OverlayTransform (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.visbio.data.DataTransform
- - loci.visbio.overlays.OverlayTransform

All Implemented Interfaces:

TransformListener, Dynamic, Saveable
```
public class OverlayTransform
extends DataTransform
implements TransformListener
```
A set of overlays on top another transform.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static RealType`	`ALPHA_TYPE` MathType for alpha color mappings.
`protected static RealType`	`BLUE_TYPE` MathType for blue color mappings.
`protected Vector`	`clipboard` Clipboard stores overlays grabbed with the copy function.
`protected int[]`	`clipboardPos` Dimensional position of overlays stored in the clipboard.
`protected OverlayWidget`	`controls` Controls for creating overlays.
`protected boolean`	`drawText` Whether to draw text.
`protected FontMetrics`	`fontMetrics` Font metrics for the current font.
`protected static RealType`	`GREEN_TYPE` MathType for green color mappings.
`protected String`	`lastToolType` Type of last tool used.
`protected boolean`	`mouseDownLeft` Whether left mouse button is currently being pressed.
`protected boolean`	`mouseDownRight` Whether right mouse button is currently being pressed.
`protected static String`	`NOT_APPLICABLE` String indicating a given field is not applicable to an overlay.
`protected Vector[]`	`overlays` List of overlays for each dimensional position.
`protected int[]`	`pos` Current dimensional position.
`protected static RealTupleType`	`RANGE_TUPLE` Overlay range type.
`protected static RealType`	`RED_TYPE` MathType for red color mappings.
`protected TransientSelectBox`	`selectBox` Transient Select Box, if active.
`protected TupleType`	`textRangeTuple` Overlay range type for text overlays.
`protected TextType`	`textType` MathType for Text mappings.
`protected boolean`	`toolChanged` Whether last tool has changed.

Fields inherited from class loci.visbio.data.DataTransform
dims, font, labels, lengths, listeners, MU, name, nextId, parent, thumbs, transformId

Constructor Summary

Constructors
Constructor and Description

OverlayTransform(DataTransform parent, String name)
Creates an overlay object for the given transform.

Constructors
Constructor and Description
`OverlayTransform(DataTransform parent, String name)` Creates an overlay object for the given transform.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addObject(OverlayObject obj)` Adds an overlay object at the current dimensional position.
`void`	`addObject(OverlayObject obj, int[] pos)` Adds an overlay object at the given dimensional position.
`void`	`addTSB(TransientSelectBox tsb)` Adds a transient selection box.
`protected void`	`configureOverlay(OverlayObject obj)` Configures the given overlay to match the current settings.
`void`	`copySelectedObjects()` Copies selected overlay objects at the current dimensional position to the clipboard.
`void`	`copySelectedObjects(int[] pos)` Copies selected overlay objects at the given dimensional position to the clipboard.
`void`	`discard()` Called when this object is being discarded in favor of another object with a matching state.
`void`	`displayChanged(DisplayEvent e)` Responds to mouse gestures with appropriate overlay interaction.
`String`	`distributeObjects()` 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.
`String`	`distributeObjects(int[] pos)` 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.
`loci.poi.hssf.usermodel.HSSFWorkbook`	`exportOverlays()` Exports the overlays as .xls to the given output file.
`String`	`getCacheId(int[] pos, boolean global)` Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching.
`JComponent`	`getControls()` Gets associated GUI controls for this transform.
`Data`	`getData(TransformLink link, int[] pos, int dim, DataCache cache)` Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
`RealTupleType`	`getDomainType()` Gets domain type (XY).
`FontMetrics`	`getFontMetrics()` Gets font metrics for the current font.
`OverlayObject[]`	`getObjects()` Gets the overlay objects at the current dimensional position.
`OverlayObject[]`	`getObjects(int[] pos)` Gets the overlay objects at the given dimensional position.
`int[]`	`getPos()` Gets transform's current dimensional position.
`TupleType`	`getRangeType()` Gets range type (RGB).
`int`	`getScalingValue()` Gets a scaling value suitable for computing an overlay size or picking threshold.
`int`	`getScalingValueX()` Gets a scaling value along the X axis, suitable for computing an overlay width or picking threshold.
`int`	`getScalingValueY()` Gets a scaling value along the Y axis, suitable for computing an overlay height or picking threshold.
`ScalarMap[]`	`getSuggestedMaps()` Retrieves a set of mappings for displaying this transform effectively.
`TupleType`	`getTextRangeType()` Gets range type for text overlays (R, G, B, text).
`Tuple`	`getTextRangeValue(String text, float r, float g, float b, float a)` Constructs a range value with the given component values.
`boolean`	`hasToolChanged()` Gets whether the current tool has changed since last mouse gesture.
`void`	`initState(Dynamic dyn)` Modifies this object's state to match that of the given object.
`boolean`	`isCompatible(Dynamic dyn)` Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
`boolean`	`isImmediate()` Overlay transforms are rendered immediately, due to frequent user interaction.
`static boolean`	`isParentRequired()` Indicates whether this transform type requires a parent transform.
`boolean`	`isTextDrawn()` Gets whether text is drawn.
`boolean`	`isValidDimension(int dim)` Gets whether this transform provides data of the given dimensionality.
`static boolean`	`isValidParent(DataTransform data)` Indicates whether this transform type would accept the given transform as its parent transform.
`void`	`loadOverlays(BufferedReader in)` Reads the overlays from the given reader.
`protected static RealTupleType`	`makeRangeTuple()` Constructs the overlay range type for most overlays.
`static DataTransform`	`makeTransform(DataManager dm)` Creates a new set of overlays, with user interaction.
`boolean`	`matches(Dynamic dyn)` Tests whether two dynamic objects are equivalent.
`void`	`pasteObjects()` Pastes copied objects at the current dimensional position.
`void`	`pasteObjects(int[] pos)` Pastes copied objects at the given dimensional position.
`protected void`	`releaseLeft(DisplayEvent e, DisplayImpl display, OverlayTool tool)` Helper method that handles left mouse button releases.
`void`	`removeObject(OverlayObject obj)` Removes an overlay object at the current dimensional position.
`void`	`removeObject(OverlayObject obj, int[] pos)` Removes an overlay object at the given dimensional position.
`void`	`removeSelectedObjects()` Removes selected overlay objects at the current dimensional position.
`void`	`removeSelectedObjects(int[] pos)` Removes selected overlay objects at the given dimensional position.
`void`	`removeTSB()` Removes transient selection box.
`void`	`saveOverlays(PrintWriter out)` Writes the overlays to the given writer.
`void`	`setFont(Font font)` Sets the font used for text overlays.
`void`	`setPos(int[] pos)` Sets transform's current dimensional position.
`void`	`setTextDrawn(boolean value)` Whether text is drawn.
`void`	`transformChanged(TransformEvent e)` Called when parent data transform's parameters are updated.
`protected void`	`updatePosition(DisplayImpl display)` Updates the dimensional position based on the current state of the given display.

