OverlayUtil (LOCI Javadocs 0-SNAPSHOT API)

java.lang.Object
- loci.visbio.overlays.OverlayUtil

public final class OverlayUtil
extends Object

Utility methods for Overlays.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static float[][]`	`ARC` Computed (X, Y) pairs for top 1/2 of a unit circle.
`protected static float`	`GLOW_ALPHA` Alpha of the selection layer.
`protected static Color`	`GLOW_COLOR` Color of the selection layer.
`protected static float`	`GLOW_WIDTH` Width of the selection layer beyond the object's boundaries.
`protected static float`	`HLT_ALPHA` Alpha of the highlight layer for noded object.
`protected static Color`	`HLT_COLOR` Color of the highlight layer for noded objects.
`protected static Color`	`OUTLINE_COLOR` Color of the outline layer.
`static String[]`	`OVERLAY_TYPES` List of all OverlayObject subclasses.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static float[][]`	`adjoin(float[][] a, float[][] b)` Connects a pair of VisAD-style 2D arrays of points.
`static Vector`	`buildNodesSets(RealTupleType domain, float[][] nodes, float width)` Given a set of nodes, creates a UnionSet of Gridded2DSets to highlight the nodes.
`static double[][]`	`floatsToPixelDoubles(DisplayImpl d, float[][] nodes)` Casts and converts an array of floats in domain coordinates to doubles in pixel coordinates.
`static DataImpl`	`getArrowLayer(OverlayObject obj, TransformLink link)` Computes selection layer for OverlayArrow objects.
`static DataImpl`	`getBoxLayer(OverlayObject obj, TransformLink link)` Computes selection layer for OverlayBox objects.
`static DataImpl`	`getLineLayer(OverlayObject obj, TransformLink link)` Returns a selection layer for OverlayLine objects.
`static DataImpl`	`getMarkerLayer(OverlayObject obj, TransformLink link)` Returns a selection layer for OverlayMarker objects.
`static float`	`getMultiplier(DisplayImpl display)` Returns a multiplier suitable for scaling distances to pixel coordinates.
`static float`	`getMultiplier(TransformLink link)` Returns a multiplier suitable for scaling distances to pixel coordinates.
`static DataImpl`	`getNodedLayer(OverlayObject obj, TransformLink link)` Computes selection layer for OverlayNodedObject objects.
`static DataImpl`	`getOutlineLayer(OverlayObject obj, TransformLink link)` Computes a standard outline layer for an OverlayObject.
`static DataImpl`	`getOvalLayer(OverlayObject obj, TransformLink link)` Computes a selection layer for OverlayOval objects.
`static String[]`	`getOverlayTypes()` Get list of all OverlayObject subclasses.
`static DataImpl`	`getSelectionLayer(OverlayObject obj, TransformLink link, boolean outline)` Computes a type-specific selection layer for the given OverlayObject.
`protected static String[]`	`getStatTypes(String overlayType)` Returns statistic names for a particular class.
`static DataImpl`	`getTextLayer(OverlayObject obj, TransformLink link)` Computes a selection layer for OverlayText objects.
`static Vector`	`makeGridded2DSets(RealTupleType domain, float[][] nodes, float[][] right, float[][] left, float width)` Makes valid Gridded2DSets from the arrays supplied.
`static void`	`print(float[] p)` Prints a point.
`static void`	`print(float[][] points)` Prints a VisAD style group of points.
`static void`	`print(float x, float y)` Prints a point.
`static float[]`	`smooth(float[] un, float[] cn1, float S)` Calculates smoothed coordinates using "single exponential smoothing" as described in Littlewood and Inman, _Computer-assisted DNA length measurements..._.

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

Field Detail
- GLOW_WIDTH
```
protected static final float GLOW_WIDTH
```
  Width of the selection layer beyond the object's boundaries.
  
  See Also:
  
  Constant Field Values
- GLOW_ALPHA
```
protected static final float GLOW_ALPHA
```
  Alpha of the selection layer.
  
  See Also:
  
  Constant Field Values
- GLOW_COLOR
```
protected static final Color GLOW_COLOR
```
  Color of the selection layer.
- HLT_COLOR
```
protected static final Color HLT_COLOR
```
  Color of the highlight layer for noded objects.
- HLT_ALPHA
```
protected static final float HLT_ALPHA
```
  Alpha of the highlight layer for noded object.
  
