaction, with the given default file.
makeTransform(DataManager) - Static method in class loci.visbio.data.ProjectionTransform: Creates a new maximum intensity projection, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.data.SpectralTransform: Creates a new spectral mapping, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.ext.ExternalProgram: Creates a new external program, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.ext.MatlabFunction: Creates a new MATLAB transform, with user interaction.
makeTransform(DataManager) - Static method in class loci.visbio.overlays.OverlayTransform: Creates a new set of overlays, with user interaction.
makeWindow() - Method in class de.sciss.jcollider.gui.NodeTreePanel: Creates a window containing this panel.
makeWindow(Server) - Static method in class de.sciss.jcollider.gui.ServerPanel: Creates a window containing a ServerPanel for the given server.
makeWindow(Server, int) - Static method in class de.sciss.jcollider.gui.ServerPanel: Creates a window with custom flags.
manager - Variable in class loci.visbio.view.DisplayWindow: Associated display manager.
managers - Variable in class loci.visbio.VisBioFrame: Logic managers.
map(double) - Method in class de.sciss.jcollider.gui.ControlSpec
map(double, ControlSpec) - Method in class de.sciss.jcollider.gui.Warp
map(int[], int[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
map(String[], int[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
map(int[], Bus[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
map(String[], Bus[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
map(String, Bus) - Method in class de.sciss.jcollider.Node: Convenience method for a single mapping.
mapChanged(ScalarMapEvent) - Method in class loci.slim.ColorWidget
mapMsg(int[], int[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_map message to map a list of the node's control parameters to be automatically read from global control busses.
mapMsg(String[], int[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_map message to map a list of the node's control parameters to be automatically read from global control busses.
mapMsg(int[], Bus[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_map message to map a list of the node's control parameters to be automatically read from global control busses.
mapMsg(String[], Bus[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_map message to map a list of the node's control parameters to be automatically read from global control busses.
mapMsg(String, Bus) - Method in class de.sciss.jcollider.Node: Convenience method for a single mapping.
mapn(int[], int[], int[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
mapn(String[], int[], int[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
mapn(int[], Bus[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
mapn(String[], Bus[]) - Method in class de.sciss.jcollider.Node: Maps a list of the node's control parameters to be automatically read from global control busses.
mapnMsg(int[], int[], int[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_map message to map a list of the node's control parameters to be automatically read from global control busses.
mapnMsg(String[], int[], int[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_mapn message to map a list of the node's control parameters to be automatically read from global control busses.
mapnMsg(int[], Bus[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_mapn message to map a list of the node's control parameters to be automatically read from global control busses.
mapnMsg(String[], Bus[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_mapn message to map a list of the node's control parameters to be automatically read from global control busses.
mapping - Variable in class loci.visbio.data.SpectralWidget: Associated spectral mapping.
maps - Variable in class loci.visbio.view.ColorPane: List of mappings from range components to RGB.
marker - Variable in class loci.visbio.overlays.MarkerTool: Marker currently being drawn.
MarkerTool - Class in loci.visbio.overlays: MarkerTool is the tool for creating measurement markers.
MarkerTool(OverlayTransform) - Constructor for class loci.visbio.overlays.MarkerTool: Constructs a measurement marker creation tool.
mask - Variable in class loci.slim.fit.BurnInRenderer
maskCount - Variable in class loci.slim.fit.BurnInRenderer
matches(Dynamic) - Method in class loci.visbio.data.ArbitrarySlice: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.data.CollapseTransform: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.data.DataSampling: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.data.Dataset: Tests whether two dynamic objects have matching states.
matches(Dynamic) - Method in class loci.visbio.data.DataTransform: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.data.ProjectionTransform: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.data.SpectralTransform: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.ext.ExternalFunction: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.overlays.OverlayTransform: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in interface loci.visbio.state.Dynamic: Tests whether two dynamic objects are equivalent.
matches(CaptureHandler) - Method in class loci.visbio.view.CaptureHandler: Tests whether two objects are in equivalent states.
matches(ColorHandler) - Method in class loci.visbio.view.ColorHandler: Tests whether two objects are in equivalent states.
matches(Dynamic) - Method in class loci.visbio.view.DisplayPosition: Tests whether two dynamic objects have matching states.
matches(Dynamic) - Method in class loci.visbio.view.DisplayWindow: Tests whether two dynamic objects are equivalent.
matches(Dynamic) - Method in class loci.visbio.view.StackLink: Tests whether two dynamic objects are equivalent.
matches(TransformHandler) - Method in class loci.visbio.view.TransformHandler: Tests whether two objects are in equivalent states.
matches(Dynamic) - Method in class loci.visbio.view.TransformLink: Tests whether two dynamic objects are equivalent.
matches(ViewHandler) - Method in class loci.visbio.view.ViewHandler: Tests whether two objects are in equivalent states.
MathUtil - Class in loci.visbio.util: MathUtil contains useful mathematical functions.
MatlabFunction - Class in loci.visbio.ext: MatlabFunction executes a MATLAB script or function on a data object.
MatlabFunction() - Constructor for class loci.visbio.ext.MatlabFunction: Creates an uninitialized MATLAB transform.
MatlabFunction(DataTransform, String, String) - Constructor for class loci.visbio.ext.MatlabFunction: Creates a MATLAB transform from the given transform.
MatlabUtil - Class in loci.visbio.ext: MatlabUtil contains useful MATLAB functions.
matrix - Variable in class loci.visbio.view.ViewHandler: Matrix representing current display projection.
max - Variable in class de.sciss.jcollider.gui.NumberSpace: Maximum allowed value or Double.POSITIVE_INFINITY
max - Variable in class de.sciss.jcollider.UGenInfo.Arg: Allowed range of its value and default value.
max - Variable in class loci.slim.fit.CurveEvent: Progress maximum for the event.
max - Variable in class loci.visbio.data.DataSampling: Maximum index value for each dimension.
MAX_DISPLAYS - Static variable in class loci.visbio.view.DisplayManager: Maximum number of simultaneous displays.
MAX_PACKET_SIZE - Static variable in class loci.jvmlink.ConnThread
MAX_POWER - Static variable in class loci.visbio.util.ColorUtil: Maximum alpha exponent for polynomial transparency curve.
MAX_VOLUME_RESOLUTION - Static variable in class loci.visbio.view.StackHandler: Maximum length of each volume rendered spatial axis.
maxFields - Variable in class loci.visbio.data.SamplingWidget: Text fields for maximum dimensional values.
maxFracDigits - Variable in class de.sciss.jcollider.gui.NumberSpace
maxIterations - Variable in class loci.slim.fit.CurveRenderer
maxNodes - Variable in class loci.visbio.overlays.OverlayNodedObject: Total number of nodes (real + buffer) nodes in the node array.
maxPeak - Variable in class loci.slim.SlimData
maxProgress - Variable in class loci.slim.fit.CurveRenderer
maxRCSE - Variable in class loci.slim.fit.CurveRenderer
maxWave - Variable in class loci.slim.SlimData
memUsage - Variable in class loci.visbio.SystemControls: Current memory usage.
mergeStates(Vector, Vector) - Static method in class loci.visbio.state.StateManager: Merges states between two lists of dynamic objects.
message - Variable in class loci.slim.fit.CurveEvent: String message describing the event.
MessagePane - Class in loci.visbio.util: MessagePane provides a dialog box for displaying a dialog to the user with an "Always display this dialog" checkbox for toggling its appearance.
MessagePane(String, JPanel, boolean) - Constructor for class loci.visbio.util.MessagePane: Creates a new message pane linked to the given checkbox.
messageReceived(OSCMessage, SocketAddress, long) - Method in class de.sciss.jcollider.OSCMultiResponder
messageReceived(OSCMessage, SocketAddress, long) - Method in class de.sciss.jcollider.OSCResponderNode: This method is called as part of the implementation of the OSCListener interface.
META_COLUMNS - Static variable in class loci.visbio.data.DatasetWidget: Column headings for metadata table.
metadata - Variable in class loci.visbio.data.DatasetWidget: Dataset's associated metadata.
metaTable - Variable in class loci.visbio.data.DatasetWidget: Table listing metadata fields.
metaTableModel - Variable in class loci.visbio.data.DatasetWidget: Table model backing metadata table.
MICRON - Static variable in class loci.visbio.data.ImageTransform: Micron unit.
micronHeight - Variable in class loci.visbio.data.ImageTransform: Physical image dimensions in microns.
micronStep - Variable in class loci.visbio.data.ImageTransform: Physical image dimensions in microns.
micronValue(Length) - Static method in class loci.plugins.stitching.TileUtils
micronValue(Length, double) - Static method in class loci.plugins.stitching.TileUtils
micronWidth - Variable in class loci.visbio.data.ImageTransform: Physical image dimensions in microns.
milestones() - Static method in class loci.backup.github.ResumePoint
MIMIC - Static variable in class de.sciss.jcollider.gui.ServerPanel: Constructor flag: shortcut for creating those GUI elements that SClang provides.
min - Variable in class de.sciss.jcollider.gui.NumberSpace: Minimum allowed value or Double.NEGATIVE_INFINITY
min - Variable in class de.sciss.jcollider.UGenInfo.Arg: Allowed range of its value and default value.
min - Variable in class loci.visbio.data.DataSampling: Minimum index value for each dimension.
MIN - Static variable in class loci.visbio.overlays.OverlayOval
MIN_VOLUME_RESOLUTION - Static variable in class loci.visbio.view.StackHandler: Minimum length of each volume rendered spatial axis.
minFields - Variable in class loci.visbio.data.SamplingWidget: Text fields for minimum dimensional values.
minFracDigits - Variable in class de.sciss.jcollider.gui.NumberSpace
MiniBioformatsTool - Class in loci.apps.SlideScannerImport
MiniBioformatsTool(String) - Constructor for class loci.apps.SlideScannerImport.MiniBioformatsTool
MINIMUM_BURN_DELAY - Static variable in class loci.visbio.view.TransformHandler: Minimum amount of time to delay burn-in.
minWave - Variable in class loci.slim.SlimData
mode - Variable in class loci.visbio.overlays.FreeformTool: Stores the current mode (INIT, ERASE, CHILL, DRAW, EDIT).
mode - Variable in class loci.visbio.overlays.PolylineTool: The current mode of the state machine represented in/by the mouse methods of this tool.
model - Variable in class loci.visbio.view.BioColorWidget: Color model: RGB or HSV.
MODSForm - Class in loci.niche: Populates a MODS template for the WID 3D Niche system.
MODSForm() - Constructor for class loci.niche.MODSForm
MODULE - Static variable in class loci.deepzoom.workflow.WorkFlow
ModuleFactory - Class in loci.deepzoom.workflow: TODO
MODULES - Static variable in class loci.deepzoom.workflow.WorkFlow
MouseBehaviorButtons - Class in loci.slim: Button bar for controlling a VisAD display's mouse behavior.
MouseBehaviorButtons(DisplayImpl, boolean, boolean) - Constructor for class loci.slim.MouseBehaviorButtons
mouseClicked(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
MouseClickListener - Class in loci.apps.SlideScannerImport
MouseClickListener(ImagePlus) - Constructor for class loci.apps.SlideScannerImport.MouseClickListener
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.ArrowTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.BoxTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.FreeformTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.LineTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.MarkerTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OvalTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PointerTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PolylineTool: Instructs this tool to respond to a mouse press.
mouseDown(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.TextTool: Instructs this tool to respond to a mouse press.
mouseDownLeft - Variable in class loci.visbio.overlays.OverlayTransform: Whether left mouse button is currently being pressed.
mouseDownRight - Variable in class loci.visbio.overlays.OverlayTransform: Whether right mouse button is currently being pressed.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.ArrowTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.BoxTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.FreeformTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.LineTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.MarkerTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OvalTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PointerTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PolylineTool: Instructs this tool to respond to a mouse drag.
mouseDrag(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.TextTool: Instructs this tool to respond to a mouse drag.
mouseDragged(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mouseDragged(ImagePlus, MouseEvent) - Method in class loci.sonification.SonificationTool
mouseEntered(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mouseExited(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mouseMoved(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mouseMoved(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to mouse movement.
mouseMoved(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PolylineTool: Instructs this tool to respond to a mouse movement.
mousePressed(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mousePressed(ImagePlus, MouseEvent) - Method in class loci.sonification.SonificationTool
mouseReleased(MouseEvent) - Method in class loci.apps.SlideScannerImport.MouseClickListener
mouseReleased(ImagePlus, MouseEvent) - Method in class loci.sonification.SonificationTool
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.ArrowTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.BoxTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.FreeformTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.LineTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.MarkerTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OvalTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.OverlayTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PointerTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.PolylineTool: Instructs this tool to respond to a mouse release.
mouseUp(DisplayEvent, int, int, float, float, int[], int) - Method in class loci.visbio.overlays.TextTool: Instructs this tool to respond to a mouse release.
MOVE - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the node has moved
moveAfter(Node) - Method in class de.sciss.jcollider.Node: Moves the node after another node in the server graph.
moveAfterMsg(Node) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_after message.
moveBefore(Node) - Method in class de.sciss.jcollider.Node: Moves the node before another node in the server graph.
moveBeforeMsg(Node) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_before message.
moveDown - Variable in class loci.visbio.view.CapturePanel: Button for moving selected position downward.
moveDown - Variable in class loci.visbio.view.TransformPanel: Button for moving data objects downward in the list.
moveNodeToHead(Node) - Method in class de.sciss.jcollider.Group
moveNodeToHeadMsg(Node) - Method in class de.sciss.jcollider.Group
moveNodeToTail(Node) - Method in class de.sciss.jcollider.Group
moveNodeToTailMsg(Node) - Method in class de.sciss.jcollider.Group
moveToHead(Group) - Method in class de.sciss.jcollider.Node: Moves the node to the head of a group in the server graph.
moveToHeadMsg(Group) - Method in class de.sciss.jcollider.Node: Creates an OSC /g_head message.
moveToTail(Group) - Method in class de.sciss.jcollider.Node: Moves the node to the tail of a group in the server graph.
moveToTailMsg(Group) - Method in class de.sciss.jcollider.Node: Creates an OSC /g_tail message.
moveTransformDown(DataTransform) - Method in class loci.visbio.view.TransformHandler: Moves the given transform down in the Z-order.
moveTransformDown(DataTransform) - Method in class loci.visbio.view.TransformPanel: Moves the given transform down in the list.
moveTransformUp(DataTransform) - Method in class loci.visbio.view.TransformHandler: Moves the given transform up in the Z-order.
moveTransformUp(DataTransform) - Method in class loci.visbio.view.TransformPanel: Moves the given transform up in the list.
moveUp - Variable in class loci.visbio.view.CapturePanel: Button for moving selected position upward.
moveUp - Variable in class loci.visbio.view.TransformPanel: Button for moving data objects upward in the list.
movieBox - Variable in class loci.visbio.view.CaptureHandler: File chooser for movie output.
movieFPS - Variable in class loci.visbio.view.CaptureHandler: Movie frames per second.
movieSmooth - Variable in class loci.visbio.view.CaptureHandler: Whether transitions use a smoothing sine function.
movieSpeed - Variable in class loci.visbio.view.CaptureHandler: Movie speed.
msg - Variable in class loci.visbio.state.ProgramState: Message to be displayed as part of "Undo" and "Redo" menu items.
MU - Static variable in class loci.visbio.data.DataTransform
MultiLUT - Class in loci.apps: An application for weighted spectral mapping.
MultiLUT() - Constructor for class loci.apps.MultiLUT
mutationFactor - Variable in class loci.slim.fit.GACurveFitter

N

name - Variable in class de.sciss.jcollider.UGenInfo.Arg: Name of the argument (same as in SClang).
NAME - Static variable in class loci.deepzoom.workflow.WorkFlow
name - Variable in class loci.multithreadedplugin.Image
name() - Method in class loci.plugins.stitching.Pt
name - Variable in class loci.visbio.ControlPanel: Name of this control panel.
name - Variable in class loci.visbio.data.DataTransform: Name of this transform.
name - Variable in class loci.visbio.ext.FunctionParam: Name of this parameter.
name - Variable in class loci.visbio.overlays.OverlayTool: Name of this tool.
name - Variable in class loci.visbio.view.BioSlideWidget: Slider name.
name - Variable in class loci.visbio.view.DisplayWindow: Name of this display.
name - Variable in class loci.visbio.WindowState: Title of the window.
namespace(String) - Static method in class loci.jar2lib.ClassList: Gets the C++ namespace fragment corresponding to the given class name.
needRefresh - Variable in class loci.visbio.overlays.OverlayWidget: Flag indicating widget components need to be refreshed.
newCurveFitter(Class) - Static method in class loci.slim.fit.CurveCollection
newFrom(Server) - Static method in class de.sciss.jcollider.NodeWatcher: Returns a NodeWatcher to monitor a given server.
newGroup - Variable in class loci.visbio.overlays.OverlayWidget: Button for creating a new overlay group.
newLinks - Variable in class loci.visbio.view.TransformHandler: List of uninitialized links.
newMsg() - Method in class de.sciss.jcollider.Group
newMsg(Group) - Method in class de.sciss.jcollider.Group
newMsg(Node, int) - Method in class de.sciss.jcollider.Group: Note: this sets the group!
newMsg() - Method in class de.sciss.jcollider.Synth
newMsg(Node) - Method in class de.sciss.jcollider.Synth
newMsg(Node, String[], float[]) - Method in class de.sciss.jcollider.Synth
newMsg(Node, String[], float[], int) - Method in class de.sciss.jcollider.Synth
newPaused(String, String[], float[], Node) - Static method in class de.sciss.jcollider.Synth
newPaused(String, String[], float[], Node, int) - Static method in class de.sciss.jcollider.Synth
next() - Static method in class de.sciss.jcollider.UniqueID: Returns the next unique ID
next - Variable in class loci.visbio.util.WizardPane: Wizard's next button.
next - Variable in class loci.visbio.view.BioSlideWidget: Next step button.
nextId - Static variable in class loci.visbio.data.DataTransform: Next free transform id number.
nextId - Variable in class loci.visbio.view.DisplayManager: Counter for display names.
nextInChainProcess(ImageWrapper) - Method in class loci.chainableplugin.AbstractPipelineProcessor: This method passes on the image to the next processor.
nextNodeID() - Method in class de.sciss.jcollider.Server: Allocates a new free node ID for a group or synth.
nextTask() - Method in class loci.visbio.util.SplashScreen: Advances task counter.
NICE_ALPHA - Static variable in class loci.visbio.view.DisplayManager: String for nicest transparency option.
nodal - Variable in class loci.visbio.overlays.FreeformExtension: Whether this freeform extension began on a node or in the middle of a segment.
Node - Class in de.sciss.jcollider: This is a client side representation of a node in the synthesis graph.
Node(Server, int) - Constructor for class de.sciss.jcollider.Node: Creates a Node representation for a given node ID.
Node(Server) - Constructor for class de.sciss.jcollider.Node: Creates a Node representation.
nodeAction(NodeEvent) - Method in class de.sciss.jcollider.gui.NodeTreeManager: This method is part of the NodeListener interface.
nodeAction(NodeEvent) - Method in interface de.sciss.jcollider.NodeListener: Called when the node status changed.
NodeEvent - Class in de.sciss.jcollider: These kind of events get delivered by a node watcher to inform listeners about node status changes.
NodeEvent(Object, int, long, Node, int, int, int, int, int, int, int) - Constructor for class de.sciss.jcollider.NodeEvent: Constructs a NodeEvent from a detailed description.
NodeIDAllocator - Class in de.sciss.jcollider: Quite a 1:1 translation from SClang, this is used as the default node allocator by the server.
NodeIDAllocator() - Constructor for class de.sciss.jcollider.NodeIDAllocator
NodeIDAllocator(int) - Constructor for class de.sciss.jcollider.NodeIDAllocator
NodeListener - Interface in de.sciss.jcollider: Objects which wish to be informed about server status changes must implement this interface and register using Server.addListener.
NODES - Static variable in class loci.visbio.overlays.OverlayIO
NODES - Static variable in class loci.visbio.overlays.OverlayNodedObject
nodes - Variable in class loci.visbio.overlays.OverlayNodedObject: Node array and associated tracking variables.
NodeScheduler - Class in loci.multithreadedplugin: Handles named data passing among nodes.
nodesSync - Variable in class loci.visbio.overlays.OverlayNodedObject: Synchronization object for nodes array.
NodeTreeManager - Class in de.sciss.jcollider.gui: A class that helps to set up a JTree with a view of a node graph.
NodeTreeManager(NodeWatcher, Node) - Constructor for class de.sciss.jcollider.gui.NodeTreeManager: Creates a new NodeTreeManager for a given NodeWatcher instance and root Node.
NodeTreeManager(NodeWatcher) - Constructor for class de.sciss.jcollider.gui.NodeTreeManager
NodeTreePanel - Class in de.sciss.jcollider.gui: A panel that contains a tree view of the nodes as monitored by a NodeWatcher.
NodeTreePanel(NodeWatcher, Node, int) - Constructor for class de.sciss.jcollider.gui.NodeTreePanel: Creates a new NodeTreePanel for a given node watcher and root element.
NodeTreePanel(NodeWatcher, Node) - Constructor for class de.sciss.jcollider.gui.NodeTreePanel: Creates a panel with default gadgets.
NodeWatcher - Class in de.sciss.jcollider: A node status managing class which has a similar concept as SCLang's NodeWatcher class, however the implementation is different and the feature set is different.
NORMAL_BRIGHTNESS - Static variable in class loci.visbio.view.ColorHandler: Starting brightness value.
NORMAL_CONTRAST - Static variable in class loci.visbio.view.ColorHandler: Starting contrast value.
NORMAL_OPACITY - Static variable in class loci.visbio.view.ColorHandler: Starting opacity value.
NOT_APPLICABLE - Static variable in class loci.visbio.overlays.OverlayIO: String indicating a given field is not applicable to an overlay.
NOT_APPLICABLE - Static variable in class loci.visbio.overlays.OverlayTransform: String indicating a given field is not applicable to an overlay.
noTabs - Variable in class loci.visbio.state.OptionPane: Non-tabbed pane.
notes - Variable in class loci.visbio.overlays.OverlayObject: Notes associated with this overlay.
notes - Variable in class loci.visbio.overlays.OverlayWidget: Text field for miscellaneous notes.
notify(boolean) - Method in class de.sciss.jcollider.Server: Sends a message to the server requesting to be notified about server actions such as nodes being added and deleted.
notifyListeners(TransformEvent) - Method in class loci.visbio.data.DataTransform: Notifies transform listeners of a parameter change.
notifyListeners(boolean) - Method in class loci.visbio.overlays.OverlayWidget: Sends a TransformEvent to the overlay transform's listeners.
notifyListeners(SpawnEvent) - Method in class loci.visbio.util.InstanceServer: Notifies application instance spawn listeners of a newly spawned application instance.
notifyListeners(OutputEvent) - Method in class loci.visbio.util.OutputConsole
NULL_TYPE - Static variable in class loci.jvmlink.ConnThread
numberChanged(NumberEvent) - Method in interface de.sciss.jcollider.gui.NumberListener: Notifies the listener that a number changed occured.
NumberEvent - Class in de.sciss.jcollider.gui: This kind of event is fired from a NumberField gadget when the user modified its contents.
NumberEvent(Object, int, long, Number, boolean) - Constructor for class de.sciss.jcollider.gui.NumberEvent: Constructs a new NumberEvent
NumberField - Class in de.sciss.jcollider.gui: A NumberField is basically a JPanel holding a JTextField whose content is limited to decimal numbers.
NumberField() - Constructor for class de.sciss.jcollider.gui.NumberField: Create a new NumberField for a given space.
NumberField(NumberSpace) - Constructor for class de.sciss.jcollider.gui.NumberField
numberFlavor - Static variable in class de.sciss.jcollider.gui.NumberField
NumberListener - Interface in de.sciss.jcollider.gui: Interface for listening the changes of the contents of a NumberField gadget
numbers - Variable in class loci.visbio.view.BioSlideWidget: Slider labels.
NumberSpace - Class in de.sciss.jcollider.gui: A number space describes a field of possible numeric values with a minimum and maximum (which can be infinity), a central value (usually zero) a quantization size which can be used to describe integers or to limit the numeric resolution.
NumberSpace(double, double, double, int, int, double) - Constructor for class de.sciss.jcollider.gui.NumberSpace: Creates a new NumberSpace with the given values.
NumberSpace(double, double, double, int, int) - Constructor for class de.sciss.jcollider.gui.NumberSpace: Creates a new NumberSpace with the given values.
NumberSpace(double, double, double) - Constructor for class de.sciss.jcollider.gui.NumberSpace: Creates a new NumberSpace with the given values.
numCols - Variable in class loci.slim.fit.CurveCollection: Full image resolution.
numCols - Variable in class loci.slim.fit.CurveRenderer
NumericOption - Class in loci.visbio.state: NumericOption is an integer option in the VisBio Options dialog.
NumericOption(String, String, String, int) - Constructor for class loci.visbio.state.NumericOption: Constructs a new option.
NumericOption(String, String, String, double) - Constructor for class loci.visbio.state.NumericOption: Constructs a new option.
NumericOption(String, String, String, String) - Constructor for class loci.visbio.state.NumericOption: Constructs a new option.
numExp - Variable in class loci.slim.SlimData
numExponentials - Variable in class loci.slim.fit.CurveRenderer
numGroups - Variable in class de.sciss.jcollider.Server.Status
numIter - Variable in class loci.slim.fit.GACurveFitter
numNodes - Variable in class loci.visbio.overlays.OverlayNodedObject: Number of real nodes in the node array.
numRange - Variable in class loci.visbio.data.DataSampling: Range component count for each image.
numRange - Variable in class loci.visbio.ext.ExternalFunction: Range component count for each image.
numRows - Variable in class loci.slim.fit.CurveCollection: Full image resolution.
numRows - Variable in class loci.slim.fit.CurveRenderer
numSynthDefs - Variable in class de.sciss.jcollider.Server.Status
numSynths - Variable in class de.sciss.jcollider.Server.Status
numUGens - Variable in class de.sciss.jcollider.Server.Status