Methods inherited from class loci.visbio.data.DataTransform
addTransformListener, canDisplay2D, canDisplay3D, getDimTypes, getFont, getHTMLDescription, getLabels, getLengths, getName, getParent, getThumbHandler, getTransformId, getUnitDescription, makeLabels, notifyListeners, removeTransformListener, restoreState, saveState, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - RED_TYPE
```
protected static final RealType RED_TYPE
```
    MathType for red color mappings.
  - GREEN_TYPE
```
protected static final RealType GREEN_TYPE
```
    MathType for green color mappings.
  - BLUE_TYPE
```
protected static final RealType BLUE_TYPE
```
    MathType for blue color mappings.
  - ALPHA_TYPE
```
protected static final RealType ALPHA_TYPE
```
    MathType for alpha color mappings.
  - RANGE_TUPLE
```
protected static final RealTupleType RANGE_TUPLE
```
    Overlay range type.
  - NOT_APPLICABLE
```
protected static final String NOT_APPLICABLE
```
    String indicating a given field is not applicable to an overlay.
    
    See Also:
    
    Constant Field Values
  - controls
```
protected OverlayWidget controls
```
    Controls for creating overlays.
  - overlays
```
protected Vector[] overlays
```
    List of overlays for each dimensional position.
  - pos
```
protected int[] pos
```
    Current dimensional position.
  - textType
```
protected TextType textType
```
    MathType for Text mappings.
  - textRangeTuple
```
protected TupleType textRangeTuple
```
    Overlay range type for text overlays.
  - mouseDownLeft
```
protected boolean mouseDownLeft
```
    Whether left mouse button is currently being pressed.
  - mouseDownRight
```
protected boolean mouseDownRight
```
    Whether right mouse button is currently being pressed.
  - fontMetrics
```
protected FontMetrics fontMetrics
```
    Font metrics for the current font.
  - drawText
```
protected boolean drawText
```
    Whether to draw text.
  - clipboard
```
protected Vector clipboard
```
    Clipboard stores overlays grabbed with the copy function.
  - clipboardPos
```
protected int[] clipboardPos
```
    Dimensional position of overlays stored in the clipboard.
  - selectBox
```
protected TransientSelectBox selectBox
```
    Transient Select Box, if active.
  - lastToolType
```
protected String lastToolType
```
    Type of last tool used.
  - toolChanged
```
protected boolean toolChanged
```
    Whether last tool has changed.
- Constructor Detail
  - OverlayTransform
```
public OverlayTransform(DataTransform parent,
                        String name)
```
    Creates an overlay object for the given transform.
- Method Detail
  - makeRangeTuple
```
protected static RealTupleType makeRangeTuple()
```
    Constructs the overlay range type for most overlays.
  - addObject
```
public void addObject(OverlayObject obj)
```
    Adds an overlay object at the current dimensional position.
  - addObject
```
public void addObject(OverlayObject obj,
                      int[] pos)
```
    Adds an overlay object at the given dimensional position.
  - removeObject
```
public void removeObject(OverlayObject obj)
```
    Removes an overlay object at the current dimensional position.
  - removeObject
```
public void removeObject(OverlayObject obj,
                         int[] pos)
```
    Removes an overlay object at the given dimensional position.
  - removeSelectedObjects
```
public void removeSelectedObjects()
```
    Removes selected overlay objects at the current dimensional position.
  - addTSB
```
public void addTSB(TransientSelectBox tsb)
```
    Adds a transient selection box.
  - removeTSB
```
public void removeTSB()
```
    Removes transient selection box.
  - removeSelectedObjects
```
public void removeSelectedObjects(int[] pos)
```
    Removes selected overlay objects at the given dimensional position.
  - copySelectedObjects
```
public void copySelectedObjects()
```
    Copies selected overlay objects at the current dimensional position to the clipboard.
  - copySelectedObjects
```
public void copySelectedObjects(int[] pos)
```
    Copies selected overlay objects at the given dimensional position to the clipboard.
