ij.plugin.frame

Class ClusterFramePlugIn

java.lang.Object

LinkedViewFrame

ij.plugin.frame.ClusterFramePlugIn

All Implemented Interfaces:

java.awt.event.FocusListener, java.awt.event.WindowListener, java.util.EventListener

public class ClusterFramePlugIn
extends LinkedViewFrame
implements java.awt.event.WindowListener, java.awt.event.FocusListener

This class provides the JTreeView library plotting functionality as an ImageJ/PhysImage plugin. This plugin also introduces quite a few methods for manipulating the content and presentation of the data. This is one of the basic PlugIn Frames whose contents can be displayed in Layouts.

Constructor Summary

Constructors

Constructor and Description
ClusterFramePlugIn(java.lang.String filename)

Method Summary

Modifier and Type	Method and Description
Range	addClusterAverageWave(java.lang.String clusterAverageWavename, java.util.ArrayList clusterNames, java.awt.Color color, ChartPlugIn frame)
void	close()
void	focusGained(java.awt.event.FocusEvent e)
void	focusLost(java.awt.event.FocusEvent e)
ImagePlus	getAnnotatedImage(int width, int height)
TreeDrawerNode	getCluster1()
TreeDrawerNode	getCluster2()
TreeDrawerNode	getCluster3()
TreeDrawerNode	getCluster4()
double	getClustersLowerBound(Range cluster1, Range cluster2, Range cluster3, Range cluster4)
double	getClustersUpperBound(Range cluster1, Range cluster2, Range cluster3, Range cluster4)
double	getContrast()
DendroView	getDendroView()
float[]	getLeftHorizontalProportions()
float[]	getLeftVerticalProportions()
int	getMiddleDividerLocation()
java.util.ArrayList	getNamesByCluster(TreeDrawerNode node)
void	getNamesByCluster(TreeDrawerNode node, java.util.ArrayList list)
Roi[]	getRoisByNames(java.util.ArrayList names)
javax.swing.JSplitPane	getSplitPane()
ChartPlugIn	plot3D()
void	removeJScrollBars()
void	removeJScrollBars(java.awt.Container container)
void	run(java.lang.String arg)
void	setContrast(double contrast)
void	setLeftHorizontalProportions(float[] widths)
void	setLeftVerticalProportions(float[] heights)
void	setMiddleDividerLocation(int dividerLocation)
void	setTreeColor(TreeDrawerNode node, java.awt.Color color)
void	setTreeColors()
java.lang.String	stripName(java.lang.String name)
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e)
void	windowDeactivated(java.awt.event.WindowEvent e)
void	windowDeiconified(java.awt.event.WindowEvent e)
void	windowIconified(java.awt.event.WindowEvent e)
void	windowOpened(java.awt.event.WindowEvent e)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ClusterFramePlugIn

public ClusterFramePlugIn(java.lang.String filename)

Method Detail

focusGained

public void focusGained(java.awt.event.FocusEvent e)

Specified by:

focusGained in interface java.awt.event.FocusListener

close

public void close()

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)

Specified by:

windowClosing in interface java.awt.event.WindowListener

windowActivated

public void windowActivated(java.awt.event.WindowEvent e)

Specified by:

windowActivated in interface java.awt.event.WindowListener

plot3D

public ChartPlugIn plot3D()

getClustersLowerBound

public double getClustersLowerBound(Range cluster1,
                                    Range cluster2,
                                    Range cluster3,
                                    Range cluster4)

getClustersUpperBound

public double getClustersUpperBound(Range cluster1,
                                    Range cluster2,
                                    Range cluster3,
                                    Range cluster4)

addClusterAverageWave

public Range addClusterAverageWave(java.lang.String clusterAverageWavename,
                                   java.util.ArrayList clusterNames,
                                   java.awt.Color color,
                                   ChartPlugIn frame)

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowClosed

public void windowClosed(java.awt.event.WindowEvent e)

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowIconified

public void windowIconified(java.awt.event.WindowEvent e)

Specified by:

windowIconified in interface java.awt.event.WindowListener

windowDeiconified

public void windowDeiconified(java.awt.event.WindowEvent e)

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowDeactivated

public void windowDeactivated(java.awt.event.WindowEvent e)

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

focusLost

public void focusLost(java.awt.event.FocusEvent e)

Specified by:

focusLost in interface java.awt.event.FocusListener

setContrast

public void setContrast(double contrast)

getContrast

public double getContrast()

getDendroView

public DendroView getDendroView()

getSplitPane

public javax.swing.JSplitPane getSplitPane()

setLeftVerticalProportions

public void setLeftVerticalProportions(float[] heights)

getLeftVerticalProportions

public float[] getLeftVerticalProportions()

setLeftHorizontalProportions

public void setLeftHorizontalProportions(float[] widths)

getLeftHorizontalProportions

public float[] getLeftHorizontalProportions()

setMiddleDividerLocation

public void setMiddleDividerLocation(int dividerLocation)

getMiddleDividerLocation

public int getMiddleDividerLocation()

removeJScrollBars

public void removeJScrollBars()

removeJScrollBars

public void removeJScrollBars(java.awt.Container container)

setTreeColors

public void setTreeColors()

getCluster1

public TreeDrawerNode getCluster1()

getCluster2

public TreeDrawerNode getCluster2()

getCluster3

public TreeDrawerNode getCluster3()

getCluster4

public TreeDrawerNode getCluster4()

getNamesByCluster

public java.util.ArrayList getNamesByCluster(TreeDrawerNode node)

getRoisByNames

public Roi[] getRoisByNames(java.util.ArrayList names)

getAnnotatedImage

public ImagePlus getAnnotatedImage(int width,
                                   int height)

stripName

public java.lang.String stripName(java.lang.String name)

getNamesByCluster

public void getNamesByCluster(TreeDrawerNode node,
                              java.util.ArrayList list)

setTreeColor

public void setTreeColor(TreeDrawerNode node,
                         java.awt.Color color)

run

public void run(java.lang.String arg)