O

objectsEqual(Object, Object) - Static method in class loci.visbio.util.ObjectUtil: Determines whether the two objects are equal.
ObjectUtil - Class in loci.visbio.util: ObjectUtil contains object and array manipulation functions.
objs - Variable in class loci.visbio.overlays.PointerTool: Array of OverlayObjects at current dimensional position.
OFF - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the node was paused
offsets - Variable in class loci.visbio.data.ThumbnailCache: Thumbnail byte offsets.
ok - Variable in class loci.visbio.util.DialogPane: Ok button.
om - Variable in class loci.visbio.state.OptionPane: Options manager.
ome.xml.version - package ome.xml.version
OMEXMLhelper - Class in loci.wiscscan: Helper class for working with OME-XML.
OMEXMLhelper() - Constructor for class loci.wiscscan.OMEXMLhelper
ON - Static variable in class de.sciss.jcollider.NodeEvent: returned by getID() : the node was resumed
on - Variable in class loci.visbio.data.ThumbnailHandler: Flag indicating background thumbnail generation is enabled.
OnFlush(int) - Method in interface loci.apps.flow.Find_Particle_Areas.MPFC_Ctrl
opacity - Variable in class loci.visbio.view.ColorPane: Slider for level of opacity.
opacityModel - Variable in class loci.visbio.view.ColorHandler: Transparency model (CONSTANT_ALPHA or CURVED_ALPHA).
opacityValue - Variable in class loci.visbio.view.ColorHandler: Opacity value.
opacityValue - Variable in class loci.visbio.view.ColorPane: Label for current opacity value.
openAperioImages(String, boolean[]) - Static method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
openFile(String, double) - Static method in class loci.apps.flow.FlowCyto
OpenLine(int, int, int) - Method in interface loci.apps.flow.Find_Particle_Areas.MPFC_Ctrl
openSampleData(String) - Method in class loci.visbio.data.DataManager: Loads the given sample dataset.
openURL(String) - Static method in class com.centerkey.utils.BareBonesBrowserLaunch: Opens the specified web page in the user's default browser
openURL(String) - Static method in class loci.visbio.util.BrowserLauncher: Attempts to open the default web browser to the given URL.
optionListToStringArray(List) - Static method in class de.sciss.jcollider.ServerOptions: Converts a list of string elements to one an array of strings
OptionManager - Class in loci.visbio.state: OptionManager is the manager encapsulating VisBio's options.
OptionManager(VisBioFrame) - Constructor for class loci.visbio.state.OptionManager: Constructs an options manager.
OptionPane - Class in loci.visbio.state: OptionPane provides a dialog box for adjusting VisBio's options.
OptionPane(OptionManager) - Constructor for class loci.visbio.state.OptionPane: Creates a new options pane.
ORDER_VALUE - Static variable in class loci.jvmlink.ConnThread
orient2D(float[], float[], float[]) - Static method in class loci.visbio.util.MathUtil: Obtains the z-coordinate of the cross product of the 2D vectors p2-p1 and p3-p2, useful for determining whether the curve p1->p2->p3 is curving to the right or left.
OrthoStack - Class in loci.visbio: Visualizes a stack of image planes in an aligned parallel projection.
OrthoStack() - Constructor for class loci.visbio.OrthoStack
OSCMultiResponder - Class in de.sciss.jcollider: Despite the name, the OSCMultiResponder mimics the SClang counter part only superficially.
OSCMultiResponder(OSCClient) - Constructor for class de.sciss.jcollider.OSCMultiResponder: Creates a new responder for the given OSCClient.
OSCResponderNode - Class in de.sciss.jcollider: Similar operation as the SClang class of the same name, but slightly different implementation, based on the new OSCMultiResponder class and NetUtil.
OSCResponderNode(Server, String, OSCListener) - Constructor for class de.sciss.jcollider.OSCResponderNode: Creates a new responder node to listen for messages coming in from the given server.
OSCResponderNode(Server, String, OSCResponderNode.Action) - Constructor for class de.sciss.jcollider.OSCResponderNode: Creates a new responder node to listen for messages coming in from the given server.
OSCResponderNode.Action - Interface in de.sciss.jcollider
otherFreefs - Variable in class loci.visbio.overlays.FreeformTool: Other freeforms on the canvas.
OUTLINE_COLOR - Static variable in class loci.visbio.overlays.OverlayUtil: Color of the outline layer.
Output - Annotation Type in loci.deepzoom.plugin.annotations: TODO
OUTPUT - Static variable in class loci.deepzoom.workflow.WorkFlow
output - Variable in class loci.niche.MODSForm
OUTPUT_ARG - Static variable in class de.sciss.jcollider.UGenInfo: Value for outputType : the ugen has a variable number which needs to be specified explictly when constructing the ugen (example : PanAz)
OUTPUT_ARRAYSIZE - Static variable in class de.sciss.jcollider.UGenInfo: Value for outputType : the ugen has a variable number of outputs depending on the length of it's array argument (example : Demand)
OUTPUT_FIXED - Static variable in class de.sciss.jcollider.UGenInfo: Value for outputType : the ugen has a fixed number of outputs
OutputConsole - Class in loci.visbio.util: OutputConsole provides an output stream that pipes to a JTextArea Swing component in its own frame (instead of to a console window).
OutputConsole(String) - Constructor for class loci.visbio.util.OutputConsole: Constructs a new instance of OutputConsole.
OutputConsole(String, String) - Constructor for class loci.visbio.util.OutputConsole: Constructs a new instance of OutputConsole, logging all output to the given log file.
OutputEvent - Class in loci.visbio.util: An event indicating an OutputConsole has produced output.
OutputEvent(Object) - Constructor for class loci.visbio.util.OutputEvent: Constructs an output console event.
outputImage(String, ItemWrapper) - Method in interface loci.deepzoom.workflow.IOutputListener: Tells listener that an output image is ready.
OutputListener - Interface in loci.visbio.util: A listener for output console events.
outputMul - Variable in class de.sciss.jcollider.UGenInfo: A tricky workaround invented for LagControl until i recognized that this isn't a real ugen.
outputProduced(OutputEvent) - Method in class loci.visbio.ConsoleManager: Handles output and error console window updates.
outputProduced(OutputEvent) - Method in interface loci.visbio.util.OutputListener: Used to notify listeners when an output console produces output.
OUTPUTS - Static variable in class loci.deepzoom.workflow.WorkFlow
outputType - Variable in class de.sciss.jcollider.UGenInfo: Defines how the number of outputs is determined.
outputVal - Variable in class de.sciss.jcollider.UGenInfo: For fixed output ugens, the number of outputs.
oval - Variable in class loci.visbio.overlays.OvalTool: Oval currently being drawn.
OvalTool - Class in loci.visbio.overlays: OvalTool is the tool for creating oval overlays.
OvalTool(OverlayTransform) - Constructor for class loci.visbio.overlays.OvalTool: Constructs an oval overlay creation tool.
overlay - Variable in class loci.visbio.overlays.OverlayObject: Associated overlay transform.
overlay - Variable in class loci.visbio.overlays.OverlayTool: Associated overlay transform.
overlay - Variable in class loci.visbio.overlays.OverlayWidget: Associated overlay object.
OVERLAY_TYPES - Static variable in class loci.visbio.overlays.OverlayUtil: List of all OverlayObject subclasses.
OverlayArrow - Class in loci.visbio.overlays: OverlayArrow is an arrow wedge overlay.
OverlayArrow(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayArrow: Constructs an uninitialized arrow wedge overlay.
OverlayArrow(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayArrow: Constructs an arrow wedge overlay.
OverlayBox - Class in loci.visbio.overlays: OverlayBox is a rectangle overlay.
OverlayBox(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayBox: Constructs an uninitialized bounding rectangle.
OverlayBox(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayBox: Constructs a bounding rectangle.
OverlayFreeform - Class in loci.visbio.overlays: OverlayFreeform is a freeform overlay.
OverlayFreeform(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayFreeform: Constructs an uninitialized freeform.
OverlayFreeform(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayFreeform: Constructs a freeform.
OverlayFreeform(OverlayTransform, float[][]) - Constructor for class loci.visbio.overlays.OverlayFreeform: Constructs a freeform from an array of nodes.
OverlayIO - Class in loci.visbio.overlays: Utility methods for saving and loading overlays to and from disk.
OverlayLine - Class in loci.visbio.overlays: OverlayLine is a measurement line overlay.
OverlayLine(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayLine: Constructs an uninitialized measurement line.
OverlayLine(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayLine: Constructs a measurement line.
overlayList - Variable in class loci.visbio.overlays.OverlayWidget: List of overlays.
overlayListModel - Variable in class loci.visbio.overlays.OverlayWidget: List model for overlay list.
overlayLoadBox - Variable in class loci.visbio.overlays.OverlayWidget: File chooser for loading overlays.
OverlayManager - Class in loci.visbio.overlays: OverlayManager is the manager encapsulating VisBio's overlay logic.
OverlayManager(VisBioFrame) - Constructor for class loci.visbio.overlays.OverlayManager: Constructs a window manager.
OverlayMarker - Class in loci.visbio.overlays: OverlayMarker is a marker crosshairs overlay.
OverlayMarker(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayMarker: Constructs an uninitialized measurement marker.
OverlayMarker(OverlayTransform, float, float) - Constructor for class loci.visbio.overlays.OverlayMarker: Constructs a measurement marker.
OverlayNodedObject - Class in loci.visbio.overlays: OverlayNodedObject is an overlay object built of nodes likely connected by lines.
OverlayNodedObject(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayNodedObject: Constructs an uninitialized noded object.
OverlayNodedObject(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayNodedObject: Constructs a noded object.
OverlayNodedObject(OverlayTransform, float[][]) - Constructor for class loci.visbio.overlays.OverlayNodedObject: Constructs a noded object from an array of nodes.
OverlayNumericStrategy - Class in loci.visbio.overlays: Provides threshholds and other constants to overlays classes.
OverlayObject - Class in loci.visbio.overlays: OverlayObject is the superclass of all overlay objects.
OverlayObject(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayObject: Constructs an overlay.
OverlayOval - Class in loci.visbio.overlays: OverlayOval is a bounding oval overlay.
OverlayOval(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayOval: Constructs an uninitialized bounding oval.
OverlayOval(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayOval: Constructs an bounding oval.
OverlayPolyline - Class in loci.visbio.overlays: OverlayFreeform is a freeform overlay.
OverlayPolyline(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayPolyline: Constructs an uninitialized freeform.
OverlayPolyline(OverlayTransform, float, float, float, float) - Constructor for class loci.visbio.overlays.OverlayPolyline: Constructs a freeform.
OverlayPolyline(OverlayTransform, float[][]) - Constructor for class loci.visbio.overlays.OverlayPolyline: Constructs a freeform from an array of nodes.
overlays - Variable in class loci.visbio.overlays.OverlayTransform: List of overlays for each dimensional position.
overlaySaveBox - Variable in class loci.visbio.overlays.OverlayWidget: File chooser for saving overlays.
OverlayText - Class in loci.visbio.overlays: OverlayText is a text string overlay.
OverlayText(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayText: Constructs an uninitialized text string overlay.
OverlayText(OverlayTransform, float, float, String) - Constructor for class loci.visbio.overlays.OverlayText: Constructs a text string overlay.
OverlayTool - Class in loci.visbio.overlays: OverlayTool is the superclass of all overlay tools.
OverlayTool(OverlayTransform, String, String, String) - Constructor for class loci.visbio.overlays.OverlayTool: Constructs a measurement line creation tool.
OverlayTransform - Class in loci.visbio.overlays: A set of overlays on top another transform.
OverlayTransform(DataTransform, String) - Constructor for class loci.visbio.overlays.OverlayTransform: Creates an overlay object for the given transform.
OverlayUtil - Class in loci.visbio.overlays: Utility methods for Overlays.
OverlayWidget - Class in loci.visbio.overlays: OverlayWidget is a set of GUI controls for an overlay transform.
OverlayWidget(OverlayTransform) - Constructor for class loci.visbio.overlays.OverlayWidget: Creates overlay GUI controls.
overlayXLSBox - Variable in class loci.visbio.overlays.OverlayWidget: File chooser for exporting overlays to .xls format.
owner - Variable in class loci.visbio.util.BreakawayPanel: Owner window for breakaway panel and its parent.

P

p - Variable in class loci.plugins.stitching.Pt
pack() - Method in class loci.visbio.help.HelpWindow: Expands tree fully before packing help window.
pack(Window) - Static method in class loci.visbio.util.SwingUtil: Packs a window, with hacks to correct for inaccuracies in certain cases.
pack - Variable in class loci.visbio.WindowInfo: Whether to pack this window the first time it is shown.
packageName(String) - Static method in class loci.jar2lib.ClassList: Gets the package name for the given fully qualified class name.
page - Variable in class loci.visbio.util.WizardPane: The current page.
pages - Variable in class loci.visbio.util.WizardPane: Panels representing the wizard's pages.
pan - Variable in class loci.slim.MouseBehaviorButtons
pan(double, double, double) - Method in class loci.visbio.view.ViewHandler: Pans the display in the given direction.
PAN_AMOUNT - Static variable in class loci.visbio.view.ViewHandler: How far display pans each time.
panDown() - Method in class loci.visbio.view.ViewHandler: Slides the display downward.
pane - Variable in class loci.visbio.util.BreakawayPanel: Pane to which GUI components can be added to the breakaway panel.
pane - Variable in class loci.visbio.util.DialogPane: Content pane for dialog.
panel - Variable in class loci.visbio.view.CaptureHandler: GUI controls for capture handler.
panel - Variable in class loci.visbio.view.TransformHandler: GUI controls for transform handler.
panel - Variable in class loci.visbio.view.ViewHandler: GUI controls for view handler.
PanelManager - Class in loci.visbio: PanelManager is the manager encapsulating VisBio's control panel logic.
PanelManager(VisBioFrame) - Constructor for class loci.visbio.PanelManager: Constructs a panel manager.
panLeft() - Method in class loci.visbio.view.ViewHandler: Slides the display to the left.
panRight() - Method in class loci.visbio.view.ViewHandler: Slides the display to the right.
panUp() - Method in class loci.visbio.view.ViewHandler: Slides the display upward.
parallel - Variable in class loci.visbio.view.ViewHandler: Whether display is in parallel projection mode.
paramFields - Variable in class loci.visbio.ext.FunctionWidget: Fields corresponding to function parameters.
paramList - Variable in class loci.visbio.ext.ExternalFunction: List of parameters and associated default values.
params - Variable in class loci.visbio.ext.ExternalFunction: Parameter values for passing to the function.
params() - Method in class loci.visbio.ext.ExternalFunction: Gets the input parameter names and corresponding default values.
params() - Method in class loci.visbio.ext.ExternalProgram: Gets the input parameter names and corresponding default values.
params() - Method in class loci.visbio.ext.MatlabFunction: Gets the input parameter names and corresponding default values.
parent - Variable in class loci.visbio.data.DataTransform: Parent transform from which this transform obtains its data.
parent - Variable in class loci.visbio.util.BreakawayPanel: Parent container.
parse(String, int) - Static method in class loci.slim.SlimData
parse(String, float) - Static method in class loci.slim.SlimData
PARSE - Static variable in class loci.visbio.overlays.OverlayIO
parseArgs(String[]) - Method in class loci.jar2lib.Jar2Lib: Parses the settings from the given command line arguments.
parseXML(File) - Static method in class loci.visbio.util.XMLUtil: Parses a DOM from the given XML file on disk.
parseXML(String) - Static method in class loci.visbio.util.XMLUtil: Parses a DOM from the given XML string.
parseXML(InputStream) - Static method in class loci.visbio.util.XMLUtil: Parses a DOM from the given XML input stream.
paste - Variable in class loci.visbio.overlays.OverlayWidget: Button for pasting copied overlays onto the current position.
pasteObjects() - Method in class loci.visbio.overlays.OverlayTransform: Pastes copied objects at the current dimensional position.
pasteObjects(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Pastes copied objects at the given dimensional position.
path - Variable in class loci.visbio.overlays.SpreadsheetLauncher: Path to spreadsheet executable.
pattern - Variable in class loci.visbio.data.Dataset: A string pattern describing this dataset.
pause(String) - Static method in class loci.visbio.util.SwingUtil: Pops up a message box, blocking the current thread.
pause(Throwable) - Static method in class loci.visbio.util.SwingUtil: Pops up a message box, blocking the current thread.
peakCPU - Variable in class de.sciss.jcollider.Server.Status
PERIM - Static variable in class loci.visbio.overlays.OverlayBox
physicalSizeX(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
physicalSizeX(IMetadata, int, double) - Static method in class loci.plugins.stitching.TileUtils
physicalSizeY(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
physicalSizeY(IMetadata, int, double) - Static method in class loci.plugins.stitching.TileUtils
physicalSizeZ(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
physicalSizeZ(IMetadata, int, double) - Static method in class loci.plugins.stitching.TileUtils
picoToBins(float) - Method in class loci.slim.SlimData: Converts value in picoseconds to histogram bins.
pitch - Variable in class loci.visbio.data.ArbitrarySlice: Vertical rotatational angle of slicing line.
pitch - Variable in class loci.visbio.data.SliceWidget: Slider for adjusting pitch.
pitchValue - Variable in class loci.visbio.data.SliceWidget: Label for current pitch value.
pixelToCursor(DisplayImpl, int, int) - Static method in class loci.slim.TwoDPane: Converts the given pixel coordinates to cursor coordinates.
PLACE - Static variable in class loci.visbio.overlays.PolylineTool
placeMeInAPane() - Method in class de.sciss.jcollider.gui.LogTextArea
play() - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents (oneshot) beginning on the first audio output.
play(boolean) - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents beginning on the first audio output.
play(boolean, float) - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents beginning on the first audio output.
play(boolean, float, int) - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents.
play(boolean, float, int, float) - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents.
play(boolean, float, int, float, Node, int) - Method in class de.sciss.jcollider.Buffer: Plays the buffer contents.
play(Group) - Method in class de.sciss.jcollider.SynthDef: Sends the def to the server and creates a synth from this def.
play(Group, String[], float[]) - Method in class de.sciss.jcollider.SynthDef: Sends the def to the server and creates a synth from this def.
play(Node, String[], float[], int) - Method in class de.sciss.jcollider.SynthDef: Sends the def to the server and creates a synth from this def.
plotData(boolean, boolean, boolean) - Method in class loci.slim.SlimPlotter
plotProbe(boolean) - Method in class loci.slim.SlimPlotter
plotRegion(boolean, boolean, boolean) - Method in class loci.slim.SlimPlotter
PLUGIN - Static variable in class loci.deepzoom.workflow.PluginModule
PluginAnnotations - Class in loci.deepzoom.workflow.plugin: The PluginAnnotations class keeps sets of input and output names based on plugin class annotations.
PluginAnnotations(Class) - Constructor for class loci.deepzoom.workflow.plugin.PluginAnnotations: Creates an instance for a given plugin class.
PluginAnnotations - Class in loci.multiinstanceplugin: The PluginAnnotations class keeps sets of input and output names based on plugin class annotations.
PluginClassException - Exception in loci.deepzoom.workflow.plugin: Exception thrown when a plugin class cannot be launched.
PluginClassException(String) - Constructor for exception loci.deepzoom.workflow.plugin.PluginClassException
PluginClassException - Exception in loci.multiinstanceplugin: Exception thrown when a plugin class cannot be launched.
PluginClassException(String) - Constructor for exception loci.multiinstanceplugin.PluginClassException
PluginLauncher - Class in loci.deepzoom.workflow.plugin: The PluginLauncher talks to the PluginScheduler and launches new instances of the plugin as needed.
PluginLauncher(Class, PluginAnnotations) - Constructor for class loci.deepzoom.workflow.plugin.PluginLauncher: Creates a launcher for a given class, that has the given input and output image name annotations.
PluginLauncher - Class in loci.multiinstanceplugin: The PluginLauncher talks to the PluginScheduler and launches new instances of the plugin as needed.
PluginLauncher(Class<?>, PluginAnnotations) - Constructor for class loci.multiinstanceplugin.PluginLauncher: Creates a launcher for a given class, that has the given input and output image name annotations.
PluginModule - Class in loci.deepzoom.workflow: TODO
PluginModule() - Constructor for class loci.deepzoom.workflow.PluginModule
PluginModule(String) - Constructor for class loci.deepzoom.workflow.PluginModule: Create an instance for a given plugin class name.
PluginModule(Class<?>) - Constructor for class loci.deepzoom.workflow.PluginModule: Create an instance for a given plugin class.
PluginModuleFactory - Class in loci.deepzoom.workflow: TODO
PluginScheduler - Class in loci.deepzoom.workflow.plugin: Schedules named image passing among plugins.
PluginScheduler - Class in loci.multiinstanceplugin: Schedules named image passing among plugins.
PointerTool - Class in loci.visbio.overlays: PointerTool is the tool for manipulating existing overlays.
PointerTool(OverlayTransform) - Constructor for class loci.visbio.overlays.PointerTool: Constructs an overlay manipulation tool.
POLYLINE_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: Maximum distance (in pixels) mouse can be from a node to be considered pointing to it.
PolylineTool - Class in loci.visbio.overlays: FreeformTool is the tool for creating freeform objects.
PolylineTool(OverlayTransform) - Constructor for class loci.visbio.overlays.PolylineTool: Constructs a creation tool.
pos - Variable in class loci.visbio.overlays.OverlayTransform: Current dimensional position.
positions - Variable in class loci.visbio.view.CaptureHandler: List of positions.
positions - Variable in class loci.visbio.view.StackHandler: Dimensional positions.
positionToRaster(int[], int...) - Static method in class loci.visbio.OrthoStack: Computes a unique 1-D index corresponding to the given multidimensional position.
posList - Variable in class loci.visbio.view.CapturePanel: Position list.
posListModel - Variable in class loci.visbio.view.CapturePanel: Position list model.
post - Variable in class loci.visbio.overlays.FreeformExtension: Chunks of curve before and after the extension.
posX(IMetadata, int, int) - Static method in class loci.plugins.stitching.TileUtils
posY(IMetadata, int, int) - Static method in class loci.plugins.stitching.TileUtils
posZ(IMetadata, int, int) - Static method in class loci.plugins.stitching.TileUtils
PowerOfTwoAllocator - Class in de.sciss.jcollider: Quite a 1:1 translation from SClang, this is used as the default bus allocator by the server.
PowerOfTwoAllocator(int) - Constructor for class de.sciss.jcollider.PowerOfTwoAllocator
PowerOfTwoAllocator(int, int) - Constructor for class de.sciss.jcollider.PowerOfTwoAllocator
PowerOfTwoAllocator.Factory - Class in de.sciss.jcollider
PrairieInjector - Class in loci.apps.prairie: Command line tool to inject OME-XML into Prairie TIFF files.
PrairieInjector() - Constructor for class loci.apps.prairie.PrairieInjector
prComments(boolean) - Static method in class loci.backup.github.ResumePoint
prComments(boolean, int) - Static method in class loci.backup.github.ResumePoint
pre - Variable in class loci.visbio.overlays.FreeformExtension: Chunks of curve before and after the extension.
PRECISION - Static variable in class loci.visbio.data.SpectralWidget: Granularity of the weighted sliders.
predict(int, int, int, String[]) - Method in class loci.visbio.ext.ExternalFunction: Predicts the width, height and number of output planes, given the width, height and number of input planes, and parameter values.
predict(int, int, int, String[]) - Method in class loci.visbio.ext.ExternalProgram: Predicts the width, height and number of output planes, given the width, height and number of input planes, and parameter values.
predict(int, int, int, String[]) - Method in class loci.visbio.ext.MatlabFunction: Predicts the width, height and number of output planes, given the width, height and number of input planes, and parameter values.
prepend(int, int, int, double[]) - Static method in class loci.visbio.ext.MatlabUtil: Prepends the given dimensions to the specified parameter list.
preview - Variable in class loci.visbio.view.ColorPane: Color preview display.
previewText - Variable in class loci.visbio.util.FontChooserPane: Text area containing preview text with the chosen font settings.
previous - Variable in class loci.visbio.view.BioSlideWidget: Previous step button.
print(String, String) - Method in class loci.visbio.overlays.FreeformTool: Prints a message for debugging.
print(float[][]) - Static method in class loci.visbio.overlays.OverlayUtil: Prints a VisAD style group of points.
print(float, float) - Static method in class loci.visbio.overlays.OverlayUtil: Prints a point.
print(float[]) - Static method in class loci.visbio.overlays.OverlayUtil: Prints a point.
print(String, String) - Method in class loci.visbio.overlays.PolylineTool: Prints a message for debugging.
printError(String, Throwable) - Static method in class de.sciss.jcollider.Server
println(String) - Method in class loci.slim.fit.LMCurveFitter.ConsoleStream
println(Object) - Method in class loci.slim.fit.LMCurveFitter.ConsoleStream
printNodes() - Method in class loci.visbio.overlays.OverlayNodedObject: Prints node array of current freeform.
printOn(PrintStream) - Method in class de.sciss.jcollider.Buffer
printOn(PrintStream) - Method in class de.sciss.jcollider.Bus
printOn(PrintStream) - Method in class de.sciss.jcollider.ControlDesc
printOn(PrintStream) - Method in class de.sciss.jcollider.Node
printOn(PrintStream) - Method in class de.sciss.jcollider.Server: Prints a textual representation of this object onto the given stream
printOn(PrintStream) - Method in class de.sciss.jcollider.SynthDef: Prints a textual representation of the synth def to the given stream.
printOn(PrintStream) - Method in class de.sciss.jcollider.UGenInfo: Prints a textual representation of this dataset onto the given stream
printPathProperty(String, String) - Static method in class SysProps
printProperties(String[]) - Static method in class SysProps
printProperty(String, String) - Static method in class SysProps
printSizes(Component) - Static method in class loci.slim.SpringUtilities: A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printStackTrace() - Method in exception loci.visbio.state.SaveException: Prints a stack trace.
printStream - Static variable in class de.sciss.jcollider.Server
printThread(String) - Static method in class loci.visbio.overlays.OverlayNodedObject: Prints current thread plus method name if provided.
priorities - Variable in class loci.visbio.util.Docker: List of window docking priorities.
prIsMerged(boolean) - Static method in class loci.backup.github.ResumePoint
prIsMerged(boolean, int) - Static method in class loci.backup.github.ResumePoint
probe - Variable in class loci.slim.MouseBehaviorButtons
process(ImageWrapper) - Method in class loci.chainableplugin.AbstractPipelineProcessor: This is the abstract method that does the work, to be implemented in the concrete class processor.
process(ImageWrapper) - Method in class loci.chainableplugin.deepzoom.CutTilesProcessor: Does the image processing.
process(ImageWrapper) - Method in class loci.chainableplugin.deepzoom.DeepZoomExporter: Processes a given image.
process(ImageWrapper) - Method in class loci.chainableplugin.deepzoom.ScaleInHalfProcessor
process(ImageWrapper) - Method in interface loci.chainableplugin.IProcessor: Method to be overridden to do the actual work of the processor.
process() - Method in interface loci.deepzoom.workflow.plugin.IPlugin: This is the body of the plugin, defined in implemenation.
process() - Method in class loci.multiinstanceplugin.deepzoom.CutTilesProcessor
process() - Method in class loci.multiinstanceplugin.deepzoom.DeepZoomExporter.LevelProcessorX
process(ImageWrapper) - Method in class loci.multiinstanceplugin.deepzoom.DeepZoomExporter: Processes a given image.
process() - Method in class loci.multiinstanceplugin.deepzoom.DeepZoomExporter.TileProcessorX
process() - Method in class loci.multiinstanceplugin.deepzoom.LevelProcessor
process() - Method in class loci.multiinstanceplugin.deepzoom.ScaleInHalfProcessor
process() - Method in class loci.multiinstanceplugin.deepzoom.TileProcessor
process() - Method in interface loci.multiinstanceplugin.IPlugin: This is the body of the plugin, defined in implemenation.
process() - Method in class loci.multithreadedplugin.AbstractNode: This is the body of the plugin, defined in subclass.
processArgument(String, String) - Method in class loci.visbio.VisBioFrame: Processes the given argument key/value pair.
processArguments(String[]) - Method in class loci.visbio.VisBioFrame: Processes the given list of arguments.
processEvent(BasicEvent) - Method in class de.sciss.jcollider.gui.NumberField
processEvent(BasicEvent) - Method in class de.sciss.jcollider.NodeWatcher: This is used to dispatch node events.
processEvent(BasicEvent) - Method in class de.sciss.jcollider.Server: This is used to dispatch server events.
processFile(String) - Method in class loci.jar2lib.StringReplace
processOptions() - Method in class loci.backup.github.CreateOrphanBranchCommand
processTemplate(VelocityEngine, VelocityContext, String, String) - Static method in class loci.jar2lib.VelocityTools
processX(ImageWrapper) - Method in class loci.multiinstanceplugin.deepzoom.CutTilesProcessor: Does the image processing.
processX(ImageWrapper) - Method in class loci.multiinstanceplugin.deepzoom.ScaleInHalfProcessor
ProgramState - Class in loci.visbio.state: A VisBio state wrapper.
ProgramState(String, Document) - Constructor for class loci.visbio.state.ProgramState: Constructs a VisBio state wrapper.
progress - Variable in class loci.visbio.BioTask: Progress bar displaying the task's progress.
progress - Variable in class loci.visbio.view.CapturePanel: Progress bar for movie capture operation.
project(FlatField[]) - Static method in class loci.visbio.data.ProjectionTransform: Performs a maximum intensity projection across the given fields.
projection - Variable in class loci.visbio.data.ProjectionWidget: Associated maximum intensity projection transform.
ProjectionTransform - Class in loci.visbio.data: ProjectionTransform performs a maximum intensity projection across a given dimensional axis.
ProjectionTransform() - Constructor for class loci.visbio.data.ProjectionTransform: Creates an uninitialized maximum intensity projection.
ProjectionTransform(DataTransform, String, int) - Constructor for class loci.visbio.data.ProjectionTransform: Creates a maximum intensity projection from the given transform.
ProjectionWidget - Class in loci.visbio.data: ProjectionWidget is a set of GUI controls for a maximum intensity projection transform.
ProjectionWidget(ProjectionTransform) - Constructor for class loci.visbio.data.ProjectionWidget: Creates a new maximum intensity projection widget.
PropertyCollection - Class in loci.chainableplugin: Concrete class for the property collection.
PropertyCollection() - Constructor for class loci.chainableplugin.PropertyCollection
Pt - Class in loci.plugins.stitching: A simple data structure for storing metadata about a tile.
Pt() - Constructor for class loci.plugins.stitching.Pt
Pt(int, double, double, Double, Double, Double) - Constructor for class loci.plugins.stitching.Pt
Pt(int, int, Integer, Integer, Integer, double, double, Double, Double, Double, Integer) - Constructor for class loci.plugins.stitching.Pt
put(ItemWrapper) - Method in class loci.deepzoom.workflow.plugin.AbstractPlugin: Puts the default output image to next in chain (if any).
put(String, ItemWrapper) - Method in class loci.deepzoom.workflow.plugin.AbstractPlugin: Puts named output image to next in chain (if any).
put(ItemWrapper) - Method in interface loci.deepzoom.workflow.plugin.IPlugin: Puts the default output image to next in chain (if any).
put(String, ItemWrapper) - Method in interface loci.deepzoom.workflow.plugin.IPlugin: Puts named output image to next in chain (if any).
put(String, ItemWrapper) - Method in class loci.deepzoom.workflow.plugin.PluginScheduler: Passes image to fully-qualified name.
put(ImageWrapper) - Method in class loci.multiinstanceplugin.AbstractPlugin: Puts the default output image to next in chain (if any).
put(String, ImageWrapper) - Method in class loci.multiinstanceplugin.AbstractPlugin: Puts named output image to next in chain (if any).
put(ImageWrapper) - Method in interface loci.multiinstanceplugin.IPlugin: Puts the default output image to next in chain (if any).
put(String, ImageWrapper) - Method in interface loci.multiinstanceplugin.IPlugin: Puts named output image to next in chain (if any).
put(String, ImageWrapper) - Method in class loci.multiinstanceplugin.PluginScheduler: Passes image to fully-qualified name.
put(Object) - Method in class loci.multithreadedplugin.AbstractNode: Puts the default output data to next in chain (if any).
put(String, Object) - Method in class loci.multithreadedplugin.AbstractNode: Puts named output data to next in chain (if any).
put(Object) - Method in interface loci.multithreadedplugin.INode: Used within the run method.
put(String, Object) - Method in interface loci.multithreadedplugin.INode: Used within the run method.
put(String, Object) - Method in class loci.multithreadedplugin.NodeScheduler: Passes data to destination node + name.
putCachedData(String, Data) - Method in class loci.visbio.data.DataCache: Sets the data in the cache at the specified key.
putData(DataTransform, int[], String, Data) - Method in class loci.visbio.data.DataCache: Puts the given data object into the cache for the specified transform at the given dimensional position.