  - pasteObjects
```
public void pasteObjects()
```
    Pastes copied objects at the current dimensional position.
  - pasteObjects
```
public void pasteObjects(int[] pos)
```
    Pastes copied objects at the given dimensional position.
  - distributeObjects
```
public String distributeObjects()
```
    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. Since there are a number of criteria necessary to perform this task properly, it returns an error string if there was a problem, or null if the operation was successful.
  - distributeObjects
```
public String distributeObjects(int[] pos)
```
    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. Since there are a number of criteria necessary to perform this task properly, it returns an error string if there was a problem, or null if the operation was successful.
  - getObjects
```
public OverlayObject[] getObjects()
```
    Gets the overlay objects at the current dimensional position.
  - getObjects
```
public OverlayObject[] getObjects(int[] pos)
```
    Gets the overlay objects at the given dimensional position.
  - setPos
```
public void setPos(int[] pos)
```
    Sets transform's current dimensional position.
  - getPos
```
public int[] getPos()
```
    Gets transform's current dimensional position.
  - loadOverlays
```
public void loadOverlays(BufferedReader in)
                  throws IOException
```
    Reads the overlays from the given reader.
    
    Throws:
    
    IOException
  - saveOverlays
```
public void saveOverlays(PrintWriter out)
```
    Writes the overlays to the given writer.
  - exportOverlays
```
public loci.poi.hssf.usermodel.HSSFWorkbook exportOverlays()
```
    Exports the overlays as .xls to the given output file.
  - getDomainType
```
public RealTupleType getDomainType()
```
    Gets domain type (XY).
  - getRangeType
```
public TupleType getRangeType()
```
    Gets range type (RGB).
  - getTextRangeType
```
public TupleType getTextRangeType()
```
    Gets range type for text overlays (R, G, B, text).
  - getTextRangeValue
```
public Tuple getTextRangeValue(String text,
                               float r,
                               float g,
                               float b,
                               float a)
```
    Constructs a range value with the given component values.
  - getScalingValue
```
public int getScalingValue()
```
    Gets a scaling value suitable for computing an overlay size or picking threshold.
  - getScalingValueX
```
public int getScalingValueX()
```
    Gets a scaling value along the X axis, suitable for computing an overlay width or picking threshold.
  - getScalingValueY
```
public int getScalingValueY()
```
    Gets a scaling value along the Y axis, suitable for computing an overlay height or picking threshold.
  - getFontMetrics
```
public FontMetrics getFontMetrics()
```
    Gets font metrics for the current font.
  - setTextDrawn
```
public void setTextDrawn(boolean value)
```
    Whether text is drawn. This toggle exists because drawing text is very slow, so some operations temporarily turn off text rendering to speed up onscreen updates.
  - isTextDrawn
```
public boolean isTextDrawn()
```
    Gets whether text is drawn.
  - hasToolChanged
```
public boolean hasToolChanged()
```
    Gets whether the current tool has changed since last mouse gesture.
  - makeTransform
```
public static DataTransform makeTransform(DataManager dm)
```
    Creates a new set of overlays, with user interaction.
  - isValidParent
```
public static boolean isValidParent(DataTransform data)
```
    Indicates whether this transform type would accept the given transform as its parent transform.
  - isParentRequired
```
public static boolean isParentRequired()
```
    Indicates whether this transform type requires a parent transform.
  - getData
```
public Data getData(TransformLink link,
                    int[] pos,
                    int dim,
                    DataCache cache)
```
    Retrieves the data corresponding to the given dimensional position, for the given display dimensionality.
    
