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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