Q

quant - Variable in class de.sciss.jcollider.gui.NumberSpace: Quantization of values or zero
query() - Method in class de.sciss.jcollider.Buffer: A debugging method for querying the current buffer parameters and printing them into the console.
query() - Method in class de.sciss.jcollider.Node: A debugging method that prints the results of an OSC /n_query message into the server's default print stream.
query(PrintStream) - Method in class de.sciss.jcollider.Node: A debugging method that prints the results of an OSC /n_query message into a given print stream.
queryAllNodes(float, ActionListener) - Method in class de.sciss.jcollider.NodeWatcher
queryDone() - Method in class de.sciss.jcollider.Buffer: Called from Server when b_info is received.
queryMsg() - Method in class de.sciss.jcollider.Buffer: Constructs an OSC message /b_query for querying the buffer's parameters.
queryMsg() - Method in class de.sciss.jcollider.Node
quit() - Method in class de.sciss.jcollider.Server: Sends an asynchronous /quit to the server and cleans up the client's resources
quit() - Method in interface loci.deepzoom.workflow.IWorkFlow: Stops processing.
quit() - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Used to shut down processing.
quit() - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Quits processing the chain.
quit() - Method in class loci.deepzoom.workflow.plugin.PluginScheduler: Tears down the chained nodes.
quit() - Method in class loci.deepzoom.workflow.WorkFlow
quit() - Method in interface loci.multiinstanceplugin.ILinkedPlugin: Quits processing images.
quit() - Method in interface loci.multiinstanceplugin.IPluginLauncher: Used to shut down processing.
quit() - Method in class loci.multiinstanceplugin.LinkedPlugin: Quits processing images.
quit() - Method in class loci.multiinstanceplugin.PluginLauncher: Quits processing the chain.
quit() - Method in class loci.multiinstanceplugin.PluginScheduler: Tears down the chained nodes.
quit() - Method in class loci.multithreadedplugin.AbstractNode: Signals quitting time.
quit() - Method in interface loci.multithreadedplugin.INode: Stops this node.
quit() - Method in class loci.multithreadedplugin.NodeScheduler: Tears down the chained nodes.
quitAll() - Static method in class de.sciss.jcollider.Server: Synchronously quits all known servers.
quitAndWait() - Method in class de.sciss.jcollider.Server: Synchronously quit the server.
quitMsg() - Method in class de.sciss.jcollider.Server: Constructs a quit message for the server