    Specified by:
    
    getData in class DataTransform
    
    Returns:
    
    null if the transform does not provide data of that dimensionality
  - isValidDimension
```
public boolean isValidDimension(int dim)
```
    Gets whether this transform provides data of the given dimensionality.
    
    Specified by:
    
    isValidDimension in class DataTransform
  - getSuggestedMaps
```
public ScalarMap[] getSuggestedMaps()
```
    Retrieves a set of mappings for displaying this transform effectively.
    
    Specified by:
    
    getSuggestedMaps in class DataTransform
  - getCacheId
```
public String getCacheId(int[] pos,
                         boolean global)
```
    Gets a string id uniquely describing this data transform at the given dimensional position, for the purposes of thumbnail caching. If global flag is true, the id is suitable for use in the default, global cache file.
    
    Specified by:
    
    getCacheId in class DataTransform
  - isImmediate
```
public boolean isImmediate()
```
    Overlay transforms are rendered immediately, due to frequent user interaction.
    
    Specified by:
    
    isImmediate in class DataTransform
  - getControls
```
public JComponent getControls()
```
    Gets associated GUI controls for this transform.
    
    Overrides:
    
    getControls in class DataTransform
  - setFont
```
public void setFont(Font font)
```
    Sets the font used for text overlays. Since changing the font changes the data (text overlay bounding boxes, this method is overridden to send a DATA_CHANGED after recomputing them.
    
    Overrides:
    
    setFont in class DataTransform
  - displayChanged
```
public void displayChanged(DisplayEvent e)
```
    Responds to mouse gestures with appropriate overlay interaction.
    
    Overrides:
    
    displayChanged in class DataTransform
  - matches
```
public boolean matches(Dynamic dyn)
```
    Tests whether two dynamic objects are equivalent.
    
    Specified by:
    
    matches in interface Dynamic
    
    Overrides:
    
    matches in class DataTransform
  - isCompatible
```
public boolean isCompatible(Dynamic dyn)
```
    Tests whether the given dynamic object can be used as an argument to initState, for initializing this dynamic object.
    
    Specified by:
    
    isCompatible in interface Dynamic
    
    Overrides:
    
    isCompatible in class DataTransform
  - initState
```
public void initState(Dynamic dyn)
```
    Modifies this object's state to match that of the given object. If the argument is null, the object is initialized according to its current state instead.
    
    Specified by:
    
    initState in interface Dynamic
    
    Overrides:
    
    initState in class DataTransform
  - discard
```
public void discard()
```
    Called when this object is being discarded in favor of another object with a matching state.
    
    Specified by:
    
    discard in interface Dynamic
    
    Overrides:
    
    discard in class DataTransform
  - transformChanged
```
public void transformChanged(TransformEvent e)
```
    Called when parent data transform's parameters are updated.
    
    Specified by:
    
    transformChanged in interface TransformListener
  - configureOverlay
```
protected void configureOverlay(OverlayObject obj)
```
    Configures the given overlay to match the current settings.
  - updatePosition
```
protected void updatePosition(DisplayImpl display)
```
    Updates the dimensional position based on the current state of the given display.
  - releaseLeft
```
protected void releaseLeft(DisplayEvent e,
                           DisplayImpl display,
                           OverlayTool tool)
```
    Helper method that handles left mouse button releases.

Class OverlayTransform

Field Summary

Fields inherited from class loci.visbio.data.DataTransform

Constructor Summary

Method Summary

Methods inherited from class loci.visbio.data.DataTransform

Methods inherited from class java.lang.Object

Field Detail

RED_TYPE

GREEN_TYPE

BLUE_TYPE

ALPHA_TYPE

RANGE_TUPLE

NOT_APPLICABLE

controls

overlays

pos

textType

textRangeTuple

mouseDownLeft

mouseDownRight

fontMetrics

drawText

clipboard

clipboardPos

selectBox

lastToolType

toolChanged

Constructor Detail

OverlayTransform

Method Detail

makeRangeTuple

addObject

addObject

removeObject

removeObject

removeSelectedObjects

addTSB

removeTSB

removeSelectedObjects

copySelectedObjects

copySelectedObjects

pasteObjects

pasteObjects

distributeObjects

distributeObjects

getObjects

getObjects

setPos

getPos

loadOverlays

saveOverlays

exportOverlays

getDomainType

getRangeType

getTextRangeType

getTextRangeValue

getScalingValue

getScalingValueX

getScalingValueY

getFontMetrics

setTextDrawn

isTextDrawn

hasToolChanged

makeTransform

isValidParent

isParentRequired

getData

isValidDimension

getSuggestedMaps

getCacheId

isImmediate

getControls

setFont

displayChanged

matches

isCompatible

initState

discard

transformChanged