  See Also:
  
  Constant Field Values
- OUTLINE_COLOR
```
protected static final Color OUTLINE_COLOR
```
  Color of the outline layer.
- ARC
```
protected static final float[][] ARC
```
  Computed (X, Y) pairs for top 1/2 of a unit circle.
- OVERLAY_TYPES
```
public static final String[] OVERLAY_TYPES
```
  List of all OverlayObject subclasses.

Method Detail

getOverlayTypes
```
public static String[] getOverlayTypes()
```
Get list of all OverlayObject subclasses.

getStatTypes

protected static String[] getStatTypes(String overlayType)

Returns statistic names for a particular class.

getSelectionLayer

public static DataImpl getSelectionLayer(OverlayObject obj,
                                         TransformLink link,
                                         boolean outline)

Computes a type-specific selection layer for the given OverlayObject.

getArrowLayer

public static DataImpl getArrowLayer(OverlayObject obj,
                                     TransformLink link)

Computes selection layer for OverlayArrow objects.

getBoxLayer

public static DataImpl getBoxLayer(OverlayObject obj,
                                   TransformLink link)

Computes selection layer for OverlayBox objects.

getLineLayer

public static DataImpl getLineLayer(OverlayObject obj,
                                    TransformLink link)

Returns a selection layer for OverlayLine objects.

getMarkerLayer

public static DataImpl getMarkerLayer(OverlayObject obj,
                                      TransformLink link)

Returns a selection layer for OverlayMarker objects.

getNodedLayer

public static DataImpl getNodedLayer(OverlayObject obj,
                                     TransformLink link)

Computes selection layer for OverlayNodedObject objects.

getOvalLayer

public static DataImpl getOvalLayer(OverlayObject obj,
                                    TransformLink link)

Computes a selection layer for OverlayOval objects.

getTextLayer

public static DataImpl getTextLayer(OverlayObject obj,
                                    TransformLink link)

Computes a selection layer for OverlayText objects.

getOutlineLayer

public static DataImpl getOutlineLayer(OverlayObject obj,
                                       TransformLink link)

Computes a standard outline layer for an OverlayObject.

getMultiplier
```
public static float getMultiplier(TransformLink link)
```
Returns a multiplier suitable for scaling distances to pixel coordinates. Useful when the location of an event are unimportant, just the properties of the display.

getMultiplier
```
public static float getMultiplier(DisplayImpl display)
```
Returns a multiplier suitable for scaling distances to pixel coordinates. Useful when the location of an event are unimportant, just the properties of the display.

adjoin

public static float[][] adjoin(float[][] a,
                               float[][] b)

Connects a pair of VisAD-style 2D arrays of points.

buildNodesSets

public static Vector buildNodesSets(RealTupleType domain,
                                    float[][] nodes,
                                    float width)

Given a set of nodes, creates a UnionSet of Gridded2DSets to highlight the nodes.

makeGridded2DSets
```
public static Vector makeGridded2DSets(RealTupleType domain,
                                       float[][] nodes,
                                       float[][] right,
                                       float[][] left,
                                       float width)
```
Makes valid Gridded2DSets from the arrays supplied.

Parameters:

nodes - The nodes of the noded object

right - The points on the right side of the noded object (supposing node indices increase from left to right across the screen)

left - The points on the left side of the noded object (again supposing node indices increase from left to right across the screen).

smooth
```
public static float[] smooth(float[] un,
                             float[] cn1,
                             float S)
```
Calculates smoothed coordinates using "single exponential smoothing" as described in Littlewood and Inman, _Computer-assisted DNA length measurements..._. Nucleic Acids Research, V 10 No. 5. (1982) p. 1694

floatsToPixelDoubles

public static double[][] floatsToPixelDoubles(DisplayImpl d,
                                              float[][] nodes)

Casts and converts an array of floats in domain coordinates to doubles in pixel coordinates.

print

public static void print(float[][] points)

Prints a VisAD style group of points.

print

public static void print(float x,
                         float y)

Prints a point.

print
```
public static void print(float[] p)
```
Prints a point.

Class OverlayUtil

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

GLOW_WIDTH

GLOW_ALPHA

GLOW_COLOR

HLT_COLOR

HLT_ALPHA

OUTLINE_COLOR

ARC

OVERLAY_TYPES

Method Detail

getOverlayTypes

getStatTypes

getSelectionLayer

getArrowLayer

getBoxLayer

getLineLayer

getMarkerLayer

getNodedLayer

getOvalLayer

getTextLayer

getOutlineLayer

getMultiplier

getMultiplier

adjoin

buildNodesSets

makeGridded2DSets

smooth

floatsToPixelDoubles

print

print

print