R

r - Variable in class loci.slim.fit.GACurveFitter
RAD - Static variable in class loci.visbio.overlays.OverlayOval
RADIUS - Static variable in class loci.visbio.overlays.OverlayNodedObject: Radius in pixels of circle indicating a node is selected.
RandomPass - Class in <Unnamed>: Generates random passwords.
RandomPass() - Constructor for class RandomPass
range - Variable in class loci.visbio.data.CollapseTransform: Range display mappings.
range - Variable in class loci.visbio.data.DataSampling: List of included range components.
range - Variable in class loci.visbio.data.ProjectionTransform: Range display mappings.
range - Variable in class loci.visbio.data.SpectralTransform: Output range components.
RANGE_TUPLE - Static variable in class loci.visbio.overlays.OverlayTransform: Overlay range type.
rangeBoxes - Variable in class loci.visbio.data.SamplingWidget: Check boxes for included range components.
raster1Dto2D(double[], int, int) - Static method in class loci.visbio.ext.MatlabUtil: Converts a double[n*x*y] into a double[n][y*x].
raster2Dto3D(double[][], int, int) - Static method in class loci.visbio.ext.MatlabUtil: Converts a double[n][y*x] into a double[y][x][n].
raster3Dto2D(double[][][]) - Static method in class loci.visbio.ext.MatlabUtil: Converts a double[y][x][n] into a double[n][y*x].
rasterToPosition(int, int...) - Static method in class loci.visbio.OrthoStack: Computes a unique N-D position corresponding to the given rasterized index value.
rasterToPosition(int[], int, int...) - Static method in class loci.visbio.OrthoStack: Computes a unique N-D position corresponding to the given rasterized index value.
rates - Variable in class de.sciss.jcollider.UGenInfo: Set of all allowed rates at which the ugen can run
rawValue(Length) - Static method in class loci.plugins.stitching.TileUtils
rawValue(Length, double) - Static method in class loci.plugins.stitching.TileUtils
read(Server, String) - Static method in class de.sciss.jcollider.Buffer: Reads a whole file into memory for PlayBuf etc.
read(Server, String, long) - Static method in class de.sciss.jcollider.Buffer: Reads a whole file into memory for PlayBuf etc., starting at a given frame.
read(Server, String, long, int) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
read(Server, String, long, int, Buffer.CompletionAction) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
read(Server, String, long, int, Buffer.CompletionAction, int) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
read(String) - Method in class de.sciss.jcollider.Buffer: Reads in as many frames from a sound file as fit into the buffer, starting at the beginning of the file.
read(String, long) - Method in class de.sciss.jcollider.Buffer: Reads in as many frames from a sound file as fit into the buffer, starting at a given frame in the file.
read(String, long, int) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer.
read(String, long, int, int) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
read(String, long, int, int, boolean) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
read(String, long, int, int, boolean, Buffer.CompletionAction) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
read(InputStream) - Static method in class de.sciss.jcollider.SynthDef: Reads a single SynthDef from an input stream (such as a harddisk file or memory buffer).
readBinaryDefinitions() - Static method in class de.sciss.jcollider.UGenInfo: Reads in the ugen definition database from a binary resource inside the libraries jar file (ugendefs.bin).
readChannel(Server, String, long, int, int[]) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a given set of channels from a file into memory for PlayBuf etc.
readChannel(Server, String, long, int, int[], Buffer.CompletionAction) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a given set of channels from a file into memory for PlayBuf etc.
readChannel(Server, String, long, int, int[], Buffer.CompletionAction, int) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a given set of channels from a file into memory for PlayBuf etc.
readChannel(String, long, int, int, boolean, int[], Buffer.CompletionAction) - Method in class de.sciss.jcollider.Buffer: Reads in frames from selected channels of a sound file into the buffer, beginning a given offset in the buffer.
readChannelMsg(String, long, int, int, boolean, int[]) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from selected channels of a sound file into the buffer, beginning a given offset in the buffer.
readChannelMsg(String, long, int, int, boolean, int[], OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from selected channels of a sound file into the buffer, beginning a given offset in the buffer.
readCoords(IMetadata) - Static method in class loci.plugins.stitching.TileUtils: Generates a list of coordinates from all series described by the provided IMetadata object.
readDefFile(URL) - Static method in class de.sciss.jcollider.SynthDef: Reads definitions from a synth def file.
readDefFile(File) - Static method in class de.sciss.jcollider.SynthDef: Reads definitions from a synth def file.
readDefFile(InputStream) - Static method in class de.sciss.jcollider.SynthDef: Reads definitions from an input stream (such as a harddisk file or memory buffer).
readDefinitions() - Static method in class de.sciss.jcollider.UGenInfo: Reads in the ugen definition database from a text resource inside the libraries jar file (ugendefs.xml).
reader - Variable in class loci.visbio.data.Dataset: Data reader.
readFile(String) - Method in class loci.jar2lib.StringReplace
readIni() - Method in class loci.visbio.state.OptionManager: Reads in configuration from configuration file.
readMsg(String) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in as many frames from a sound file as fit into the buffer, starting at the beginning of the file, closing the file after reading.
readMsg(String, long) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in as many frames from a sound file as fit into the buffer, starting at a given frame in the file, closing the file after reading.
readMsg(String, long, int) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from a sound file into the buffer, closing the file after reading.
readMsg(String, long, int, int) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from a sound file into the buffer, beginning a given offset in the buffer, closing the file after reading.
readMsg(String, long, int, int, boolean) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from a sound file into the buffer, beginning a given offset in the buffer.
readMsg(String, long, int, int, boolean, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_read message to read in frames from a sound file into the buffer, beginning a given offset in the buffer.
readNoUpdate(Server, String) - Static method in class de.sciss.jcollider.Buffer: Reads a whole file into memory for PlayBuf etc.
readNoUpdate(Server, String, long) - Static method in class de.sciss.jcollider.Buffer: Reads a whole file into memory for PlayBuf etc.
readNoUpdate(Server, String, long, int) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
readNoUpdate(Server, String, long, int, Buffer.CompletionFunction) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
readNoUpdate(Server, String, long, int, Buffer.CompletionFunction, int) - Static method in class de.sciss.jcollider.Buffer: Reads a section of a file into memory for PlayBuf etc.
readNoUpdate(String) - Method in class de.sciss.jcollider.Buffer: Reads in as many frames from a sound file as fit into the buffer, starting at the beginning of the file.
readNoUpdate(String, long) - Method in class de.sciss.jcollider.Buffer: Reads in as many frames from a sound file as fit into the buffer, starting at a given frame in the file.
readNoUpdate(String, long, int) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer.
readNoUpdate(String, long, int, int) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
readNoUpdate(String, long, int, int, boolean) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
readNoUpdate(String, long, int, int, boolean, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Reads in frames from a sound file into the buffer, beginning a given offset in the buffer.
readThumbnail(String, String) - Static method in class CreateThumbnail: Creates a thumbnail for a given image file.
realloc() - Method in class de.sciss.jcollider.Bus
reAutoScale(DisplayImpl, ScalarMap) - Static method in class loci.visbio.util.ColorUtil: Recomputes autoscaled color bounds for the given color map.
reAutoScale() - Method in class loci.visbio.view.ColorHandler: Recomputes autoscaled color range bounds.
rebuild(boolean) - Method in class loci.visbio.view.TransformHandler: Rebuilds sliders and display mappings for all linked transforms.
recompute - Variable in class loci.visbio.data.SliceWidget: Check box for whether slice is recomputed on the fly.
reconnect(int, double, boolean) - Method in class loci.visbio.overlays.FreeformExtension: Reconnects the extension with the freeform.
RECONNECT_THRESH - Static variable in class loci.visbio.overlays.FreeformExtension: Threshhold within which click must occur to invoke extend mode or reconnect a freeformExtension.
RECONNECT_THRESH - Static variable in class loci.visbio.overlays.FreeformTool: Threshhold within which click must occur to invoke extend mode or reconnect a freeformExtension.
RECONNECT_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: Threshhold within which click must occur to invoke extend mode or reconnect a freeformExtension.
recreateROIListRelativeToStartPoint() - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
recreateROIListRelativeToStartPoint(ArrayList<ArrayList<Float>>, double[]) - Static method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
recvMsg() - Method in class de.sciss.jcollider.SynthDef: Constructs a message to sends to a server for providing the synth def.
recvMsg(OSCMessage) - Method in class de.sciss.jcollider.SynthDef: Constructs a message to sends to a server for providing the synth def.
red - Variable in class loci.visbio.view.ColorHandler: Red, green and blue components of images.
red - Variable in class loci.visbio.view.ColorPane: Color map widgets.
RED_TYPE - Static variable in class loci.visbio.overlays.OverlayTransform: MathType for red color mappings.
redrawMessages(DisplayImpl) - Static method in class loci.visbio.util.DisplayUtil: Redraws exception messages in a display's bottom left-hand corner.
ref - Variable in class loci.visbio.view.TransformLink: Data reference linking data to the display.
references - Variable in class loci.visbio.view.StackLink: Data references linking data to the display.
refresh() - Method in class loci.visbio.view.DisplayControls: Refreshes GUI components based on current selection.
refresh() - Method in class loci.visbio.view.DisplayWindow: Refreshes GUI components.
refreshCurrentFont() - Method in class loci.visbio.overlays.OverlayWidget: Sets the font text field to reflect the currently chosen font.
refreshFont() - Method in class loci.visbio.util.FontChooserPane: Refreshes font to match latest GUI state.
refreshListObjects() - Method in class loci.visbio.overlays.OverlayWidget: Updates items on overlay list based on current transform state.
refreshListSelection() - Method in class loci.visbio.overlays.OverlayWidget: Updates overlay list's selection based on current transform state.
refreshPasteComponent(boolean) - Method in class loci.visbio.overlays.OverlayWidget: Updates copy and paste widget components to display data relevant to currently selected overlays.
refreshPreviewData() - Method in class loci.visbio.view.ColorHandler: Refreshes preview data from the transform link.
refreshTimer - Variable in class loci.visbio.overlays.OverlayWidget: Timer for refreshing widget components 5 times per second.
refreshWidget() - Method in class loci.visbio.data.SliceWidget: Updates the widget to reflect the arbitrary slice's current values.
refreshWidgetComponents() - Method in class loci.visbio.overlays.OverlayWidget: Updates right-hand widget components to display data relevant to currently selected overlays.
region - Variable in class loci.slim.MouseBehaviorButtons
register() - Method in class de.sciss.jcollider.Node
register(boolean) - Method in class de.sciss.jcollider.Node
register(Node) - Method in class de.sciss.jcollider.NodeWatcher: Adds a node to the list of known nodes.
register(Node, boolean) - Method in class de.sciss.jcollider.NodeWatcher
register(String, IModuleFactory) - Method in class loci.deepzoom.workflow.ModuleFactory
registerDataType(Class<?>, String) - Method in class loci.visbio.data.DataManager: Registers the given subclass of DataTransform with the data manager, using the given label as a description.
release() - Method in class de.sciss.jcollider.Node: Releases a node with default release time.
release(float) - Method in class de.sciss.jcollider.Node: Releases a node.
releaseLeft(DisplayEvent, DisplayImpl, OverlayTool) - Method in class loci.visbio.overlays.OverlayTransform: Helper method that handles left mouse button releases.
releaseMsg() - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to release a node with default release time.
releaseMsg(float) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to release a node.
remove() - Method in class de.sciss.jcollider.OSCResponderNode: Removes the node from the list of actively listening nodes.
remove - Variable in class loci.visbio.overlays.OverlayWidget: Button for removing selected overlays.
remove - Variable in class loci.visbio.view.CapturePanel: Button for removing selected position.
remove - Variable in class loci.visbio.view.DisplayControls: Button for removing a display from the list.
removeActionListener(ActionListener) - Method in class de.sciss.jcollider.gui.EZSlider
removeAllAxes() - Method in class loci.visbio.view.TransformPanel: Removes all dimensional axes.
removeAllListeners() - Method in class loci.visbio.util.InstanceServer: Removes all application instance spawn listeners.
removeAllOutputListeners() - Method in class loci.visbio.util.OutputConsole
removeAllTransforms() - Method in class loci.visbio.view.DisplayWindow: Unlinks all data transforms from the display.
removeAllTransforms() - Method in class loci.visbio.view.TransformHandler: Unlinks all data transforms from the display.
removeAllTransforms() - Method in class loci.visbio.view.TransformPanel: Removes all data transforms from the list.
removeAllWindows() - Method in class loci.visbio.util.Docker: Removes all windows from the dockable group.
removeCurveListener(CurveListener) - Method in class loci.slim.fit.CurveCollection
removeCurveListener(CurveListener) - Method in interface loci.slim.fit.CurveReporter
removeData(DataTransform) - Method in class loci.visbio.data.DataControls: Removes a data object from the data object tree.
removeData(DataTransform, boolean) - Method in class loci.visbio.data.DataControls: Removes a data object from the data object tree, confirming with the user first if confirm flag is set and the object has derivative objects.
removeData(DataTransform) - Method in class loci.visbio.data.DataManager: Removes a data object from the list.
removeData(DataTransform, boolean) - Method in class loci.visbio.data.DataManager: Removes a data object from the list.
removeDisplay(DisplayWindow) - Method in class loci.visbio.view.DisplayControls: Removes a display from the list of current displays.
removeDisplay(DisplayWindow) - Method in class loci.visbio.view.DisplayManager: Removes a display from the list of current displays.
removeDoWhenBooted(Server.CompletionAction) - Method in class de.sciss.jcollider.Server: Unregisters an action from being executed after the boot process.
removeEmptyFreeforms(OverlayFreeform[]) - Method in class loci.visbio.overlays.FreeformTool: Removes any freeforms with one or fewer nodes.
removeItemListener(ItemListener) - Method in class loci.visbio.view.BioColorWidget: Removes an item listener from this widget.
removeListener(NumberListener) - Method in class de.sciss.jcollider.gui.NumberField: Unregister a NumberListener from receiving number change events.
removeListener(NodeListener) - Method in class de.sciss.jcollider.NodeWatcher: Unregisters a listener from being informed about node status changes.
removeListener(ServerListener) - Method in class de.sciss.jcollider.Server: Unregisters a listener from being informed about server status changes.
removeNode(OSCResponderNode) - Method in class de.sciss.jcollider.OSCMultiResponder
removeNode(int) - Method in class loci.visbio.overlays.OverlayNodedObject: Deletes a node from the freeform object, creating two new freeforms if the node deleted is an interior node.
removeNullFromString(String) - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
removeNullFromString(String) - Static method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
removeObject(OverlayObject) - Method in class loci.visbio.overlays.OverlayTransform: Removes an overlay object at the current dimensional position.
removeObject(OverlayObject, int[]) - Method in class loci.visbio.overlays.OverlayTransform: Removes an overlay object at the given dimensional position.
removeOutputListener(OutputListener) - Method in class loci.visbio.util.OutputConsole
removeSelectedObjects() - Method in class loci.visbio.overlays.OverlayTransform: Removes selected overlay objects at the current dimensional position.
removeSelectedObjects(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Removes selected overlay objects at the given dimensional position.
removeSpawnListener(SpawnListener) - Method in class loci.visbio.util.InstanceServer: Removes an application instance spawn listener.
removeTask(BioTask) - Method in class loci.visbio.TaskControls: Removes a task from the tasks pane.
removeTransform(DataTransform) - Method in class loci.visbio.view.DisplayWindow: Removes the given data transform from the display.
removeTransform(DataTransform) - Method in class loci.visbio.view.TransformHandler: Removes the given data transform from the display.
removeTransform - Variable in class loci.visbio.view.TransformPanel: Button for removing selected data transform.
removeTransform(DataTransform) - Method in class loci.visbio.view.TransformPanel: Removes the given data transform from the list.
removeTransformListener(TransformListener) - Method in class loci.visbio.data.DataTransform: Removes the given listener from the list of listeners.
removeTSB() - Method in class loci.visbio.overlays.OverlayTransform: Removes transient selection box.
removeUpdate(DocumentEvent) - Method in class loci.slim.ColorWidget
removeUpdate(DocumentEvent) - Method in class loci.slim.SlimPlotter
removeUpdate(DocumentEvent) - Method in class loci.slim.TwoDPane
removeUpdate(DocumentEvent) - Method in class loci.visbio.overlays.OverlayWidget
removeUpdate(DocumentEvent) - Method in class loci.visbio.view.ColorPane: Handles text field deletions.
removeUpdate(DocumentEvent) - Method in class loci.visbio.view.ViewPanel: Handles text removals from a text field.
removeWhenDone() - Method in class de.sciss.jcollider.OSCResponderNode: Tags the node to remove itself after the next unfiltered message arrived.
removeWindow(Window) - Method in class loci.visbio.util.Docker: Removes a window from the dockable group.
rend - Variable in class loci.visbio.view.TransformLink: Data renderer for toggling data's visibility and other parameters.
render - Variable in class loci.visbio.view.StackPanel: Checkbox indicating whether volume rendering is enabled.
renderers - Variable in class loci.slim.fit.RendererSwitcher
renderers - Variable in class loci.visbio.view.StackLink: Data renderers for toggling data's visibility and other parameters.
RendererSwitcher - Class in loci.slim.fit: Renderer manager capable of switching between multiple renderers.
RendererSwitcher(ICurveRenderer[]) - Constructor for class loci.slim.fit.RendererSwitcher
renderRes - Variable in class loci.visbio.view.StackPanel: Spinner for volume rendering resolution.
repack() - Method in class loci.visbio.util.BreakawayPanel: Enlarges the window to its preferred size if it is too small.
repack(Window) - Static method in class loci.visbio.util.SwingUtil: Enlarges a window to its preferred width and/or height if it is too small.
repack() - Method in class loci.visbio.util.WizardPane: Resizes and centers dialog based on its contents.
repack() - Method in class loci.visbio.view.DisplayWindow: Enlarges the display to its preferred width and/or height if it is too small, keeping the display itself square.
replace(Node) - Static method in class de.sciss.jcollider.Group
replace(Node, String) - Static method in class de.sciss.jcollider.Synth
replace(Node, String, String[], float[]) - Static method in class de.sciss.jcollider.Synth
repoCollab() - Static method in class loci.backup.github.ResumePoint
repoHooks() - Static method in class loci.backup.github.ResumePoint
repoIssues() - Static method in class loci.backup.github.ResumePoint
repoIssues(boolean) - Static method in class loci.backup.github.ResumePoint
repoPR() - Static method in class loci.backup.github.ResumePoint
repoPR(boolean) - Static method in class loci.backup.github.ResumePoint
reportNewPlugin(String) - Method in class loci.deepzoom.workflow.plugin.PluginScheduler: This is just for debugging.
reportNewPlugin(String) - Method in class loci.multiinstanceplugin.PluginScheduler: This is just for debugging.
repoTeam() - Static method in class loci.backup.github.ResumePoint
repoUser() - Static method in class loci.backup.github.ResumePoint
res - Variable in class loci.visbio.data.ArbitrarySlice: Resolution of arbitrary slice.
res - Variable in class loci.visbio.data.SliceWidget: Slider for adjusting resolution.
resample(FlatField, int[], boolean[]) - Static method in class loci.visbio.util.DataUtil: Resamples the given FlatField to the specified resolution, keeping only the flagged range components (or null to keep them all), leaving the domain set's low and high values untouched.
resample(FlatField, int[], boolean[], boolean) - Static method in class loci.visbio.util.DataUtil: Resamples the given FlatField to the specified resolution, keeping only the flagged range components (or null to keep them all), forcing the result onto an IntegerSet of appropriate length if the relevant flag is set.
resample(FlatField, int[], boolean[], float[], float[]) - Static method in class loci.visbio.util.DataUtil: Resamples the given FlatField to the specified resolution, keeping only the flagged range components (or null to keep them all), and using the given minimum and maximum domain set values.
rescale(float) - Method in class loci.visbio.overlays.OverlayMarker: Rescales an OverlayMarker.
rescale(float) - Method in class loci.visbio.overlays.OverlayObject: Rescales this overlay object.
reserve(int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator
reserve(int, int) - Method in class de.sciss.jcollider.ContiguousBlockAllocator
reset - Variable in class de.sciss.jcollider.gui.NumberSpace: Reset value, i.e.
reset() - Method in class de.sciss.jcollider.NodeIDAllocator
reset() - Method in class loci.visbio.view.ViewHandler: Restores the display's zoom and orientation to the original values.
resetComponents() - Method in class loci.visbio.data.ExportPane: Resets the wizard pane's components to their default states.
resetComponents() - Method in class loci.visbio.state.OptionPane: Resets the dialog pane's components to their default states.
resetComponents() - Method in class loci.visbio.util.DialogPane: Resets the dialog pane's components to their default states.
resetComponents() - Method in class loci.visbio.util.WizardPane: Resets the wizard pane's components to their default states.
resetComponents() - Method in class loci.visbio.view.ColorPane: Resets the color pane's components to their default states.
resetComponents() - Method in class loci.visbio.view.SliceToggler: Resets the slice toggler's components to their default states.
reshow() - Method in class loci.visbio.util.BreakawayPanel: If breakaway panel is in a separate window, ensures it is visible.
resizeNodeArray(int) - Method in class loci.visbio.overlays.OverlayNodedObject: Resizes the node array, truncating if necessary.
resolution - Variable in class loci.visbio.data.ThumbnailHandler: Resolution of each thumbnail dimension.
ResolutionOption - Class in loci.visbio.state: ResolutionOption is an option for changing image resolution (two positive integers) in the VisBio Options dialog.
ResolutionOption(String, String, int, int) - Constructor for class loci.visbio.state.ResolutionOption: Constructs a new option.
ResolutionToggleOption - Class in loci.visbio.state: ResolutionToggleOption is an option for toggling image resolution (two positive integers) in the VisBio Options dialog.
ResolutionToggleOption(String, char, String, boolean, int, int) - Constructor for class loci.visbio.state.ResolutionToggleOption: Constructs a new option.
respond(OSCResponderNode, OSCMessage, long) - Method in class de.sciss.jcollider.NodeWatcher: This method is part of the implementation of the OSCResponderNode.Action interface.
respond(OSCResponderNode, OSCMessage, long) - Method in interface de.sciss.jcollider.OSCResponderNode.Action
restoreState(Element) - Method in class loci.visbio.data.ArbitrarySlice: Restores the current state from the given DOM element ("ArbitrarySlice").
restoreState(Element) - Method in class loci.visbio.data.CollapseTransform: Restores the current state from the given DOM element ("DimensionalCollapse").
restoreState(Element) - Method in class loci.visbio.data.DataManager: Restores the current state from the given DOM element ("VisBio").
restoreState(Element) - Method in class loci.visbio.data.DataSampling: Restores the current state from the given DOM element ("DataSampling").
restoreState(Element) - Method in class loci.visbio.data.Dataset: Restores the current state from the given DOM element ("Dataset").
restoreState(Element) - Method in class loci.visbio.data.DataTransform: Restores the current state from the given DOM element (a child of "DataTransforms").
restoreState(Element) - Method in class loci.visbio.data.ImageTransform: Restores the current state from the given DOM element (a child of "DataTransforms").
restoreState(Element) - Method in class loci.visbio.data.ProjectionTransform: Restores the current state from the given DOM element ("MaximumIntensityProjection").
restoreState(Element) - Method in class loci.visbio.data.SpectralTransform: Restores the current state from the given DOM element ("SpectralMapping").
restoreState(Element) - Method in class loci.visbio.ext.ExternalFunction: Restores the current state from the given DOM element ("ExternalFunction").
restoreState(Element) - Method in class loci.visbio.LogicManager: Restores the current state from the given DOM element.
restoreState(Element) - Method in class loci.visbio.state.BioOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.state.BooleanOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.state.ListOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.state.NumericOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.state.OptionManager: Restores the current state from the given DOM element ("VisBio").
restoreState(Element) - Method in class loci.visbio.state.ResolutionOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.state.ResolutionToggleOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in interface loci.visbio.state.Saveable: Restores the current state from the given DOM element.
restoreState(Element) - Method in class loci.visbio.state.SpreadsheetLaunchOption: Restores the current state from the given DOM element ("Options").
restoreState(File) - Method in class loci.visbio.state.StateManager: Restores the current state from the given state file.
restoreState(Element) - Method in class loci.visbio.state.StateManager: Restores the current state from the given DOM element ("VisBio").
restoreState(Element) - Method in class loci.visbio.state.StringOption: Restores the current state from the given DOM element ("Options").
restoreState(Element) - Method in class loci.visbio.view.CaptureHandler: Restores the current state from the given DOM element ("Display").
restoreState(Element) - Method in class loci.visbio.view.ColorHandler: Restores the current state from the given DOM element ("TransformLink").
restoreState(Element) - Method in class loci.visbio.view.DisplayManager: Restores the current state from the given DOM element ("VisBio").
restoreState(Element) - Method in class loci.visbio.view.DisplayPosition: Restores the current state from the given DOM element ("DisplayPosition").
restoreState(Element) - Method in class loci.visbio.view.DisplayWindow: Restores the current state from the given DOM element ("Display").
restoreState(Element) - Method in class loci.visbio.view.StackHandler: Restores the current state from the given DOM element ("Display").
restoreState(Element) - Method in class loci.visbio.view.StackLink: Restores the current state from the given DOM element ("StackLink").
restoreState(Element) - Method in class loci.visbio.view.TransformHandler: Restores the current state from the given DOM element ("Display").
restoreState(Element) - Method in class loci.visbio.view.TransformLink: Restores the current state from the given DOM element ("TransformLink").
restoreState(Element) - Method in class loci.visbio.view.ViewHandler: Restores the current state from the given DOM element ("Display").
restoreState(Element) - Method in class loci.visbio.WindowManager: Restores the current state from the given DOM element ("VisBio").
restoreWindows() - Method in class loci.visbio.WindowManager: Restores all previously hidden windows.
RESUME_FILE - Static variable in class loci.backup.github.GitHubBackup: File name of the temporary resume file.
RESUME_THRESH - Static variable in class loci.visbio.overlays.FreeformTool: How close mouse must be to end node to resume drawing.
RESUME_THRESH - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: How close mouse must be to end node to resume drawing.
ResumePoint - Class in loci.backup.github: A static utility class providing consistent name patterns that can be used to mark resume points in GitHubBackup when the API access limit is reached.
ResumePoint() - Constructor for class loci.backup.github.ResumePoint
resValue - Variable in class loci.visbio.data.SliceWidget: Label for current resolution value.
resX - Variable in class loci.visbio.data.DataSampling: Width of each image.
resX - Variable in class loci.visbio.ext.ExternalFunction: Width of each image.
resY - Variable in class loci.visbio.data.DataSampling: Height of each image.
resY - Variable in class loci.visbio.ext.ExternalFunction: Height of each image.
retrieve(String) - Method in class loci.visbio.data.ThumbnailCache: Retrieves the thumbnail with the given id string from the disk cache.
reverseNodes() - Method in class loci.visbio.overlays.OverlayNodedObject: Reverses the node array (and therefore its internal orientation).
rgb - Variable in class loci.visbio.view.ColorPane: Color model options.
RGB_MODEL - Static variable in class loci.visbio.util.ColorUtil: RGB color space model.
right - Variable in class loci.visbio.util.BreakawayPanel: Arrow buttons.
RoiMap - Class in loci.plugins: TODO
RoiMap() - Constructor for class loci.plugins.RoiMap
rotate - Variable in class loci.slim.MouseBehaviorButtons
rotate(double, double, double) - Method in class loci.visbio.view.ViewHandler: Rotates the display in the given direction.
rotateClockwise() - Method in class loci.visbio.view.ViewHandler: Rotates the display clockwise (2D and 3D).
rotateClockwise90(ArrayList<ArrayList<Float>>) - Static method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
rotateClockwise90(ArrayList<ArrayList<Float>>) - Static method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
rotateCounterclockwise() - Method in class loci.visbio.view.ViewHandler: Rotates the display counterclockwise (2D and 3D).
rotateDown() - Method in class loci.visbio.view.ViewHandler: Rotates the display downward (3D only).
rotateLeft() - Method in class loci.visbio.view.ViewHandler: Rotates the display to the left (3D only).
rotateRight() - Method in class loci.visbio.view.ViewHandler: Rotates the display to the right (3D only).
rotateUp() - Method in class loci.visbio.view.ViewHandler: Rotates the display upward (3D only).
ROTATION_AMOUNT - Static variable in class loci.visbio.view.ViewHandler: How far display rotates each time.
rt - Static variable in class loci.visbio.ext.ExternalProgram: Runtime object for running JVM.
run() - Method in class de.sciss.jcollider.Node: Resumes the node if it was paused.
run(boolean) - Method in class de.sciss.jcollider.Node: Pauses or resumes the node.
run() - Method in class de.sciss.jcollider.NodeWatcher: Part of internal message queueing.
run(ImageProcessor) - Method in class loci.apps.flow.Find_Particle_Areas
run(String) - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
run(String) - Method in class loci.apps.SlideScannerImport.SIFT_ExtractPointRoi
run() - Method in class loci.backup.github.GitHubBackup: Run the backup.
run(String) - Method in class loci.deepzoom.DeepZoom
run() - Method in class loci.jvmlink.ConnThread
run() - Method in class loci.jvmlink.JVMLinkServer: Continually listens for incoming client connections.
run() - Method in class loci.multithreadedplugin.AbstractNode: Loops until quitting time.
run() - Method in interface loci.multithreadedplugin.INode: The implementation of this method gets and puts data to do the data processing work of the node.
run() - Method in class loci.niche.MODSForm
run(String) - Method in class loci.plugins.DumpStack
run(ImageProcessor) - Method in class loci.plugins.ExportAsText
run(ImageProcessor) - Method in class loci.plugins.RoiMap
run(String) - Method in class loci.plugins.stitching.StitchOmeTiff
run(String) - Method in class loci.plugins.stitching.StitchPrairieTiff
run(String) - Method in class loci.plugins.stitching.VisualizeTiles
run() - Method in class loci.slim.fit.BurnInRenderer
run() - Method in class loci.slim.fit.CurveRenderer
run() - Method in interface loci.slim.fit.ICurveRenderer
run() - Method in class loci.slim.fit.RendererSwitcher
run() - Method in class loci.slim.SlimPlotter
run(String) - Method in class loci.sonification.Sonification
run(String) - Method in class loci.sonification.SonificationTool
run() - Method in class loci.visbio.data.ThumbnailHandler: Loads all thumbnails in the background.
run(String) - Method in class loci.visbio.OrthoStack
run() - Method in class loci.visbio.overlays.OverlayWidget: Refreshes the list selection.
run() - Method in class loci.visbio.SystemManager: Performs garbage collection, displaying a wait cursor while doing so.
run() - Method in class loci.visbio.util.InstanceServer: Listens for connections from newly spawned application instances and passes their arguments to all registered listeners.
run() - Method in class loci.visbio.view.TransformHandler: Animates the display.
run() - Method in class loci.visbio.view.TransformLink: Executes full-resolution burn-in operations.
run() - Method in class loci.visbio.VisBio: Launches the VisBio GUI with no arguments.
run() - Method in class loci.visbio.VisBioFrame: Preloads relevant classes.
runMsg() - Method in class de.sciss.jcollider.Node: Creates an OSC [ /n_run, <nodeID>, 1 ] message for the node.
runMsg(boolean) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_run message for the node.
RUNNING - Static variable in class de.sciss.jcollider.ServerEvent: returned by getID() : the server started running
rval - Variable in class loci.visbio.util.DialogPane: Return value of dialog.

S

S - Static variable in class loci.visbio.overlays.FreeformTool: Smoothing factor for "single exponential smoothing".
s_folder - Static variable in class loci.multiinstanceplugin.deepzoom.TileProcessor
s_format - Static variable in class loci.multiinstanceplugin.deepzoom.TileProcessor
s_name - Static variable in class loci.multiinstanceplugin.deepzoom.TileProcessor
s_singleInstance - Static variable in class loci.deepzoom.workflow.plugin.PluginLauncher
s_singleInstance - Static variable in class loci.multiinstanceplugin.PluginLauncher
s_suffix - Static variable in class loci.multiinstanceplugin.deepzoom.TileProcessor
SAMPLE_PREFIX - Static variable in class loci.visbio.data.DataManager: URL prefix for sample datasets.
sampleRate - Variable in class de.sciss.jcollider.Server.Status
sampling - Variable in class loci.visbio.data.SamplingWidget: Associated data sampling.
SamplingThumbHandler - Class in loci.visbio.data: Provides logic for handling data sampling thumbnails.
SamplingThumbHandler(DataTransform, String) - Constructor for class loci.visbio.data.SamplingThumbHandler: Creates a thumbnail handler.
SamplingWidget - Class in loci.visbio.data: SamplingWidget is a set of GUI controls for a DataSampling transform.
SamplingWidget(DataSampling) - Constructor for class loci.visbio.data.SamplingWidget
save(String, FlatField) - Method in class loci.visbio.data.ThumbnailCache: Saves the given data object to the end of the cache file.
save - Variable in class loci.visbio.overlays.OverlayWidget: Button for saving overlays to disk.
Saveable - Interface in loci.visbio.state: The Saveable interface provides methods for saving and restoring the implementing object's state to and from a data stream.
saveColorTable(float[][], File) - Static method in class loci.visbio.util.ColorUtil: Saves the given color table into the specified file.
SaveException - Exception in loci.visbio.state: Exception indicating a problem with saving or restoring an object state.
SaveException(String) - Constructor for exception loci.visbio.state.SaveException: Constructs a save exception with the given message.
SaveException(Exception) - Constructor for exception loci.visbio.state.SaveException: Constructs a save exception based on the given exception.
saveOverlays(PrintWriter, OverlayTransform) - Static method in class loci.visbio.overlays.OverlayIO: Writes the overlays to the given writer.
saveOverlays(PrintWriter) - Method in class loci.visbio.overlays.OverlayTransform: Writes the overlays to the given writer.
saveSettings() - Method in class loci.visbio.overlays.StatsOptionsPane: Saves current pane selections to OptionManager.
saveSnapshot() - Method in class loci.visbio.OrthoStack
saveSnapshot() - Method in class loci.visbio.view.CaptureHandler: Saves a snapshot of the display to a file specified by the user.
saveState(Element) - Method in class loci.visbio.data.ArbitrarySlice: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.data.CollapseTransform: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.data.DataManager: Writes the current state to the given DOM element ("VisBio").
saveState(Element) - Method in class loci.visbio.data.DataSampling: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.data.Dataset: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.data.DataTransform: Writes the current state to the given DOM element (a child of "DataTransforms").
saveState(Element) - Method in class loci.visbio.data.ImageTransform: Writes the current state to the given DOM element (a child of "DataTransforms").
saveState(Element) - Method in class loci.visbio.data.ProjectionTransform: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.data.SpectralTransform: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.ext.ExternalFunction: Writes the current state to the given DOM element ("DataTransforms").
saveState(Element) - Method in class loci.visbio.LogicManager: Writes the current state to the given DOM element.
saveState(Element) - Method in class loci.visbio.state.BioOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.state.BooleanOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.state.ListOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.state.NumericOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.state.OptionManager: Writes the current state to the given DOM element ("VisBio").
saveState(Element) - Method in class loci.visbio.state.ResolutionOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.state.ResolutionToggleOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in interface loci.visbio.state.Saveable: Writes the current state to the given DOM element.
saveState(Element) - Method in class loci.visbio.state.SpreadsheetLaunchOption: Writes the current state to the given DOM element ("Options").
saveState(File) - Method in class loci.visbio.state.StateManager: Saves the current state to the given state file.
saveState(Element) - Method in class loci.visbio.state.StateManager: Writes the current state to the given DOM element ("VisBio").
saveState(Element) - Method in class loci.visbio.state.StringOption: Writes the current state to the given DOM element ("Options").
saveState(Element) - Method in class loci.visbio.view.CaptureHandler: Writes the current state to the given DOM element ("Display").
saveState(Element) - Method in class loci.visbio.view.ColorHandler: Writes the current state to the given DOM element ("TransformLink").
saveState(Element) - Method in class loci.visbio.view.DisplayManager: Writes the current state to the given DOM element ("VisBio").
saveState(Element) - Method in class loci.visbio.view.DisplayPosition: Writes the current state to the given DOM element ("Capture").
saveState(Element) - Method in class loci.visbio.view.DisplayWindow: Writes the current state to the given DOM element ("Displays").
saveState(Element) - Method in class loci.visbio.view.StackLink: Writes the current state to the given DOM element ("LinkedData").
saveState(Element) - Method in class loci.visbio.view.TransformHandler: Writes the current state to the given DOM element ("Display").
saveState(Element) - Method in class loci.visbio.view.TransformLink: Writes the current state to the given DOM element ("LinkedData").
saveState(Element) - Method in class loci.visbio.view.ViewHandler: Writes the current state to the given DOM element ("Display").
saveState(Element) - Method in class loci.visbio.WindowManager: Writes the current state to the given DOM element ("VisBio").
scalarMultiply(float[], float) - Static method in class loci.visbio.util.MathUtil: Multiplies an N-D vector by a scalar.
scalars - Variable in class loci.visbio.view.BioColorWidget: List of range component scalars.
ScaleInHalfProcessor - Class in loci.chainableplugin.deepzoom: A processor that takes an image and scales it in half.
ScaleInHalfProcessor() - Constructor for class loci.chainableplugin.deepzoom.ScaleInHalfProcessor
ScaleInHalfProcessor - Class in loci.multiinstanceplugin.deepzoom: A processor that takes an image and scales it in half.
ScaleInHalfProcessor() - Constructor for class loci.multiinstanceplugin.deepzoom.ScaleInHalfProcessor
scaleROIStoLowresImage() - Method in class loci.apps.SlideScannerImport.AperioScannerInterpreter
scaleROIStoLowresImage() - Method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
scaleROIStoLowresImage(ArrayList<ArrayList<Float>>, double[]) - Static method in class loci.apps.SlideScannerImport.VentanaScannerInterpreter
SCGF_VERSION - Static variable in class de.sciss.jcollider.SynthDef: Currently supported synth def file version (1).
scrollPane - Variable in class loci.visbio.util.BreakawayPanel: Scroll pane (if any).
seg - Variable in class loci.visbio.overlays.FreeformTool.DistanceQuery: The index of the first node of the closest segment.
Segment2D - Class in loci.visbio.util: A 2D line segment.
Segment2D(float[], float[]) - Constructor for class loci.visbio.util.Segment2D: Constructor.
select - Variable in class loci.visbio.overlays.PointerTool: The selection box which may be created by this tool.
SELECT - Static variable in class loci.visbio.overlays.PolylineTool
selectBox - Variable in class loci.visbio.overlays.OverlayTransform: Transient Select Box, if active.
selected - Variable in class loci.visbio.overlays.OverlayObject: Flag indicating this overlay is currently selected.
selected - Variable in class loci.visbio.overlays.PointerTool: Array of whether objects are selected at time of mouse press.
SELECTED_TAIL - Static variable in class loci.visbio.overlays.PolylineTool
selectedNode - Variable in class loci.visbio.overlays.PolylineTool: Nearest node on selected PolyLine.
selectionContainsGroups - Variable in class de.sciss.jcollider.gui.NodeTreePanel
selectionContainsPausing - Variable in class de.sciss.jcollider.gui.NodeTreePanel
selectionContainsPlaying - Variable in class de.sciss.jcollider.gui.NodeTreePanel
selectionContainsSynths - Variable in class de.sciss.jcollider.gui.NodeTreePanel
selectNode(DefaultMutableTreeNode) - Method in class loci.visbio.data.DataControls: Selects the given tree node.
selector - Variable in class loci.visbio.view.ColorPane: Combo box for choosing color widgets.
send(Server) - Method in class de.sciss.jcollider.SynthDef: Sends the definition to a server.
send(Server, OSCMessage) - Method in class de.sciss.jcollider.SynthDef: Sends the definition to a server.
send() - Method in class loci.visbio.data.SendToIJPane: Sends the data to ImageJ according to the current input parameters.
sendArguments(String[], int) - Static method in class loci.visbio.util.InstanceServer: Attempts to send the given arguments to an instance server running on the specified port.
sendBundle(OSCBundle) - Method in class de.sciss.jcollider.Server: Sends an OSC bundle for scheduling to the server
sendBundleSync(OSCBundle, String, float) - Method in class de.sciss.jcollider.Server: Sends a bundle and waits for a /done reply for a given command name from the server.
sendBundleSync(OSCBundle, String, String, int, Object, float) - Method in class de.sciss.jcollider.Server: Sends a bundle and waits for a corresponding reply or failure message from the server.
sendBundleSync(OSCBundle, String, String, int[], Object[], int[], Object[], float) - Method in class de.sciss.jcollider.Server: Sends a bundle and waits for a corresponding reply or failure message from the server.
sendDataToImageJ(ImageTransform) - Method in class loci.visbio.data.DataControls: Sends part of a data object to an instance of ImageJ.
sendDataToImageJ() - Method in class loci.visbio.data.DataManager: Sends the selected data object to an instance of ImageJ.
sendDataToImageJ(ImageTransform) - Method in class loci.visbio.data.DataManager: Sends the given data object to an instance of ImageJ.
sendMsg(OSCMessage) - Method in class de.sciss.jcollider.Server: Sends an OSC message to the server
sendMsgSync(OSCMessage, float) - Method in class de.sciss.jcollider.Server: Sends a message and waits for a corresponding /done reply from the server.
sendMsgSync(OSCMessage, String, String, int, Object, float) - Method in class de.sciss.jcollider.Server: Sends a message and waits for a corresponding reply or failure message from the server.
sendMsgSync(OSCMessage, String, String, int[], Object[], int[], Object[], float) - Method in class de.sciss.jcollider.Server: Sends a message and waits for a corresponding reply or failure message from the server.
SendToIJPane - Class in loci.visbio.data: SendToIJPane provides options for exporting part of a multidimensional data series directly to an ImageJ instance.
SendToIJPane(VisBioFrame) - Constructor for class loci.visbio.data.SendToIJPane: Creates a dialog for specifying ImageJ export parameters.
sendToImageJ(String, Image) - Static method in class loci.visbio.util.ImageJUtil: Displays the given image object within ImageJ, launching ImageJ if necessary.
sendToImageJ(String, Image, VisBioFrame) - Static method in class loci.visbio.util.ImageJUtil: Displays the given image object within ImageJ, launching ImageJ if necessary.
sendToImageJ(String, FlatField[], VisBioFrame) - Static method in class loci.visbio.util.ImageJUtil: Displays the given FlatFields as an image stack within ImageJ, launching ImageJ if necessary.
sendToImageJ(ImagePlus, VisBioFrame) - Static method in class loci.visbio.util.ImageJUtil: Displays the given image object within ImageJ, launching ImageJ if necessary.
sendToImageJ(ImagePlus) - Static method in class loci.visbio.util.ImageJUtil: Displays the given image object within ImageJ, launching ImageJ if necessary.
sendToImageJ() - Method in class loci.visbio.view.CaptureHandler: Sends a snapshot of the display to ImageJ.
server - Variable in class de.sciss.jcollider.gui.ServerPanel
server - Variable in class de.sciss.jcollider.NodeWatcher
Server - Class in de.sciss.jcollider: Closely following SClang's server class, this is the client side representation of a supercollider server.
Server(String, InetSocketAddress, ServerOptions, int) - Constructor for class de.sciss.jcollider.Server: Creates a new Server representation object.
Server(String, InetSocketAddress, ServerOptions) - Constructor for class de.sciss.jcollider.Server: Creates a server representation for the default client (0).
Server(String, InetSocketAddress) - Constructor for class de.sciss.jcollider.Server: Creates a server representation for the default client (0), using default options.
Server(String) - Constructor for class de.sciss.jcollider.Server: Creates a representation for a server which listens at the loopback address (127.0.0.1:57110).
Server.CompletionAction - Interface in de.sciss.jcollider: This interface is used to describe an action to be executed after some process such as booting the server has completed.
Server.Status - Class in de.sciss.jcollider: A static field only class describing the snapshot of the server status as delivered by getStatus
serverAction(ServerEvent) - Method in class de.sciss.jcollider.gui.ServerPanel: This class implements the ServerListener interface to be notified about the server booting and quitting, and for tracking the status.
serverAction(ServerEvent) - Method in interface de.sciss.jcollider.ServerListener: Called when the server status changed.
serverAction(ServerEvent) - Method in class loci.sonification.Sonification
serverAction(ServerEvent) - Method in class loci.sonification.SonificationTool
serverBooting - Variable in class de.sciss.jcollider.Server
ServerEvent - Class in de.sciss.jcollider: These kind of events get delivered by a server represenation to inform listeners about server status changes
ServerEvent(Object, int, long, Server) - Constructor for class de.sciss.jcollider.ServerEvent
ServerListener - Interface in de.sciss.jcollider: Objects which wish to be informed about server status changes must implement this interface and register using Server.addListener.
ServerOptions - Class in de.sciss.jcollider: A class full of getter/setter methods to describe the options to boot a local scsynth server.
ServerOptions() - Constructor for class de.sciss.jcollider.ServerOptions: Creates a new instance with default options
ServerPanel - Class in de.sciss.jcollider.gui: A quick hack to provide a GUI element looking similar to SCLang's server window.
ServerPanel(Server, int) - Constructor for class de.sciss.jcollider.gui.ServerPanel: Creates a new ServerPanel for the given server and with GUI elements specified by the flags.
serverSocket - Variable in class loci.visbio.util.InstanceServer: Server socket listening for client connections.
set(float) - Method in class de.sciss.jcollider.Bus
set(int[], float[]) - Method in class de.sciss.jcollider.Bus
set(String, float) - Method in class de.sciss.jcollider.Node: Sets a node's control parameter to a new value.
set(int, float) - Method in class de.sciss.jcollider.Node: Sets a node's control parameter to a new value.
set(String[], float[]) - Method in class de.sciss.jcollider.Node: Sets a list of the node's control parameters to new values.
set(int[], float[]) - Method in class de.sciss.jcollider.Node: Sets a list of the node's control parameters to new values.
set(String, Object) - Method in interface loci.chainableplugin.IPropertyCollection: Sets a string/value association.
set(String, Object) - Method in class loci.chainableplugin.PropertyCollection: Sets a value.
set3DTexturing(boolean) - Method in class loci.visbio.view.DisplayWindow: Sets whether volume rendering uses 3D texturing.
setActiveColor(Color) - Method in class loci.visbio.overlays.OverlayWidget: Sets currently active overlay color.
setActiveGroup(String) - Method in class loci.visbio.overlays.OverlayWidget: Sets currently active overlay group.
setAll(Map<String, Object>) - Method in interface loci.chainableplugin.IPropertyCollection: Sets the map of all associations.
setAll(Map<String, Object>) - Method in class loci.chainableplugin.PropertyCollection: Sets the entire string/object map.
setAlphaTable(ScalarMap[], float[]) - Static method in class loci.visbio.util.ColorUtil: Assigns the given alpha channel to the specified mappings.
setAnimating(boolean) - Method in class loci.visbio.view.TransformHandler: Toggles animation of the display.
setAnimationAxis(int) - Method in class loci.visbio.view.TransformHandler: Assigns the given axis as the animation axis.
setAnimationRate(int) - Method in class loci.visbio.view.TransformHandler: Sets animation rate.
setAspect(double, double, double) - Method in class loci.visbio.view.ViewHandler: Adjusts the aspect ratio.
setAspect(double, double, double) - Method in class loci.visbio.view.ViewPanel: Updates aspect ratio GUI controls.
setAutoPopup(boolean) - Method in class loci.visbio.ConsoleManager: Sets whether consoles are automatically shown when output occurs.
setAutoRegister(boolean) - Method in class de.sciss.jcollider.NodeWatcher: Decides whether unknown nodes should be automatically added to the node watcher (usefull for debugging).
setAutoRegister() - Method in class de.sciss.jcollider.NodeWatcher: Queries whether automatic node registration is enabled.
setAutoSize(boolean) - Method in class loci.visbio.util.BreakawayPanel: Sets whether changing the edge intelligently resizes the owner window.
setAxis(int) - Method in class loci.visbio.data.ArbitrarySlice: Sets the axis through which to slice.
setBlockAllocFactory(BlockAllocator.Factory) - Method in class de.sciss.jcollider.ServerOptions
setBlockSize(int) - Method in class de.sciss.jcollider.ServerOptions
setBooting(boolean) - Method in class de.sciss.jcollider.Server
setBoundaries(float, float) - Method in class loci.visbio.overlays.OverlayObject: Sets value of largest and smallest x, y values.
setBoundingBox(boolean) - Method in class loci.visbio.OrthoStack
setBoundingBoxVisible(boolean) - Method in class loci.visbio.view.StackLink: Enables or disables visibility of the yellow bounding box.
setBurnDelay(long) - Method in class loci.visbio.view.TransformHandler: Sets the delay in milliseconds before full-resolution burn-in occurs.
setClasspathJars(List<String>) - Method in class loci.jar2lib.Jar2Lib
setClipboardContents(String) - Method in class loci.slim.TextTransfer
setColor(Color) - Method in class loci.visbio.overlays.OverlayObject: Sets color of this overlay.
setColorMode(DisplayImpl, int) - Static method in class loci.visbio.util.ColorUtil: Sets the given display's color mode to use either averaging or sums, depending on the specified color model.
setColorRange(DisplayImpl, ScalarMap, double, double, boolean) - Static method in class loci.visbio.util.ColorUtil: Assigns the given color range to the specified display and mapping.
setColorRanges(DisplayImpl, ScalarMap[], double[], double[], boolean[]) - Static method in class loci.visbio.util.ColorUtil: Assigns the given color ranges to the specified display and mappings.
setColors(int, int, int, RealType, RealType, RealType, boolean) - Method in class loci.visbio.view.ColorHandler: Updates color settings to those given.
setColorTables(ScalarMap[], float[][][]) - Static method in class loci.visbio.util.ColorUtil: Assigns the given color tables to the specified mappings.
setCompleted() - Method in class loci.visbio.BioTask: Marks a task as completed.
setCompleted(BioTask) - Method in class loci.visbio.TaskManager: Removes the given task from the task list.
setComponentCount(int) - Method in class loci.slim.fit.BurnInRenderer
setComponentCount(int) - Method in class loci.slim.fit.CurveCollection: Sets how many exponentials are expected to be fitted.
setComponentCount(int) - Method in class loci.slim.fit.CurveFitter: Sets how many exponentials are expected to be fitted.
setComponentCount(int) - Method in class loci.slim.fit.CurveRenderer
setComponentCount(int) - Method in interface loci.slim.fit.ICurveFitter: Sets how many exponentials are expected to be fitted.
setComponentCount(int) - Method in interface loci.slim.fit.ICurveRenderer
setComponentCount(int) - Method in class loci.slim.fit.RendererSwitcher
setConflictsPath(String) - Method in class loci.jar2lib.Jar2Lib
setContentPane(Container) - Method in class loci.visbio.util.BreakawayPanel: Sets pane containing GUI components.
setControlSpec(ControlSpec) - Method in class de.sciss.jcollider.gui.EZSlider
setCoords(float, float) - Method in class loci.visbio.overlays.OverlayNodedObject: Changes coordinates of the overlay's first endpoint.
setCoords(float, float) - Method in class loci.visbio.overlays.OverlayObject: Changes coordinates of the overlay's first endpoint.
setCoords2(float, float) - Method in class loci.visbio.overlays.OverlayObject: Changes coordinates of the overlay's second endpoint.
setCorePath(String) - Method in class loci.jar2lib.Jar2Lib
setCorner(int, int) - Method in class loci.visbio.overlays.TransientSelectBox: Sets coordinates of draggable box corner.
setCurrent(int) - Method in class loci.slim.fit.RendererSwitcher
setCursor(Component, Cursor) - Static method in class loci.visbio.util.SwingUtil: Sets the cursor for the given component and all child components to the given cursor.
setCurve(double[][]) - Method in class loci.slim.fit.CurveFitter: Sets the current curve estimate, useful if information about the curve is already known.
setCurve(double[][]) - Method in interface loci.slim.fit.ICurveFitter: Sets the current curve estimate, useful if information about the curve is already known.
setCurveLength(double) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets length of curve.
setData(int[]) - Method in class loci.slim.fit.CurveFitter: Sets the data to be used to generate curve estimates.
setData(int[], int, int) - Method in class loci.slim.fit.CurveFitter
setData(int[]) - Method in interface loci.slim.fit.ICurveFitter: Sets the data to be used to generate curve estimates.
setData(int[], int, int) - Method in interface loci.slim.fit.ICurveFitter
setData(ImageTransform) - Method in class loci.visbio.data.ExportPane: Associates the given data object with the export pane.
setData(ImageTransform) - Method in class loci.visbio.data.SendToIJPane: Associates the given data object with the export pane.
setData(Data, DataReference, DataRenderer, boolean, double) - Method in class loci.visbio.view.StackLink: Assigns the given data object to the specified data reference, switching to the proper types if the flag is set.
setData(Data) - Method in class loci.visbio.view.TransformLink: Assigns the given data object to the data reference.
setData(Data, boolean) - Method in class loci.visbio.view.TransformLink: Assigns the given data object to the data reference, switching to the proper types if the flag is set.
setData(Data, DataReference) - Method in class loci.visbio.view.TransformLink: Assigns the given data object to the given data reference.
setData(Data, DataReference, boolean) - Method in class loci.visbio.view.TransformLink: Assigns the given data object to the given data reference, switching to the proper types if the flag is set.
setDebug(boolean) - Method in class loci.jvmlink.JVMLinkServer
setDebug(boolean) - Method in class loci.visbio.ConsoleManager: Sets whether debugging mode is enabled.
setDeepFont(Container, Font) - Static method in class de.sciss.jcollider.JCollider: Set a font for a container and all children we can find in this container (calling this method recursively).
setDevice(String) - Method in class de.sciss.jcollider.ServerOptions
setDisplayDisabled(DisplayImpl, boolean) - Static method in class loci.visbio.util.DisplayUtil: Enables or disables the given display.
setDistributedMenus(boolean) - Method in class loci.visbio.WindowManager: Sets whether all registered frames should have a duplicate of the main VisBio menu bar.
setDocking(boolean) - Method in class loci.visbio.WindowManager: Sets whether window docking features are enabled.
setDoubleValue(double) - Method in class loci.visbio.DoubleSlider
setDownEnabled(boolean) - Method in class loci.visbio.util.BreakawayPanel: Toggles availability of down arrow button.
setDrawing(boolean) - Method in class loci.visbio.overlays.OverlayObject: Sets whether this overlay is still being initially drawn.
setEdge(String) - Method in class loci.visbio.util.BreakawayPanel: Sets the edge upon which the breakaway panel lies.
setEnabled(boolean) - Method in class loci.visbio.util.Docker: Sets whether docker should perform docking operations.
setEnabled(boolean) - Method in class loci.visbio.view.BioSlideWidget: Enables or disables this dimensional slider widget.
setExtrasPath(String) - Method in class loci.jar2lib.Jar2Lib
setEyeSeparation(DisplayImpl, double) - Static method in class loci.visbio.util.DisplayUtil: Sets the eye separation for a stereo 3D display.
setFilled(boolean) - Method in class loci.visbio.overlays.OverlayObject: Sets whether overlay is solid.
setFilled(boolean) - Method in class loci.visbio.overlays.OverlayWidget: Sets whether current overlay is filled.
setFireAllNodes(boolean) - Method in class de.sciss.jcollider.NodeWatcher: Decides whether node changes for any node or only for registered nodes are delivered to event listeners.
setFixed(boolean[][]) - Method in class loci.slim.fit.CurveCollection: Sets which parameters should be fixed, versus allowed to converge.
setFixed(boolean[][]) - Method in class loci.slim.fit.CurveFitter
setFixed(boolean[][]) - Method in class loci.slim.fit.CurveRenderer
setFixed(boolean[][]) - Method in interface loci.slim.fit.ICurveFitter: For each parameter, sets whether it should be fixed at the current value, or allowed to iterate toward an optimal value.
setFixed(boolean[][]) - Method in interface loci.slim.fit.ICurveRenderer
setFixed(boolean[][]) - Method in class loci.slim.fit.RendererSwitcher
setFlags(int) - Method in class de.sciss.jcollider.gui.NumberField
setFont(Font) - Method in class loci.visbio.data.DataTransform: Sets the font used for this transform's text mappings.
setFont(Font) - Method in class loci.visbio.overlays.OverlayTransform: Sets the font used for text overlays.
setFPS(int) - Method in class loci.visbio.view.CapturePanel: Sets movie frames per second.
setFullStackOption(boolean) - Method in class loci.apps.flow.Find_Particle_Areas
setGroup(Group) - Method in class de.sciss.jcollider.Node: Sets the node's group.
setGroup(String) - Method in class loci.visbio.overlays.OverlayObject: Sets group to which this overlay belongs.
setHardwareBufferSize(int) - Method in class de.sciss.jcollider.ServerOptions
setHeaderPath(String) - Method in class loci.jar2lib.Jar2Lib
setHeadNode(Node) - Method in class de.sciss.jcollider.Group
setHideAll(boolean) - Method in class loci.visbio.WindowManager: Sets whether minimizing the main VisBio window hides the other VisBio windows.
setHighlightNode(int) - Method in class loci.visbio.overlays.OverlayNodedObject: Highlight a node.
setImagePlus(ImagePlus) - Method in class loci.visbio.OrthoStack
setInform(boolean) - Static method in class de.sciss.jcollider.Server: Turns on or off verbose messaging of the server representation.
setInputStreamsEnabled(String) - Method in class de.sciss.jcollider.ServerOptions
setLabel(String) - Method in class de.sciss.jcollider.gui.EZSlider
setLabelWidth(int) - Method in class de.sciss.jcollider.gui.EZSlider
setLastNode(float, float) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets coordinates of last node.
setLastNode(float[]) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets coordinates of last node.
setLeftEnabled(boolean) - Method in class loci.visbio.util.BreakawayPanel: Toggles availability of left arrow button.
setLibraryJars(List<String>) - Method in class loci.jar2lib.Jar2Lib
setLineVisible(boolean) - Method in class loci.visbio.data.ArbitrarySlice: Sets whether white line is shown.
setLoadDefs(boolean) - Method in class de.sciss.jcollider.ServerOptions
setLocation(float) - Method in class loci.visbio.data.ArbitrarySlice: Sets the location for the arbitrary slice.
setM_password(String) - Method in class loci.wiscscan.auth.Credentials
setM_username(String) - Method in class loci.wiscscan.auth.Credentials
setMask(boolean[][]) - Method in class loci.slim.fit.BurnInRenderer
setMask(boolean[][]) - Method in class loci.slim.fit.CurveRenderer
setMask(boolean[][]) - Method in interface loci.slim.fit.ICurveRenderer
setMask(boolean[][]) - Method in class loci.slim.fit.RendererSwitcher
setMatrix(double[]) - Method in class loci.visbio.view.ViewHandler: Sets the display's projection matrix to match the given one.
setMax(int) - Method in class loci.checks.BlankLinesCheck: Sets the maximum allowed number of consecutive blank lines.
setMax(double) - Method in class loci.visbio.DoubleSlider
setMaxIterations(int) - Method in class loci.slim.fit.CurveRenderer
setMaxIterations(int) - Method in interface loci.slim.fit.ICurveRenderer
setMaxIterations(int) - Method in class loci.slim.fit.RendererSwitcher
setMaxNodes(int) - Method in class de.sciss.jcollider.ServerOptions
setMaxRCSE(double) - Method in class loci.slim.fit.CurveRenderer
setMaxRCSE(double) - Method in interface loci.slim.fit.ICurveRenderer
setMaxRCSE(double) - Method in class loci.slim.fit.RendererSwitcher
setMaxSynthDefs(int) - Method in class de.sciss.jcollider.ServerOptions
setMemSize(int) - Method in class de.sciss.jcollider.ServerOptions
setMessage(String) - Method in class loci.visbio.view.TransformLink: Sets status messages displayed in display's bottom left-hand corner.
setMin(double) - Method in class loci.visbio.DoubleSlider
setMnemonic(char) - Method in class loci.visbio.view.BioColorWidget: Sets the mnemonic for this widget.
setModel(int) - Method in class loci.visbio.view.BioColorWidget: Sets the widget's color model (RGB, HSV or COMPOSITE).
setMsg(float) - Method in class de.sciss.jcollider.Bus: Set the value of a monophonic bus.
setMsg(int[], float[]) - Method in class de.sciss.jcollider.Bus
setMsg(String, float) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to change a node's control parameter to a new value.
setMsg(int, float) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to change a node's control parameter to a new value.
setMsg(String[], float[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to adjust a list of the node's control parameters to new values.
setMsg(int[], float[]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_set message to adjust a list of the node's control parameters to new values.
setn(float[]) - Method in class de.sciss.jcollider.Bus
setn(int[], float[][]) - Method in class de.sciss.jcollider.Bus
setn(String[], float[][]) - Method in class de.sciss.jcollider.Node: Sets ranges of the node's control parameters to new values.
setn(int[], float[][]) - Method in class de.sciss.jcollider.Node: Sets ranges of the node's control parameters to new values.
setName(String) - Method in class de.sciss.jcollider.Node: Set a custom name for the node.
setName(String) - Method in class loci.backup.github.CreateOrphanBranchCommand
setName(String) - Method in interface loci.deepzoom.workflow.IModule: Sets name of module.
setName(String) - Method in class loci.deepzoom.workflow.PluginModule: Sets name of component.
setName(String) - Method in class loci.deepzoom.workflow.WorkFlow
setNextNode(float, float) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets next node coordinates.
setNextNode(float[]) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets next node coordinates.
setnMsg(float[]) - Method in class de.sciss.jcollider.Bus
setnMsg(int[], float[][]) - Method in class de.sciss.jcollider.Bus
setnMsg(String[], float[][]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_setn message to adjust ranges of the node's control parameters to new values.
setnMsg(int[], float[][]) - Method in class de.sciss.jcollider.Node: Creates an OSC /n_setn message to adjust ranges of the node's control parameters to new values.
setNodeCoords(int, float, float) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets coordinates of an existing node.
setNodes(float[][]) - Method in class loci.visbio.overlays.OverlayNodedObject: Sets the node array to that provided--for loading from saved.
setNotes(String) - Method in class loci.visbio.overlays.OverlayObject: Sets notes for this overlay.
setNotes(String) - Method in class loci.visbio.overlays.OverlayWidget: Sets notes for current overlay.
setNumAudioBusChannels(int) - Method in class de.sciss.jcollider.ServerOptions
setNumber(Number) - Method in class de.sciss.jcollider.gui.NumberField: Set the gadget contents to a new number.
setNumberWidth(int) - Method in class de.sciss.jcollider.gui.EZSlider
setNumBuffers(int) - Method in class de.sciss.jcollider.ServerOptions
setNumChannels(int) - Method in class de.sciss.jcollider.Buffer
setNumControlBusChannels(int) - Method in class de.sciss.jcollider.ServerOptions
setNumFrames(int) - Method in class de.sciss.jcollider.Buffer
setNumInputBusChannels(int) - Method in class de.sciss.jcollider.ServerOptions
setNumOutputBusChannels(int) - Method in class de.sciss.jcollider.ServerOptions
setNumRGens(int) - Method in class de.sciss.jcollider.ServerOptions
setNumWireBufs(int) - Method in class de.sciss.jcollider.ServerOptions
setOpacity(int, int, boolean) - Method in class loci.visbio.view.ColorHandler: Sets opacity.
setOutputListener(IOutputListener) - Method in interface loci.deepzoom.workflow.IModule: Listen for default output image.
setOutputListener(String, IOutputListener) - Method in interface loci.deepzoom.workflow.IModule: Listen for named output image.
setOutputListener(IOutputListener) - Method in class loci.deepzoom.workflow.PluginModule: Listen for output image.
setOutputListener(String, IOutputListener) - Method in class loci.deepzoom.workflow.PluginModule: Listen for output image.
setOutputListener(IOutputListener) - Method in class loci.deepzoom.workflow.WorkFlow
setOutputListener(String, IOutputListener) - Method in class loci.deepzoom.workflow.WorkFlow
setOutputPath(String) - Method in class loci.jar2lib.Jar2Lib
setOutputStreamsEnabled(String) - Method in class de.sciss.jcollider.ServerOptions
setPage(int) - Method in class loci.visbio.util.WizardPane: Sets the current page to the given value.
setPages(JPanel[]) - Method in class loci.visbio.util.WizardPane: Sets wizard's pages to match the given panels.
setParallelProjection(boolean) - Method in class loci.visbio.OrthoStack
setParallelProjection(DisplayImpl, boolean) - Static method in class loci.visbio.util.DisplayUtil: Sets whether the given 3D display uses a parallel projection.
setParameters(int, float, float, float, int, boolean, boolean) - Method in class loci.visbio.data.ArbitrarySlice: Sets the parameters for the arbitrary slice, recomputing the slice if the compute flag is set.
setParameters(int) - Method in class loci.visbio.data.CollapseTransform: Assigns the parameters for this dimensional collapse.
setParameters(int[], int[], int[], int, int, boolean[]) - Method in class loci.visbio.data.DataSampling: Assigns the parameters for this data sampling.
setParameters(int) - Method in class loci.visbio.data.ProjectionTransform: Assigns the parameters for this maximum intensity projection.
setParameters(double[][]) - Method in class loci.visbio.data.SpectralTransform: Assigns the parameters for this spectral mapping.
setParameters(String[]) - Method in class loci.visbio.ext.ExternalFunction: Assigns the parameters for this external function transform.
setParameters(String[], boolean) - Method in class loci.visbio.ext.ExternalFunction: Assigns the parameters for this external function transform.
setPitch(float) - Method in class loci.visbio.data.ArbitrarySlice: Sets the pitch for the slicing line.
setPlaying(boolean) - Method in class de.sciss.jcollider.Node: Specifies whether the node is playing (not paused).
setPos(int[]) - Method in class loci.visbio.overlays.OverlayTransform: Sets transform's current dimensional position.
setPositions(Vector) - Method in class loci.visbio.view.CapturePanel: Sets positions on the list.
setPredNode(Node) - Method in class de.sciss.jcollider.Node: Sets the node's predecessor node.
setPreviewData(FlatField) - Method in class loci.visbio.view.ColorPane: Sets the data displayed in the preview display to that given.
setPrintStream(PrintStream) - Static method in class de.sciss.jcollider.Server: Changes the stream to which messages are printed.
setProgram(String) - Static method in class de.sciss.jcollider.Server: Changes the path at which scsynth is supposed to located on the local harddisk.
setProgress(ProgressMonitor, int) - Static method in class loci.slim.SlimPlotter
setProgress(ProgressMonitor, int, int, double) - Static method in class loci.slim.SlimPlotter
setProgress(ProgressMonitor, int, boolean) - Static method in class loci.slim.SlimPlotter
setProgress(int, String) - Method in class loci.visbio.view.CaptureHandler: Sets capture panel's progress bar percentage value and message.
setProgressMessage(String) - Method in class loci.visbio.view.CapturePanel: Sets the progress bar's message.
setProgressValue(int) - Method in class loci.visbio.view.CapturePanel: Sets the progress bar's value.
setProjectId(String) - Method in class loci.jar2lib.Jar2Lib
setProjectName(String) - Method in class loci.jar2lib.Jar2Lib
setProtocol(String) - Method in class de.sciss.jcollider.ServerOptions
setRanges(double[], double[], boolean[]) - Method in class loci.visbio.view.ColorHandler: Updates map ranges to those given.
setRendezvous(boolean) - Method in class de.sciss.jcollider.ServerOptions
setResolution(int) - Method in class loci.visbio.data.ArbitrarySlice: Sets the resolution for the slicing line.
setResolution(int[]) - Method in class loci.visbio.data.ThumbnailHandler: Sets resolution of computed thumbnails.
setRestoring(boolean) - Method in class loci.visbio.state.StateManager: Sets whether state is currently being restored.
setRightEnabled(boolean) - Method in class loci.visbio.util.BreakawayPanel: Toggles availability of right arrow button.
setRoot(Node) - Method in class de.sciss.jcollider.gui.NodeTreeManager
setRunning(boolean) - Method in class de.sciss.jcollider.Node: Specifies whether the node exists on the server.
setRunning(boolean) - Method in class de.sciss.jcollider.Server
setSampleRate(double) - Method in class de.sciss.jcollider.Buffer
setSampleRate(double) - Method in class de.sciss.jcollider.ServerOptions
setSelected(boolean) - Method in class loci.visbio.overlays.OverlayObject: Sets whether this overlay is currently selected.
setSelectedData(DataTransform) - Method in class loci.visbio.data.DataControls: Selects the given data object in the tree.
setSelectedItem(RealType) - Method in class loci.visbio.view.BioColorWidget: Sets the currently selected RealType.
setSliceComputed(boolean) - Method in class loci.visbio.data.ArbitrarySlice: Sets whether arbitrary slice is computed.
setSliceVisible(int, boolean) - Method in class loci.visbio.view.StackLink: Enables or disables visibility at the specified slice index.
setSliderWidth(int) - Method in class de.sciss.jcollider.gui.EZSlider
setSmooth(boolean) - Method in class loci.visbio.view.CapturePanel: Sets whether transitions use a smoothing sine function.
setSnapThreshold(int) - Method in class loci.visbio.util.Docker: Sets the docking threshold in pixels.
setSnapToScreenEdges(boolean) - Method in class loci.visbio.util.Docker: Sets whether windows should snap to the screen edges when close.
setSourcePath(String) - Method in class loci.jar2lib.Jar2Lib
setSpace(NumberSpace) - Method in class de.sciss.jcollider.gui.NumberField
setSpecialIndex(int) - Method in class de.sciss.jcollider.UGen: This is called by SynthDef when assembling controls.
setSpeed(int) - Method in class loci.visbio.view.CapturePanel: Sets movie speed.
setSplashStatus(String) - Method in class loci.visbio.VisBioFrame: Updates the splash screen to report the given status message.
setStackAxis(int) - Method in class loci.visbio.view.StackLink: Assigns the given axis as the stack axis.
setStartPoint(String) - Method in class loci.backup.github.CreateOrphanBranchCommand
setStartPoint(RevCommit) - Method in class loci.backup.github.CreateOrphanBranchCommand
setState(WindowState) - Method in class loci.visbio.WindowInfo: Sets the window to match the given state.
setStatistics(String) - Method in class loci.visbio.overlays.OverlayWidget: Sets statistics for current overlay.
setStatus(int, int) - Method in class loci.visbio.BioTask: Updates the status of this task.
setStatus(String) - Method in class loci.visbio.BioTask: Updates the status of this task.
setStatus(int, int, String) - Method in class loci.visbio.BioTask: Updates the status of this task.
setStep(double) - Method in class loci.visbio.DoubleSlider
setStoppable(boolean) - Method in class loci.visbio.BioTask: Toggles whether the task can be stopped midway.
setSuccNode(Node) - Method in class de.sciss.jcollider.Node: Sets the node's successor node.
setTables(float[][][]) - Method in class loci.visbio.view.ColorHandler: Updates color tables to those given.
setTailNode(Node) - Method in class de.sciss.jcollider.Group
setTaskCount(int) - Method in class loci.visbio.util.SplashScreen: Sets the number of tasks for splash screen progress bar.
setTaskManager(TaskManager) - Method in class loci.visbio.data.ThumbnailHandler: Sets the task manager to use for reporting thumbnail generation progress.
setText(String) - Method in class de.sciss.jcollider.gui.LogTextArea: Replaces the gadget's text.
setText(String) - Method in class loci.visbio.overlays.OverlayObject: Changes text to render.
setText(String) - Method in class loci.visbio.util.SplashScreen: Changes the currently displayed text.
setTextDrawn(boolean) - Method in class loci.visbio.overlays.OverlayTransform: Whether text is drawn.
setTextureMapping(boolean) - Method in class loci.visbio.view.DisplayWindow: Sets wehther texture mapping is enabled.
setThumb(int[], FlatField) - Method in class loci.visbio.data.ThumbnailHandler: Sets the thumbnail at the given dimensional position.
setToolTipText(String) - Method in class loci.visbio.view.BioColorWidget: Sets the tool tip for this widget.
setTransform(DataTransform) - Method in class loci.visbio.view.SliceToggler: Sets the transform affected by this slice toggler.
setTransparencyMode(boolean) - Method in class loci.visbio.view.DisplayWindow: Sets whether transparency mode is nicest vs fastest.
setUnitsWidth(int) - Method in class de.sciss.jcollider.gui.EZSlider
setUnmappedValue(double) - Method in class de.sciss.jcollider.gui.EZSlider
setup(String, ImagePlus) - Method in class loci.apps.flow.Find_Particle_Areas: Original setup method called by ImageJ when plugin is run.
setup(String, ImagePlus) - Method in class loci.plugins.ExportAsText
setup(String, ImagePlus) - Method in class loci.plugins.RoiMap
setUpEnabled(boolean) - Method in class loci.visbio.util.BreakawayPanel: Toggles availability of up arrow button.
setValue(double) - Method in class de.sciss.jcollider.gui.EZSlider
setValue(String) - Method in class loci.visbio.state.CustomOption: Does nothing for a custom option.
setValue(String) - Method in class loci.visbio.state.NumericOption: Sets the GUI component to reflect the given value.
setValueAction(double) - Method in class de.sciss.jcollider.gui.EZSlider
SETVAR - Static variable in class loci.jvmlink.ConnThread
setVerbosity(int) - Method in class de.sciss.jcollider.ServerOptions
setVisible(boolean) - Method in class loci.visbio.util.OutputConsole
setVisible(boolean) - Method in class loci.visbio.view.DisplayWindow: Shows or hides this window.
setVisible(boolean) - Method in class loci.visbio.view.StackLink: Toggles visibility of the transform.
setVisible(boolean) - Method in class loci.visbio.view.TransformLink: Toggles visibility of the transform.
setVolumeRendered(boolean) - Method in class loci.visbio.view.StackLink: Enables or disables volume rendering.
setVolumeResolution(int) - Method in class loci.visbio.view.StackLink: Sets maximum resolution per axis of rendered volumes.
setWaitCursor(Component, boolean) - Static method in class loci.visbio.util.SwingUtil: Toggles the cursor for the given component and all child components between the wait cursor and the normal one.
setWaitCursor(boolean) - Method in class loci.visbio.WindowManager: Toggles the cursor between hourglass and normal pointer mode.
setWidgetTable(float[][]) - Method in class loci.slim.ColorWidget: Sets the currently selected range component's color widget table.
setWidgetTable(float[][]) - Method in class loci.visbio.view.ColorPane: Sets the currently selected range component's color widget table.
setWindowTitle(Window, String) - Static method in class loci.visbio.util.SwingUtil: Sets the title of the given window.
setX(float) - Method in class loci.visbio.overlays.OverlayObject: Changes X coordinate of the overlay's first endpoint.
setX2(float) - Method in class loci.visbio.overlays.OverlayObject: Changes X coordinate of the overlay's second endpoint.
setY(float) - Method in class loci.visbio.overlays.OverlayObject: Changes Y coordinate of the overlay's first endpoint.
setY2(float) - Method in class loci.visbio.overlays.OverlayObject: Changes Y coordinate of the overlay's second endpoint.
setYaw(float) - Method in class loci.visbio.data.ArbitrarySlice: Sets the yaw for the slicing line.
setZLevel(DataRenderer, double, int) - Method in class loci.visbio.view.StackLink: Assigns the given value to the specified data renderer's ConstantMap to the Z axis.
shiftLocation(Window, int, int) - Method in class loci.visbio.util.Docker: Shifts the given window's location by the given amount, without generating a ComponentEvent.
SHORT_TYPE - Static variable in class loci.jvmlink.ConnThread
shortString(int) - Static method in class loci.visbio.data.SpectralWidget: Converts a number between -1000 and 1000 into a number between -1.000 and 1.000, with exactly three digits after the decimal point.
show() - Method in class loci.visbio.util.OutputConsole
show - Variable in class loci.visbio.view.DisplayControls: Button for showing a display onscreen.
showColorDialog() - Method in class loci.visbio.view.ColorHandler: Displays the color dialog pane onscreen and alters the color scheme as requested.
showControls(DataTransform) - Method in class loci.visbio.data.DataControls: Shows frame containing controls for the given data object.
showControls(DataTransform) - Method in class loci.visbio.data.DataManager: Shows dialog containing controls for the given data object.
showDialog() - Method in class loci.visbio.data.SendToIJPane: Lays out components before displaying the dialog.
showDialog(Component) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog(Frame) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog(Dialog) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog(Component, boolean) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog(Frame, boolean) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog(Dialog, boolean) - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDialog() - Method in class loci.visbio.util.DialogPane: Displays a dialog using this dialog pane.
showDisplay() - Method in class loci.visbio.view.DisplayControls: Shows the selected display onscreen.
showHideConsole(boolean) - Method in class de.sciss.jcollider.gui.ServerPanel
showImage(String, int, int, byte[]) - Static method in class loci.apps.flow.FlowCyto
showLine - Variable in class loci.visbio.data.ArbitrarySlice: Flag indicating whether slicing line should be shown.
showLine - Variable in class loci.visbio.data.SliceWidget: Check box for whether slicing line is shown.
showScale - Variable in class loci.visbio.view.ViewHandler: Whether scale is visible.
showSystemInfo() - Method in class loci.visbio.SystemManager: Displays the system information window.
showWindow() - Method in class loci.visbio.WindowInfo: Displays the window onscreen.
showWindow(Window) - Method in class loci.visbio.WindowManager: Shows the given window.
shutServer() - Method in class loci.jvmlink.JVMLinkServer: Orders the server to terminate.
SIFT_ExtractPointRoi - Class in loci.apps.SlideScannerImport: Extract landmark correspondences in two images as PointRoi.
SIFT_ExtractPointRoi() - Constructor for class loci.apps.SlideScannerImport.SIFT_ExtractPointRoi
simpleName(File) - Static method in class loci.jar2lib.VelocityAutogen: Gets a simple name prefix with only alphameric characters.
sin - Static variable in class de.sciss.jcollider.gui.Warp
sine(double) - Static method in class loci.visbio.view.CaptureHandler: Evaluates a smooth sine function at the given value.
size - Variable in class loci.visbio.util.BioArrowButton: Size of the arrow button in pixels.
sizeC - Variable in class loci.niche.MODSForm
sizeT - Variable in class loci.niche.MODSForm
sizeX - Variable in class loci.niche.MODSForm
sizeX(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
sizeY - Variable in class loci.niche.MODSForm
sizeY(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
sizeZ - Variable in class loci.niche.MODSForm
sizeZ(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
slice - Variable in class loci.visbio.data.SliceWidget: Associated arbitrary slice.
SliceToggler - Class in loci.visbio.view: SliceToggler is a dialog pane for mass toggling stack slices.
SliceToggler(StackHandler) - Constructor for class loci.visbio.view.SliceToggler: Constructs a control panel for adjusting viewing parameters.
sliceToggler - Variable in class loci.visbio.view.StackPanel: Dialog box for toggling individual slices.
sliceVisible - Variable in class loci.visbio.view.StackPanel: Checkbox for choosing whether current slice is visible.
SliceWidget - Class in loci.visbio.data: SliceWidget is a set of GUI controls for an arbitrary slice.
SliceWidget(ArbitrarySlice) - Constructor for class loci.visbio.data.SliceWidget: Creates a new arbitrary slice widget.
slider - Variable in class loci.visbio.view.BioSlideWidget: Main slider component.
sliderPanel - Variable in class loci.visbio.view.TransformHandler: Panel containing dimensional slider widgets.
sliders - Variable in class loci.visbio.view.DisplayWindow: Panel containing dimensional slider widgets.
sliders - Variable in class loci.visbio.view.TransformHandler: Dimensional slider widgets for linked transforms.
SlimData - Class in loci.slim: Data structure for housing raw experimental data, as well as various derived data such as subsamplings and curve estimates.
SlimData(String, ProgressMonitor) - Constructor for class loci.slim.SlimData: Extracts data from the given file.
SlimPlotter - Class in loci.slim: A tool for visualization of spectral lifetime data.
SlimPlotter(String[]) - Constructor for class loci.slim.SlimPlotter
SlimTypes - Class in loci.slim: Data structure encapsulating shared VisAD math types and domain sets.
SlimTypes(int, int, int, double, double) - Constructor for class loci.slim.SlimTypes
smooth(float[], float[], float) - Static method in class loci.visbio.overlays.OverlayUtil: Calculates smoothed coordinates using "single exponential smoothing" as described in Littlewood and Inman, _Computer-assisted DNA length measurements..._.
smooth - Variable in class loci.visbio.view.CapturePanel: Check box for animation smoothness.
SMOOTHING_FACTOR - Static variable in class loci.visbio.overlays.FreeformExtension: Smoothing factor for "single exponential smoothing".
SMOOTHING_FACTOR - Static variable in class loci.visbio.overlays.OverlayNumericStrategy: Smoothing factor for "single exponential smoothing".
SOLID - Static variable in class loci.visbio.util.ColorUtil: RealType for indicating uniformly solid color component.
Sonification - Class in loci.sonification
Sonification() - Constructor for class loci.sonification.Sonification
SonificationTool - Class in loci.sonification
SonificationTool() - Constructor for class loci.sonification.SonificationTool
SortList - Class in <Unnamed>: Sorts a text file alphabetically, removing duplicates.
SortList() - Constructor for class SortList
spatial - Variable in class loci.visbio.data.Dataset: Types mapped to spatial components (X, Y).
SpawnEvent - Class in loci.visbio.util: An event indicating another application instance was spawned.
SpawnEvent(String[]) - Constructor for class loci.visbio.util.SpawnEvent: Constructs an application instance spawn event.
SpawnListener - Interface in loci.visbio.util: A listener for application instance spawn events.
spec - Variable in class de.sciss.jcollider.gui.EZSlider
specials - Variable in class de.sciss.jcollider.UGenInfo: Maps special names (Strings) to specialIndex values (Integers).
SpectralTransform - Class in loci.visbio.data: SpectralTransform is a mapping of spectral bands onto an RGB or grayscale color space, as specified by the user with weighted sliders.
SpectralTransform() - Constructor for class loci.visbio.data.SpectralTransform: Creates an uninitialized spectral mapping.
SpectralTransform(DataTransform, String, int) - Constructor for class loci.visbio.data.SpectralTransform: Creates a spectral mapping from the given transform.
SpectralWidget - Class in loci.visbio.data: SpectralWidget is a set of GUI controls for a spectral mapping transform.
SpectralWidget(SpectralTransform, String[]) - Constructor for class loci.visbio.data.SpectralWidget: Creates a new spectral mapping widget with weighted sliders.
speed - Variable in class loci.visbio.view.CapturePanel: Slider for adjusting movie speed.
splash - Variable in class loci.visbio.VisBioFrame: Associated splash screen.
SplashScreen - Class in loci.visbio.util: An application splash screen.
SplashScreen(URL, String[], Color) - Constructor for class loci.visbio.util.SplashScreen: Constructs a splash screen using the given logo image, informative messages and message background color.
SplashScreen(URL, String[], Color, Color) - Constructor for class loci.visbio.util.SplashScreen: Constructs a splash screen using the given logo image, informative messages, message background color and progress bar color.
SpreadsheetLauncher - Class in loci.visbio.overlays: Launches an external spreadsheet application.
SpreadsheetLauncher() - Constructor for class loci.visbio.overlays.SpreadsheetLauncher: Constructs a spreadsheet launcher.
SpreadsheetLaunchException - Exception in loci.visbio.overlays: Exception thrown when spreadsheet launch command fails.
SpreadsheetLaunchException(String) - Constructor for exception loci.visbio.overlays.SpreadsheetLaunchException: Constructs a new SpreadsheetLaunchException.
SpreadsheetLaunchOption - Class in loci.visbio.state: Option to toggle whether spreadsheet automatically launches when overlays are exported.
SpreadsheetLaunchOption(char, String, boolean) - Constructor for class loci.visbio.state.SpreadsheetLaunchOption: Constructs a new option.
SpreadsheetOptionStrategy - Class in loci.visbio.state: Strings related to the SpreadsheetLaunchOption option.
SpringUtilities - Class in loci.slim: A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class loci.slim.SpringUtilities
SRC - Static variable in class loci.deepzoom.workflow.WorkFlow
STACK_ANIMATION_RATE - Static variable in class loci.visbio.view.StackHandler: Starting FPS for animation for image stacks.
STACK_LIMIT - Static variable in class loci.visbio.view.DisplayManager: String for image stack resolution limit option.
stackAxis - Variable in class loci.visbio.view.StackLink: Dimensional axis to use for image stacks.
stackBox - Variable in class loci.visbio.view.StackPanel: List of axes for stacking.
StackHandler - Class in loci.visbio.view: Provides logic for linking data transforms to a 3D display as a stack of images.
StackHandler(DisplayWindow) - Constructor for class loci.visbio.view.StackHandler: Creates a 3D display transform handler.
stackLabel - Variable in class loci.visbio.view.StackPanel: Label for stack axis combo box.
StackLink - Class in loci.visbio.view: Represents a link between a data transform and a display that produces an image stack.
StackLink(StackHandler) - Constructor for class loci.visbio.view.StackLink: Constructs an uninitialized stack link.
StackLink(StackHandler, DataTransform) - Constructor for class loci.visbio.view.StackLink: Creates a link between the given data transform and the specified stack handler's display.
StackPanel - Class in loci.visbio.view: Provides GUI controls for a display stack handler.
StackPanel(StackHandler) - Constructor for class loci.visbio.view.StackPanel: Creates a panel containing view handler GUI controls.
stageLabelX(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
stageLabelY(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
stageLabelZ(IMetadata, int) - Static method in class loci.plugins.stitching.TileUtils
stallGenerations - Variable in class loci.slim.fit.GACurveFitter
start() - Method in class de.sciss.jcollider.NodeWatcher: Starts the OSC responders that trace incoming node notification events.
start() - Method in class de.sciss.jcollider.Server
start(Map<String, ItemWrapper>, Map<String, String>) - Method in class loci.deepzoom.workflow.plugin.AbstractPlugin: Starts up processing.
start(Map<String, ItemWrapper>, Map<String, String>) - Method in interface loci.deepzoom.workflow.plugin.IPluginInternal: Starts up processing.
start(Map<String, ImageWrapper>, Map<String, String>) - Method in class loci.multiinstanceplugin.AbstractPlugin: Starts up processing.
start(Map<String, ImageWrapper>, Map<String, String>) - Method in interface loci.multiinstanceplugin.IPluginInternal: Starts up processing.
start - Variable in class loci.visbio.overlays.FreeformExtension: The index of the last node of the freeform extension.
startAliveThread() - Method in class de.sciss.jcollider.Server: Begins to ping the server in regular intervals to detect a newly established connection, the loss of the connection and the current server status.
startAliveThread(float, float, int) - Method in class de.sciss.jcollider.Server: Starts the ping-thread with specified initial delay and ping period.
startAnimation() - Method in class loci.visbio.view.TransformHandler: Starts a new thread for animation.
startImageJ() - Static method in class loci.apps.flow.FlowCyto
startProgram() - Static method in class loci.visbio.VisBio: Launches the VisBio GUI with no arguments, in a separate thread.
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayArrow
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayBox
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayLine
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayMarker
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayNodedObject
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayOval
STAT_TYPES - Static variable in class loci.visbio.overlays.OverlayText
state - Variable in class loci.visbio.state.ProgramState: State object for use in state restoration.
STATE_CHANGED - Static variable in class loci.visbio.VisBioEvent: Indicates the state of one of VisBio's logic managers has changed.
STATE_EXTENSION - Static variable in class loci.visbio.state.StateManager: Extension for VisBio state files.
stateBox - Variable in class loci.visbio.state.StateManager: File chooser for state saves.
stateChanged(ChangeEvent) - Method in class loci.slim.SlimPlotter: Handles slider changes.
stateChanged(ChangeEvent) - Method in class loci.slim.TwoDPane: Handles slider changes.
stateChanged(ChangeEvent) - Method in class loci.visbio.data.SliceWidget: Handles slider and check box updates.
stateChanged(ChangeEvent) - Method in class loci.visbio.util.FontChooserPane: Handles GUI events.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.BioSlideWidget: Called when the linked dimensional slider changes.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.CapturePanel: Called when slider or spinner is adjusted.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.ColorPane: Handles slider changes.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.StackPanel: Handles spinner changes.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.TransformHandler: Handles slider updates.
stateChanged(ChangeEvent) - Method in class loci.visbio.view.TransformPanel: Handles spinner changes.
StateManager - Class in loci.visbio.state: StateManager is the manager encapsulating VisBio's state logic.
StateManager(VisBioFrame) - Constructor for class loci.visbio.state.StateManager: Constructs a VisBio state management object.
StateManager(VisBioFrame, String) - Constructor for class loci.visbio.state.StateManager: Constructs a VisBio state management object.
stats - Variable in class loci.visbio.overlays.OverlayWidget: Text area for overlay statistics.
StatsOptionsPane - Class in loci.visbio.overlays: A tabbed pane full of checkboxes.
StatsOptionsPane() - Constructor for class loci.visbio.overlays.StatsOptionsPane: Creates an StatsOptionsPane object.
status - Variable in class de.sciss.jcollider.Server
status() - Method in class de.sciss.jcollider.Server
Status() - Constructor for class de.sciss.jcollider.Server.Status
status - Variable in class loci.visbio.BioTask: Label displaying current status message for the task.
status - Variable in class loci.visbio.view.TransformLink: Status message, to be displayed in bottom left corner.
step - Variable in class loci.visbio.data.DataSampling: Index step value for each dimension.
step(boolean) - Method in class loci.visbio.view.BioSlideWidget: Steps the slider in the given direction.
step - Variable in class loci.visbio.view.SliceToggler: Slice step increment.
stepFields - Variable in class loci.visbio.data.SamplingWidget: Text fields for dimensional step values.
STEREO - Static variable in class loci.visbio.view.DisplayWindow: Stereo graphics configuration.
StitchOmeTiff - Class in loci.plugins.stitching: A plugin to parse stage position information from the OME-TIFF dataset's metadata block using Bio-Formats, and convert it to a format compatible with Fiji's 2D and 3D Stitching plugins.
StitchOmeTiff() - Constructor for class loci.plugins.stitching.StitchOmeTiff
StitchOmeTiff.FusionMethod - Enum in loci.plugins.stitching
StitchPrairieTiff - Class in loci.plugins.stitching: A plugin to parse stage position information from a Prairie TIFF dataset's XML metadata file, and convert it to a format compatible with Fiji's 2D and 3D Stitching plugins.
StitchPrairieTiff() - Constructor for class loci.plugins.stitching.StitchPrairieTiff
StitchPrairieTiff.FusionMethod - Enum in loci.plugins.stitching
stop() - Method in class de.sciss.jcollider.NodeWatcher: Stops the OSC responders that trace incoming node notification events.
stop() - Method in class loci.slim.fit.CurveRenderer
stop() - Method in interface loci.slim.fit.ICurveRenderer
stop() - Method in class loci.slim.fit.RendererSwitcher
stop - Variable in class loci.visbio.BioTask: Button for halting and resuming the task.
stop - Variable in class loci.visbio.overlays.FreeformExtension: The index of the last node of the freeform extension.
stop() - Method in class loci.visbio.util.InstanceServer: Stops this instance server's thread.
stopAliveThread() - Method in class de.sciss.jcollider.Server: Stops the ping-thread.
STOPPED - Static variable in class de.sciss.jcollider.ServerEvent: returned by getID() : the server stopped running
stopped - Variable in class loci.visbio.BioTask: Whether the task has been stopped.
store(String, FlatField) - Method in class loci.visbio.data.ThumbnailCache: Stores the given thumbnail in the disk cache.
straddles(Segment2D) - Method in class loci.visbio.util.Segment2D: Whether another segment crosses the line defined by this segment.
string - Variable in class loci.visbio.view.DisplayWindow: String representation of this display.
STRING_TYPE - Static variable in class loci.jvmlink.ConnThread
stringArrayToConsoleString(String[]) - Static method in class de.sciss.jcollider.ServerOptions: Converts an array of strings to a string which can be used in a Un*x console.
StringOption - Class in loci.visbio.state: StringOption is a user-supplied string option in the VisBio Options dialog.
StringOption(String, String, String, String) - Constructor for class loci.visbio.state.StringOption: Constructs a new option.
StringReplace - Class in loci.jar2lib: A program to filter and replace strings in a file—in other words, a poor man's pure Java version of sed.
StringReplace(String, String) - Constructor for class loci.jar2lib.StringReplace
stringToBooleanArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of booleans.
stringToByteArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of bytes.
stringToCharArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of chars.
stringToColor(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given string into a Color object.
stringToDouble(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given string into a double value.
stringToDoubleArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of doubles.
stringToFloat(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given string into a float value.
stringToFloatArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of floats.
stringToIntArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of ints.
stringToLongArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of longs.
stringToShortArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of shorts.
stringToStringArray(String) - Static method in class loci.visbio.util.ObjectUtil: Converts the given String into an array of Strings.
submissionNumber - Variable in class loci.niche.MODSForm
subsampleLevel - Variable in class loci.slim.fit.CurveRenderer
SUFFIX - Static variable in class de.sciss.jcollider.SynthDef: Default file suffix when writing defs to disk.
supportedFlavors - Static variable in class de.sciss.jcollider.gui.NumberField
SwingUtil - Class in loci.visbio.util: SwingUtil contains useful Swing functions.
switchType(FlatField, FunctionType) - Static method in class loci.visbio.util.DataUtil: Converts a FlatField's MathType into the one given (if compatible).
switchType(FlatField, FunctionType, Unit[]) - Static method in class loci.visbio.util.DataUtil: Converts a FlatField's MathType into the one given (if compatible), and uses the specified domain set units.
sync(float) - Method in class de.sciss.jcollider.Server: Sends a /sync message to the server and waits for a corresponding /synced reply.
sync(OSCBundle, float) - Method in class de.sciss.jcollider.Server: Attaches a /sync message to the list of messages in a bundle and sends the bundle to server, waiting for a corresponding /synced reply.
syncBootThread - Variable in class de.sciss.jcollider.Server
syncMenuItem(JMenuItem, JMenuItem) - Static method in class loci.visbio.util.SwingUtil: Brings the destination menu item into sync with the source item.
SYNTH - Static variable in class de.sciss.jcollider.NodeEvent: returned by getType() : the node is a synth
Synth - Class in de.sciss.jcollider: Mimics SCLang's Synth class, that is, it's a client side representation of a synth in the synthesis graph
Synth(String, Node) - Constructor for class de.sciss.jcollider.Synth
Synth(String, String[], float[], Node) - Constructor for class de.sciss.jcollider.Synth
Synth(String, String[], float[], Node, int) - Constructor for class de.sciss.jcollider.Synth
SynthDef - Class in de.sciss.jcollider: This is the representation of a UGen graph, a prototype for a synth node.
SynthDef(String, GraphElem) - Constructor for class de.sciss.jcollider.SynthDef: Constructs a new SynthDef from the given graph element.
SynthDefDiagram - Class in de.sciss.jcollider.gui: An experimental view of a SynthDef's graph.
SynthDefDiagram(SynthDef) - Constructor for class de.sciss.jcollider.gui.SynthDefDiagram: Creates a new frame displaying the diagram of the provided SynthDef.
SysProps - Class in <Unnamed>: Dumps all Java system properties.
SysProps() - Constructor for class SysProps
SystemControls - Class in loci.visbio: SystemControls is the control panel for reporting system information.
SystemControls(LogicManager) - Constructor for class loci.visbio.SystemControls: Constructs a control panel for viewing system information.
SystemManager - Class in loci.visbio: SystemManager is the manager encapsulating VisBio's system information report logic.
SystemManager(VisBioFrame) - Constructor for class loci.visbio.SystemManager: Constructs a system manager.

T

t - Variable in class loci.plugins.stitching.Pt
TABLE - Static variable in class loci.visbio.overlays.OverlayIO
tabs - Variable in class loci.visbio.overlays.StatsOptionsPane: The tabbed pane contained in this object.
tabs - Variable in class loci.visbio.state.OptionPane: Tabbed pane.
tail(Group) - Static method in class de.sciss.jcollider.Group
tail(Group, String) - Static method in class de.sciss.jcollider.Synth
tail(Node, String, String[], float[]) - Static method in class de.sciss.jcollider.Synth
TaskControls - Class in loci.visbio: TaskControls is the control panel for managing tasks.
TaskControls(LogicManager) - Constructor for class loci.visbio.TaskControls: Constructs a tool panel for controlling tasks.
taskControls - Variable in class loci.visbio.TaskManager: Tasks control panel.
TaskManager - Class in loci.visbio: TaskManager is the manager encapsulating VisBio's multitasking logic.
TaskManager(VisBioFrame) - Constructor for class loci.visbio.TaskManager: Constructs a tasks manager.
TCP - Static variable in class de.sciss.jcollider.ServerOptions: Protocol type : transport control protocol
teamMembers() - Static method in class loci.backup.github.ResumePoint
teamMembers(int) - Static method in class loci.backup.github.ResumePoint
TeardownException - Exception in loci.deepzoom.workflow.plugin: Exception thrown when a plugin chain is shutting down.
TeardownException(String) - Constructor for exception loci.deepzoom.workflow.plugin.TeardownException
TeardownException - Exception in loci.multiinstanceplugin: Exception thrown when a plugin chain is shutting down.
TeardownException(String) - Constructor for exception loci.multiinstanceplugin.TeardownException
TeardownException - Exception in loci.multithreadedplugin: TODO
TeardownException(String) - Constructor for exception loci.multithreadedplugin.TeardownException
TemplateFiller - Class in loci.niche: TODO
TemplateFiller() - Constructor for class loci.niche.TemplateFiller
TestMem - Class in <Unnamed>: A little GUI for testing Java memory behavior.
TestMem() - Constructor for class TestMem
text - Variable in class loci.visbio.overlays.OverlayObject: Text string to render.
text - Variable in class loci.visbio.overlays.OverlayWidget: Text field for text labels.
text - Variable in class loci.visbio.overlays.TextTool: Text currently being rendered.
text - Variable in class loci.visbio.state.BioOption: String identifying this option.
textRangeTuple - Variable in class loci.visbio.overlays.OverlayTransform: Overlay range type for text overlays.
TextTool - Class in loci.visbio.overlays: TextTool is the tool for creating text overlays.
TextTool(OverlayTransform) - Constructor for class loci.visbio.overlays.TextTool: Constructs a text overlay creation tool.
TextTransfer - Class in loci.slim: Helper class for clipboard interaction, stolen from Java Practices.
TextTransfer() - Constructor for class loci.slim.TextTransfer
textType - Variable in class loci.visbio.overlays.OverlayTransform: MathType for Text mappings.
TEXTURE3D - Static variable in class loci.visbio.view.DisplayManager: String for 3D texturing option.
TEXTURE_MAP - Static variable in class loci.visbio.view.DisplayManager: String for texture mapping option.
theC - Variable in class loci.plugins.stitching.Pt
theT - Variable in class loci.plugins.stitching.Pt
theZ - Variable in class loci.plugins.stitching.Pt
threeD - Variable in class loci.visbio.view.DisplayWindow: True if this display is 3D, false if 2D.
THRESH - Static variable in class loci.visbio.overlays.PolylineTool: Maximum distance (in pixels) mouse can be from a node to be considered pointing to it.
thresh - Variable in class loci.visbio.util.Docker: Pixel threshold for windows to snap next to one another.
THUMB_RES - Static variable in class loci.visbio.data.DataManager: String for thumbnail resolution option.
ThumbnailCache - Class in loci.visbio.data: Disk cache for thumbnails generated from datasets.
ThumbnailCache(String) - Constructor for class loci.visbio.data.ThumbnailCache: Constructs a thumbnail cache that uses the given disk file.
ThumbnailHandler - Class in loci.visbio.data: Provides logic for handling data transform thumbnails.
ThumbnailHandler(DataTransform, String) - Constructor for class loci.visbio.data.ThumbnailHandler: Creates a thumbnail handler.
thumbs - Variable in class loci.visbio.data.DataTransform: Handles logic for creating thumbnails from transform data.
thumbs - Variable in class loci.visbio.data.ThumbnailHandler: Thumbnail data computed from data transform.
TIFFINFO(String) - Static method in class loci.apps.SlideScannerImport.MiniBioformatsTool
TileProcessor - Class in loci.multiinstanceplugin.deepzoom: XInnerX class that chains from the CutTileProcessor.
TileProcessor() - Constructor for class loci.multiinstanceplugin.deepzoom.TileProcessor
TileProcessorX() - Constructor for class loci.multiinstanceplugin.deepzoom.DeepZoomExporter.TileProcessorX
TileUtils - Class in loci.plugins.stitching: Utility methods for stitching plugins.
timeBins - Variable in class loci.slim.SlimData
timeRange - Variable in class loci.slim.SlimData
tip - Variable in class loci.visbio.ControlPanel: Tip for this control panel.
tip - Variable in class loci.visbio.overlays.FreeformExtension: The index of the tip node of the freeform extension.
TIP - Static variable in class loci.visbio.overlays.OverlayArrow: The names of the statistics this object reports.
tip - Variable in class loci.visbio.overlays.OverlayTool: Tool tip text.
title - Variable in class loci.niche.MODSForm
TITLE - Static variable in class loci.slim.SlimData
title - Variable in class loci.visbio.BioTask: Label displaying name of the task.
title - Variable in class loci.visbio.util.DialogPane: Dialog's title.
TITLE - Static variable in class loci.visbio.VisBio: Application title.
tm - Variable in class loci.visbio.BioTask: Task manager associated with the task.
tm - Variable in class loci.visbio.data.ThumbnailHandler: Task manager used for reporting background thumbnail generation progress.
toggleAllTabs() - Method in class loci.visbio.overlays.StatsOptionsPane: Selects or deselects all checkboxes in current tab.
toggleBoundingBox(boolean) - Method in class loci.visbio.view.ViewHandler: Toggles visibility of the display's bounding box.
toggleCurrentTab() - Method in class loci.visbio.overlays.StatsOptionsPane: Selects or deselects all checkboxes in current tab.
toggleGeneration(boolean) - Method in class loci.visbio.data.ThumbnailHandler: Starts or stops background thumbnail generation.
toggleParallel(boolean) - Method in class loci.visbio.view.ViewHandler: Toggles whether 3D display uses a parallel projection.
toggleScale(boolean) - Method in class loci.visbio.view.ViewHandler: Toggles visibility of scale.
toggleSlices - Variable in class loci.visbio.view.StackPanel: Button for bringing up slice toggler dialog box.
toLabel - Variable in class loci.visbio.view.ColorPane: Label for fixed color scale.
toolChanged - Variable in class loci.visbio.overlays.OverlayTransform: Whether last tool has changed.
tools - Variable in class loci.visbio.overlays.OverlayWidget: List of overlay tools.
toOptionList(int) - Method in class de.sciss.jcollider.ServerOptions: Creates a list of all the server options, omitting those whose value equals the default value.
toOptionList(int, boolean) - Method in class de.sciss.jcollider.ServerOptions: Creates a list of all the server options.
top - Variable in class loci.visbio.util.BreakawayPanel: Arrow buttons.
toString() - Method in class de.sciss.jcollider.Buffer
toString() - Method in class de.sciss.jcollider.Bus
toString() - Method in class de.sciss.jcollider.Group
toString() - Method in class de.sciss.jcollider.Synth
toString() - Method in class loci.deepzoom.plugin.ImageWrapper: Displayable info for the image.
toString() - Method in enum loci.plugins.stitching.StitchOmeTiff.FusionMethod
toString() - Method in enum loci.plugins.stitching.StitchPrairieTiff.FusionMethod
toString() - Method in class loci.slim.fit.CurveEvent: Gets a string representation of the event.
toString() - Method in class loci.visbio.data.DataTransform: Gets a string representation of this transform.
toString() - Method in class loci.visbio.overlays.OverlayArrow: Gets a short string representation of this overlay arrow.
toString() - Method in class loci.visbio.overlays.OverlayBox: Gets a short string representation of this overlay box.
toString() - Method in class loci.visbio.overlays.OverlayFreeform: Gets a short string representation of this freeform.
toString() - Method in class loci.visbio.overlays.OverlayLine: Gets a short string representation of this measurement line.
toString() - Method in class loci.visbio.overlays.OverlayMarker: Gets a short string representation of this measurement marker.
toString() - Method in class loci.visbio.overlays.OverlayOval: Gets a short string representation of this overlay oval.
toString() - Method in class loci.visbio.overlays.OverlayPolyline: Gets a short string representation of this freeform.
toString() - Method in class loci.visbio.overlays.OverlayText: Gets a short string representation of this overlay text.
toString() - Method in class loci.visbio.util.Segment2D
toString() - Method in class loci.visbio.view.DisplayPosition: Gets the position's string representation (name).
toString() - Method in class loci.visbio.view.DisplayWindow: Gets a string representation of this display (just its name).
toString() - Method in class loci.visbio.VisBioEvent: Gets a string representation of this event.
toString() - Method in class loci.visbio.WindowState: Gets a string representation of this window state.
totalIterations - Variable in class loci.slim.fit.CurveRenderer
toXML() - Method in interface loci.deepzoom.workflow.IModule: Saves module as XML string representation.
toXML() - Method in interface loci.deepzoom.workflow.IWorkFlow: Saves chained components as XML string representation.
toXML() - Method in class loci.deepzoom.workflow.PluginModule: Saves component as XML string representation.
toXML() - Method in class loci.deepzoom.workflow.WorkFlow
trace() - Method in class de.sciss.jcollider.Node: Sends an OSC /n_trace message to the server.
traceMsg() - Method in class de.sciss.jcollider.Node: Creates an OSC /n_trace message for the node.
trans - Variable in class loci.visbio.view.TransformLink: Data transform linked to the display.
transform - Variable in class loci.visbio.view.SliceToggler: Data transform upon which this slice toggler operates.
transformChanged(TransformEvent) - Method in class loci.visbio.data.ArbitrarySlice: Called when parent data transform's parameters are updated.
transformChanged(TransformEvent) - Method in class loci.visbio.data.DataControls: Updates data info panel if a data transform changes while selected.
transformChanged(TransformEvent) - Method in class loci.visbio.data.SpectralTransform: Called when parent data transform's parameters are updated.
transformChanged(TransformEvent) - Method in class loci.visbio.data.ThumbnailHandler: Handles data transform parameter changes.
transformChanged(TransformEvent) - Method in interface loci.visbio.data.TransformListener: Called when a data transform's parameters are updated.
transformChanged(TransformEvent) - Method in class loci.visbio.overlays.OverlayTransform: Called when parent data transform's parameters are updated.
transformChanged(TransformEvent) - Method in class loci.visbio.overlays.OverlayWidget: Handles font changes.
transformChanged(TransformEvent) - Method in class loci.visbio.view.TransformLink: Called when a data transform's parameters are updated.
TransformEvent - Class in loci.visbio.data: TransformEvent is the event generated when a data transform's parameters are updated.
TransformEvent(Object) - Constructor for class loci.visbio.data.TransformEvent: Constructs a new transform event indicating data has changed.
TransformEvent(Object, int) - Constructor for class loci.visbio.data.TransformEvent: Constructs a new data event.
transformHandler - Variable in class loci.visbio.view.DisplayWindow: Handles logic for linking data transforms to the VisAD display.
TransformHandler - Class in loci.visbio.view: Provides logic for linking data transforms to a display.
TransformHandler(DisplayWindow) - Constructor for class loci.visbio.view.TransformHandler: Creates a display transform handler.
transformId - Variable in class loci.visbio.data.DataTransform: ID number for this data transform.
transformLabels - Variable in class loci.visbio.data.DataManager: List of registered data transform type labels.
TransformLink - Class in loci.visbio.view: Represents a link between a data transform and a display that produces a single image.
TransformLink(TransformHandler) - Constructor for class loci.visbio.view.TransformLink: Constructs an uninitialized transform link.
TransformLink(TransformHandler, DataTransform) - Constructor for class loci.visbio.view.TransformLink: Creates a link between the given data transform and the specified transform handler's display.
transformList - Variable in class loci.visbio.view.TransformPanel: List of linked data transforms.
TransformListener - Interface in loci.visbio.data: Interface for listeners of data transform changes.
transformModel - Variable in class loci.visbio.view.TransformPanel: List model for linked data transform list.
TransformPanel - Class in loci.visbio.view: Provides GUI controls for a display transform handler.
TransformPanel(TransformHandler) - Constructor for class loci.visbio.view.TransformPanel: Creates a panel containing view handler GUI controls.
transforms - Variable in class loci.visbio.view.BioSlideWidget: Transforms affected by this widget.
transformTypes - Variable in class loci.visbio.data.DataManager: List of registered data transform type classes.
transformXML(String, String) - Static method in class loci.wiscscan.XSLTTools: Transforms the given XML string using the specified XSLT stylesheet.
TransientSelectBox - Class in loci.visbio.overlays: TransientSelectBox represents the square that appears in a VisBio display as a user drags the mouse to select overlays.
TransientSelectBox(OverlayTransform, DisplayImpl, int, int) - Constructor for class loci.visbio.overlays.TransientSelectBox: Constructs a selection box.
treeNodesChanged(TreeModelEvent) - Method in class de.sciss.jcollider.gui.NodeTreePanel: This method is part of the TreeModelListener interface.
treeNodesInserted(TreeModelEvent) - Method in class de.sciss.jcollider.gui.NodeTreePanel: This method is part of the TreeModelListener interface.
treeNodesRemoved(TreeModelEvent) - Method in class de.sciss.jcollider.gui.NodeTreePanel: This method is part of the TreeModelListener interface.
treeStructureChanged(TreeModelEvent) - Method in class de.sciss.jcollider.gui.NodeTreePanel: This method is part of the TreeModelListener interface.
TrigControl - Class in de.sciss.jcollider: Class for the TrigControl UGen.
truncateNodeArray() - Method in class loci.visbio.overlays.OverlayNodedObject: Deletes buffer nodes from the tail of the node array.
tryLogin(String, String) - Static method in class loci.wiscscan.auth.KerberosAuth: Attempts to log-in with the specified username and password.
turnOffHighlighting() - Method in class loci.visbio.overlays.OverlayNodedObject: Turn off node highlighting.
TwoDPane - Class in loci.slim: SLIM Plotter's 2D image pane.
TwoDPane(SlimPlotter, SlimData, SlimTypes) - Constructor for class loci.slim.TwoDPane
type - Variable in class loci.visbio.view.BioColorWidget: Color type: 1=Red/Hue, 2=Green/Saturation, 3=Blue/Value.

U

UDP - Static variable in class de.sciss.jcollider.ServerOptions: Protocol type : universal datagram protocol
UGen - Class in de.sciss.jcollider: The client side represenation of a unit generator.
UGen(String, Object, Object[], UGenInput[], int) - Constructor for class de.sciss.jcollider.UGen: This constructor is used by SynthDef when building the UGen from a def file.
UGenChannel - Class in de.sciss.jcollider: Represents one output channel of a (potentially multi-ouput) UGen.
UGenChannel(UGen, int) - Constructor for class de.sciss.jcollider.UGenChannel: You do not directly create UGenChannels but retrieve them from a UGen by calling its getChannel method
UGenInfo - Class in de.sciss.jcollider: As stated elsewhere, it was decided to not implement separate classes for the different unit generators in JCollider.
UGenInfo.Arg - Class in de.sciss.jcollider: Descriptor for a ugen input argument.
UGenInput - Interface in de.sciss.jcollider: A subinterface of GraphElem that represents elements in a graph that can directly be used as inputs to a ugen.
undock(Window, Window) - Method in class loci.visbio.util.Docker: Undocks window A from window B.
UniqueID - Class in de.sciss.jcollider: Utility class for outputting unique incremental numbers.
UniqueID() - Constructor for class de.sciss.jcollider.UniqueID
uniqueInstance(String) - Method in class loci.multithreadedplugin.AbstractNode: Builds a name that is tied to this instance of the subclass.
uniqueInstance(String) - Method in interface loci.multithreadedplugin.IScheduledNode: Adds a unique instance identifier to the name.
uniqueName(String) - Method in interface loci.deepzoom.workflow.plugin.IPluginLauncher: Given a name, makes it unique for this plugin launcher instance.
uniqueName(String) - Method in class loci.deepzoom.workflow.plugin.PluginLauncher: Generates a unique input image name for this launcher.
uniqueName(String) - Method in interface loci.multiinstanceplugin.IPluginLauncher: Given a name, makes it unique for this plugin launcher instance.
uniqueName(String) - Method in class loci.multiinstanceplugin.PluginLauncher: Generates a unique input image name for this launcher.
UniqueTraces - Class in <Unnamed>: Reads in a bunch of stack traces from standard input, filters out duplicates and outputs what's left.
UniqueTraces() - Constructor for class UniqueTraces
unit(float[]) - Static method in class loci.visbio.util.MathUtil: Computes the N-D unit vector in the direction of the vector supplied.
UNKNOWN - Static variable in class de.sciss.jcollider.NodeEvent: returned by getType() : the node type is unknown
unlink() - Method in class loci.visbio.view.StackLink: Unlinks this stack from the display.
unlink() - Method in class loci.visbio.view.TransformLink: Unlinks this transform from the display.
unmap(double) - Method in class de.sciss.jcollider.gui.ControlSpec
unmap(double, ControlSpec) - Method in class de.sciss.jcollider.gui.Warp
unregister(Node) - Method in class de.sciss.jcollider.NodeWatcher: Unregister a node, that is remove it from the list of known nodes.
UnusedImports - Class in <Unnamed>: Scans Java source files for unused and package imports.
UnusedImports() - Constructor for class UnusedImports
updateBigName() - Method in class de.sciss.jcollider.gui.ServerPanel
updateBoundingBox() - Method in class loci.visbio.overlays.OverlayNodedObject: Updates the coordinates of the bounding box of a noded object by checking the entire node array.
updateColorScale() - Method in class loci.slim.ColorWidget
updateControls() - Method in class loci.visbio.view.StackPanel: Updates controls to reflect current handler status.
updateControls() - Method in class loci.visbio.view.TransformPanel: Updates controls to reflect current handler status.
updateInfo(Buffer.CompletionAction) - Method in class de.sciss.jcollider.Buffer: Asynchronously updates the buffer parameters (such as number of frames or sample rate).
updateManualOverride() - Method in class loci.slim.ColorWidget: Updates min/max text field availability to match the current override value.
updateManualOverride(boolean) - Method in class loci.slim.ColorWidget: Updates manual override checkbox and min/max text field availaability to match the given value.
updateMinMaxFields() - Method in class loci.slim.ColorWidget: Updates text field range values to match map values.
updatePosition(DisplayImpl) - Method in class loci.visbio.overlays.OverlayTransform: Updates the dimensional position based on the current state of the given display.
updateScalarMap(float, float) - Method in class loci.slim.ColorWidget: Updates scalar map range to match the given values.
updateSlice() - Method in class loci.visbio.data.SliceWidget: Updates arbitrary slice to match current user interface settings.
upDownBox - Variable in class loci.visbio.view.TransformPanel: List of axes for up/down arrow mapping.
URL_CHECKSTYLE - Static variable in class loci.checks.About: URL of Checkstyle web page.
URL_LOCI_SOFTWARE - Static variable in class loci.checks.About: URL of LOCI Software web page.
URL_OME_VERSIONING - Static variable in class ome.xml.version.About: URL for OME-XML versioning web page.
URL_VISBIO - Static variable in class loci.visbio.help.HelpManager: URL of VisBio web page.
USE_TABS - Static variable in class loci.visbio.state.OptionPane: Flag indicating options should be divided into separate tabs.
useLogFile - Variable in class de.sciss.jcollider.gui.LogTextArea
userFollowers() - Static method in class loci.backup.github.ResumePoint
userFollows() - Static method in class loci.backup.github.ResumePoint
userOrgs() - Static method in class loci.backup.github.ResumePoint

V

validateInputs() - Method in class loci.jar2lib.Jar2Lib: Checks that the current settings for project production are valid.
value - Variable in class de.sciss.jcollider.gui.EZSlider
value - Variable in class de.sciss.jcollider.gui.NumberField
value(Double, double) - Static method in class loci.plugins.stitching.TileUtils
value(PositiveInteger) - Static method in class loci.plugins.stitching.TileUtils
value - Variable in class loci.slim.fit.CurveEvent: Progress value for the event.
value - Variable in class loci.visbio.ext.FunctionParam: Default value of this parameter.
valueChanged(TreeSelectionEvent) - Method in class de.sciss.jcollider.gui.NodeTreePanel: This method is part of the TreeSelectionListener interface.
valueChanged(TreeSelectionEvent) - Method in class loci.visbio.data.DataControls: Handles tree selection changes.
valueChanged(TreeSelectionEvent) - Method in class loci.visbio.help.HelpWindow: Updates help topic based on user selection.
valueChanged(ListSelectionEvent) - Method in class loci.visbio.overlays.OverlayWidget: Handles list selection changes.
valueChanged(ListSelectionEvent) - Method in class loci.visbio.view.CapturePanel: Called when the a new display position is selected.
valueChanged(ListSelectionEvent) - Method in class loci.visbio.view.DisplayControls: Handles list selection changes.
valueChanged(ListSelectionEvent) - Method in class loci.visbio.view.TransformPanel: Handles list selection changes.
valueOf(String) - Static method in enum loci.plugins.stitching.StitchOmeTiff.FusionMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum loci.plugins.stitching.StitchPrairieTiff.FusionMethod: Returns the enum constant of this type with the specified name.
values() - Static method in enum loci.plugins.stitching.StitchOmeTiff.FusionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum loci.plugins.stitching.StitchPrairieTiff.FusionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
vector(float[], float[]) - Static method in class loci.visbio.util.MathUtil: Creates the vector p2-(minus) p1.
VelocityAutogen - Class in loci.jar2lib: Automatically generates code for a Jar2Lib project.
VelocityAutogen(String) - Constructor for class loci.jar2lib.VelocityAutogen
VelocityException - Exception in loci.jar2lib: VelocityException is the exception thrown when something goes wrong with an Apache Velocity operation.
VelocityException() - Constructor for exception loci.jar2lib.VelocityException
VelocityException(String) - Constructor for exception loci.jar2lib.VelocityException
VelocityException(String, Throwable) - Constructor for exception loci.jar2lib.VelocityException
VelocityException(Throwable) - Constructor for exception loci.jar2lib.VelocityException
VelocityTools - Class in loci.jar2lib: Useful methods for working with Apache Velocity.
VelocityTools() - Constructor for class loci.jar2lib.VelocityTools
VentanaScannerInterpreter - Class in loci.apps.SlideScannerImport
VentanaScannerInterpreter(String, String, String) - Constructor for class loci.apps.SlideScannerImport.VentanaScannerInterpreter
VERBOSE - Variable in class de.sciss.jcollider.gui.NodeTreeManager: Set this to true for debugging the incoming node notifications and tree model updates
VERBOSE - Variable in class de.sciss.jcollider.NodeWatcher: Set this to true for debugging all relevant actions of the watcher, such as starting, stopping, registering nodes, and updating node status.
VERSION - Static variable in class de.sciss.jcollider.JCollider
VERSION - Static variable in class loci.visbio.VisBio: Application version (of the form "#.##").
vertGridCount - Variable in class loci.visbio.overlays.OverlayObject: Number of horizontal and vertical dividing lines for selection grid.
viewHandler - Variable in class loci.visbio.view.DisplayWindow: Handles logic for controlling the VisAD display's view.
ViewHandler - Class in loci.visbio.view: Provides logic for controlling a VisAD display's view.
ViewHandler(DisplayWindow) - Constructor for class loci.visbio.view.ViewHandler: Creates a display view handler.
ViewPanel - Class in loci.visbio.view: Provides GUI controls for a display view handler.
ViewPanel(ViewHandler) - Constructor for class loci.visbio.view.ViewPanel: Creates a panel containing view handler GUI controls.
VisBio - Class in loci.visbio: VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data.
visbio - Static variable in class loci.visbio.VisBioFrame: Running instance of VisBio.
VisBioEvent - Class in loci.visbio: VisBioEvent is the event generated when something in VisBio changes.
VisBioEvent(Object, int, String, boolean) - Constructor for class loci.visbio.VisBioEvent: Constructs a VisBio event.
VisBioFrame - Class in loci.visbio: VisBioFrame is the main GUI frame for VisBio.
VisBioFrame() - Constructor for class loci.visbio.VisBioFrame: Constructs a new VisBio frame with no splash screen.
VisBioFrame(SplashScreen) - Constructor for class loci.visbio.VisBioFrame: Constructs a new VisBio frame with the associated splash screen.
VisBioFrame(SplashScreen, String[]) - Constructor for class loci.visbio.VisBioFrame: Constructs a new VisBio frame with the associated splash screen and command line arguments.
visible - Variable in class loci.visbio.view.SliceToggler: Option for showing selected slices.
visible - Variable in class loci.visbio.view.TransformLink: Whether data transform is visible onscreen.
visible - Variable in class loci.visbio.view.TransformPanel: Checkbox for toggling data transform visibility.
visible - Variable in class loci.visbio.WindowManager: List of windows that were visible before VisBio was minimized.
visible - Variable in class loci.visbio.WindowState: Visibility of the window.
visSlices - Variable in class loci.visbio.view.StackLink: Flags indicating visibility of each slice of the stack.
VisualizeTiles - Class in loci.plugins.stitching: A plugin to visualize the tile layout of a multi-tile dataset in 3D.
VisualizeTiles() - Constructor for class loci.plugins.stitching.VisualizeTiles
volume - Variable in class loci.visbio.view.StackLink: Whether volume rendering is currently enabled.
volumeRef - Variable in class loci.visbio.view.StackLink: Data reference for volume rendered cube.
volumeRes - Variable in class loci.visbio.view.StackLink: Resolution of rendered volumes.
vType - Variable in class loci.slim.SlimTypes
vType2 - Variable in class loci.slim.SlimTypes
vTypeFit - Variable in class loci.slim.SlimTypes
vTypeRes - Variable in class loci.slim.SlimTypes
vv - Variable in class loci.slim.SlimTypes

W

w - Variable in class loci.plugins.stitching.Pt
WAIT - Static variable in class loci.visbio.overlays.OverlayIO
WAIT - Static variable in class loci.visbio.overlays.PolylineTool: The Different modes of this tool.
waitForBufInfo() - Method in class de.sciss.jcollider.Server: For internal use by Buffer objects.
waiting - Variable in class loci.visbio.WindowManager: Number of queued wait cursors.
waitingBufs - Variable in class de.sciss.jcollider.Server
waitingForBufInfo - Variable in class de.sciss.jcollider.Server
WARN_IMAGEJ - Static variable in class loci.visbio.view.DisplayManager: String for ImageJ quit warning.
WarningPane - Class in loci.visbio.util: WarningPane provides a dialog box for displaying a warning to the user.
WarningPane(String, boolean) - Constructor for class loci.visbio.util.WarningPane: Creates a new warning pane linked to the given warning checkbox.
Warp - Class in de.sciss.jcollider.gui: Helper classes for warping a control value.
Warp() - Constructor for class de.sciss.jcollider.gui.Warp
waveStep - Variable in class loci.slim.SlimData
WD - Static variable in class loci.visbio.overlays.OverlayBox
weights - Variable in class loci.visbio.data.SpectralTransform: Spectral channel weights.
weights - Variable in class loci.visbio.data.SpectralWidget: Weighted sliders for spectral transform.
widgetPane - Variable in class loci.visbio.view.ColorPane: GUI panel for color table widget.
width - Variable in class loci.slim.SlimData
width - Variable in class loci.visbio.overlays.OverlayMarker: The default width of the marker.
width - Variable in class loci.visbio.WindowState: Dimensions of the window.
widthField - Variable in class loci.visbio.data.SamplingWidget: Text field for image width.
WIN_PATH - Static variable in class loci.visbio.overlays.SpreadsheetLauncher: Default path to spreadsheet (Excel) on Windows computers.
window - Variable in class loci.visbio.util.BreakawayPanel: Floating window containing the breakaway panel.
window - Variable in class loci.visbio.view.CaptureHandler: Associated display window.
window - Variable in class loci.visbio.view.TransformHandler: Associated display window.
window - Variable in class loci.visbio.view.ViewHandler: Associated display window.
window - Variable in class loci.visbio.WindowInfo: Window for which this object stores additional information.
windowActivated(WindowEvent) - Method in class loci.slim.SlimPlotter
windowActivated(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowActivated(WindowEvent) - Method in class loci.visbio.OrthoStack
windowActivated(WindowEvent) - Method in class loci.visbio.WindowInfo
windowActivated(WindowEvent) - Method in class loci.visbio.WindowManager
windowClosed(WindowEvent) - Method in class loci.slim.SlimPlotter
windowClosed(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowClosed(WindowEvent) - Method in class loci.visbio.OrthoStack
windowClosed(WindowEvent) - Method in class loci.visbio.WindowInfo
windowClosed(WindowEvent) - Method in class loci.visbio.WindowManager
windowClosing(WindowEvent) - Method in class loci.slim.SlimPlotter
windowClosing(WindowEvent) - Method in class loci.visbio.ExitManager: Called when something tries to shut down VisBio.
windowClosing(WindowEvent) - Method in class loci.visbio.OrthoStack
windowClosing(WindowEvent) - Method in class loci.visbio.WindowInfo
windowClosing(WindowEvent) - Method in class loci.visbio.WindowManager
windowConsole(String) - Method in class loci.visbio.ConsoleManager: Displays the given output console window.
windowDeactivated(WindowEvent) - Method in class loci.slim.SlimPlotter
windowDeactivated(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowDeactivated(WindowEvent) - Method in class loci.visbio.OrthoStack
windowDeactivated(WindowEvent) - Method in class loci.visbio.WindowInfo
windowDeactivated(WindowEvent) - Method in class loci.visbio.WindowManager
windowDeiconified(WindowEvent) - Method in class loci.slim.SlimPlotter
windowDeiconified(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowDeiconified(WindowEvent) - Method in class loci.visbio.OrthoStack
windowDeiconified(WindowEvent) - Method in class loci.visbio.WindowInfo
windowDeiconified(WindowEvent) - Method in class loci.visbio.WindowManager
windowIconified(WindowEvent) - Method in class loci.slim.SlimPlotter
windowIconified(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowIconified(WindowEvent) - Method in class loci.visbio.OrthoStack
windowIconified(WindowEvent) - Method in class loci.visbio.WindowInfo
windowIconified(WindowEvent) - Method in class loci.visbio.WindowManager
WindowInfo - Class in loci.visbio: A class for keeping track of information about a window.
WindowInfo(Window, boolean) - Constructor for class loci.visbio.WindowInfo: Creates a new window information object for the given window, with the pack flag indicating whether the window is to be packed prior to being shown for the first time.
WindowManager - Class in loci.visbio: WindowManager is the manager encapsulating VisBio's window logic, including docking, resizing, minimization and cursor control.
WindowManager(VisBioFrame) - Constructor for class loci.visbio.WindowManager: Constructs a window manager.
windowOpened(WindowEvent) - Method in class loci.slim.SlimPlotter
windowOpened(WindowEvent) - Method in class loci.visbio.ExitManager: Unused WindowListener method.
windowOpened(WindowEvent) - Method in class loci.visbio.OrthoStack
windowOpened(WindowEvent) - Method in class loci.visbio.WindowInfo
windowOpened(WindowEvent) - Method in class loci.visbio.WindowManager
windows - Variable in class loci.visbio.util.Docker: List of windows able to be docked to one another.
windows - Variable in class loci.visbio.WindowManager: Table for keeping track of registered windows.
WindowState - Class in loci.visbio: A class containing a window's state.
WindowState(String, boolean, int, int, int, int) - Constructor for class loci.visbio.WindowState: Creates a new window state object.
windowStates - Variable in class loci.visbio.WindowManager: Table of window states read during state restore.
wire(IModule, IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default output of one component to default input of another.
wire(IModule, String, IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named output of one component to default input of another.
wire(IModule, IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default output of one component to named input of another.
wire(IModule, String, IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named output of one component to named input of another.
Wire - Class in loci.deepzoom.workflow: Data structure that describes a chained connection.
WIRE - Static variable in class loci.deepzoom.workflow.WorkFlow
wire(IModule, IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wire(IModule, String, IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wire(IModule, IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
wire(IModule, String, IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
wireInput(IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default workflow input to default input of component.
wireInput(IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default workflow input to named input of component.
wireInput(String, IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named workflow input to default input of component.
wireInput(String, IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named workflow input to named input of component.
wireInput(IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wireInput(IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
wireInput(String, IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wireInput(String, IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
wireOutput(IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default component output to default workflow output.
wireOutput(IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named component output to default workflow output.
wireOutput(String, IModule) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains default component output to named workflow output.
wireOutput(String, IModule, String) - Method in interface loci.deepzoom.workflow.IWorkFlow: Chains named component output to named workflow output.
wireOutput(IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wireOutput(IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
wireOutput(String, IModule) - Method in class loci.deepzoom.workflow.WorkFlow
wireOutput(String, IModule, String) - Method in class loci.deepzoom.workflow.WorkFlow
WIRES - Static variable in class loci.deepzoom.workflow.WorkFlow
WizardPane - Class in loci.visbio.util: WizardPane provides an extensible interface for creating multi-page wizard dialogs with Cancel, Back, Next and Finish buttons.
WizardPane(String) - Constructor for class loci.visbio.util.WizardPane: Creates a file series chooser dialog.
WorkFlow - Class in loci.deepzoom.workflow: Builds a workflow consisting of chained components.
WorkFlow() - Constructor for class loci.deepzoom.workflow.WorkFlow
WORKFLOW - Static variable in class loci.deepzoom.workflow.WorkFlow
WorkFlowFactory - Class in loci.deepzoom.workflow: TODO
write(String) - Method in class de.sciss.jcollider.Buffer: Writes the buffer contents to a sound file, using AIFF integer 24 bit format.
write(String, String, String) - Method in class de.sciss.jcollider.Buffer: Writes the buffer contents to a sound file.
write(String, String, String, int) - Method in class de.sciss.jcollider.Buffer: Writes the buffer contents to a sound file.
write(String, String, String, int, int) - Method in class de.sciss.jcollider.Buffer: Writes a section of the buffer to a sound file.
write(String, String, String, int, int, boolean) - Method in class de.sciss.jcollider.Buffer: Writes a section of the buffer to a sound file.
write(String, String, String, int, int, boolean, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Writes a section of the buffer to a sound file.
write(OutputStream) - Method in class de.sciss.jcollider.SynthDef: Writes this def to an output stream (such as a file or a memory buffer).
write(int) - Method in class loci.visbio.util.OutputConsole
write(byte[], int, int) - Method in class loci.visbio.util.OutputConsole
writeBinaryDefinitions(File) - Static method in class de.sciss.jcollider.UGenInfo: Writes the infos out as a binary file that can be read in again using the readBinaryDefinitions method.
writeDefFile(File, SynthDef[]) - Static method in class de.sciss.jcollider.SynthDef: Writes an array of definitions to a file.
writeDefFile(File) - Method in class de.sciss.jcollider.SynthDef: Writes this def to a definition file.
writeFile(String, Vector<String>) - Method in class loci.jar2lib.StringReplace
writeIni() - Method in class loci.visbio.state.OptionManager: Writes out configuration to configuration file.
writeMsg(String) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write the buffer contents to a sound file, using AIFF integer 24 bit format.
writeMsg(String, String, String) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write the buffer contents to a sound file.
writeMsg(String, String, String, int) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write the buffer contents to a sound file.
writeMsg(String, String, String, int, int) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write a section of the buffer to a sound file.
writeMsg(String, String, String, int, int, boolean) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write a section of the buffer to a sound file.
writeMsg(String, String, String, int, int, boolean, OSCMessage) - Method in class de.sciss.jcollider.Buffer: Creates an OSC /b_write message to write a section of the buffer to a sound file.
writeScript(int, String, String) - Method in class loci.visbio.SystemManager: Updates the VisBio launch parameters to specify the given maximum heap and look and feel settings.
writeWiscScanXYZ() - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
writeWiscScanXYZ(String, ArrayList<ArrayList<Float>>) - Method in class loci.apps.SlideScannerImport.Import_Slide_Scanner_ROIs
writeXML(File, Document) - Static method in class loci.visbio.util.XMLUtil: Writes the given DOM to the specified file on disk.
writeXML(Document) - Static method in class loci.visbio.util.XMLUtil: Writes the given DOM to a string.
writeXML(OutputStream, Document) - Static method in class loci.visbio.util.XMLUtil: Writes the given DOM to the specified output stream.
wt - Variable in class loci.visbio.overlays.FreeformTool.DistanceQuery: The weight, between 0.0 and 1.0, representing the relative distance along the segment (seg, seg+1) that must be traveled from the node at index seg to reach the closest point on the curve.

X

X - Static variable in class loci.chainableplugin.deepzoom.CutTilesProcessor
X - Static variable in class loci.multiinstanceplugin.deepzoom.CutTilesProcessor
x - Variable in class loci.plugins.stitching.Pt
x - Variable in class loci.visbio.WindowState: Position of the window.
x1 - Variable in class loci.visbio.overlays.OverlayObject: Endpoint coordinates.
x1 - Variable in class loci.visbio.overlays.OverlayWidget: Text fields for (X, Y) coordinate pairs.
x2 - Variable in class loci.visbio.overlays.OverlayObject: Endpoint coordinates.
x2 - Variable in class loci.visbio.overlays.OverlayWidget: Text fields for (X, Y) coordinate pairs.
xasp - Variable in class loci.visbio.view.ViewHandler: Aspect ratio of the display.
xGrid1 - Variable in class loci.visbio.overlays.OverlayObject: Top-left endpoint of selection grid rectangle.
xGrid2 - Variable in class loci.visbio.overlays.OverlayObject: Top-right endpoint of selection grid rectangle.
xGrid3 - Variable in class loci.visbio.overlays.OverlayObject: Bottom-left endpoint of selection grid rectangle.
xGrid4 - Variable in class loci.visbio.overlays.OverlayObject: Bottom-right endpoint of selection grid rectangle.
XMLException - Exception in loci.deepzoom.util.xmllight: TODO
XMLException(String) - Constructor for exception loci.deepzoom.util.xmllight.XMLException
XMLParser - Class in loci.deepzoom.util.xmllight: XML-light Parser.
XMLParser() - Constructor for class loci.deepzoom.util.xmllight.XMLParser
XMLTag - Class in loci.deepzoom.util.xmllight: Tag data structure returned when parsing.
XMLTag() - Constructor for class loci.deepzoom.util.xmllight.XMLTag: Creates an empty tag.
XMLTag(String, String, String) - Constructor for class loci.deepzoom.util.xmllight.XMLTag: Creates a given tag.
XMLUtil - Class in loci.visbio.util: XMLUtil contains useful functions for manipulating DOMs.
XMLWriter - Class in loci.deepzoom.util.xmllight: XML-light Writer.
XMLWriter(StringBuilder) - Constructor for class loci.deepzoom.util.xmllight.XMLWriter: Constructs a helper for writing to given string.
XSLTTools - Class in loci.wiscscan: Helper class for working with XML stylesheet transforms.
XSLTTools() - Constructor for class loci.wiscscan.XSLTTools
xType - Variable in class loci.slim.SlimTypes
xType - Variable in class loci.visbio.data.ImageTransform: X-axis type.
xy - Variable in class loci.slim.SlimTypes
xySet - Variable in class loci.slim.SlimTypes
xyvFunc - Variable in class loci.slim.SlimTypes

Y

Y - Static variable in class loci.chainableplugin.deepzoom.CutTilesProcessor
Y - Static variable in class loci.multiinstanceplugin.deepzoom.CutTilesProcessor
y - Variable in class loci.plugins.stitching.Pt
y - Variable in class loci.visbio.WindowState: Position of the window.
y1 - Variable in class loci.visbio.overlays.OverlayObject: Endpoint coordinates.
y1 - Variable in class loci.visbio.overlays.OverlayWidget: Text fields for (X, Y) coordinate pairs.
y2 - Variable in class loci.visbio.overlays.OverlayObject: Endpoint coordinates.
y2 - Variable in class loci.visbio.overlays.OverlayWidget: Text fields for (X, Y) coordinate pairs.
yasp - Variable in class loci.visbio.view.ViewHandler: Aspect ratio of the display.
yaw - Variable in class loci.visbio.data.ArbitrarySlice: Horizontal rotational angle of slicing line.
yaw - Variable in class loci.visbio.data.SliceWidget: Slider for adjusting yaw.
yawValue - Variable in class loci.visbio.data.SliceWidget: Label for current yaw value.
yGrid1 - Variable in class loci.visbio.overlays.OverlayObject: Top-left endpoint of selection grid rectangle.
yGrid2 - Variable in class loci.visbio.overlays.OverlayObject: Top-right endpoint of selection grid rectangle.
yGrid3 - Variable in class loci.visbio.overlays.OverlayObject: Bottom-left endpoint of selection grid rectangle.
yGrid4 - Variable in class loci.visbio.overlays.OverlayObject: Bottom-right endpoint of selection grid rectangle.
yType - Variable in class loci.slim.SlimTypes
yType - Variable in class loci.visbio.data.ImageTransform: Y-axis type.

Z

z - Variable in class loci.plugins.stitching.Pt
zasp - Variable in class loci.visbio.view.ViewHandler: Aspect ratio of the display.
zero() - Method in class de.sciss.jcollider.Buffer
zero(OSCMessage) - Method in class de.sciss.jcollider.Buffer
ZEROED - Static variable in class loci.visbio.util.ColorUtil: Zeroed out color table componented used in several presets.
zeroMsg() - Method in class de.sciss.jcollider.Buffer
zeroMsg(OSCMessage) - Method in class de.sciss.jcollider.Buffer
zoom - Variable in class loci.slim.MouseBehaviorButtons
zoom(double) - Method in class loci.visbio.view.ViewHandler: Zooms the display by the given amount.
ZOOM_AMOUNT - Static variable in class loci.visbio.view.ViewHandler: How far display zooms in or out each time.
zoomIn() - Method in class loci.visbio.view.ViewHandler: Zooms in on the display.
zoomOut() - Method in class loci.visbio.view.ViewHandler: Zooms out on the display.
zType - Variable in class loci.visbio.data.ImageTransform: Z-axis type.

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