Class ClusterGramCanvas

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Canvas
              |
              +--ClusterGramCanvas

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

class ClusterGramCanvas

extends java.awt.Canvas

Create a ClusterGram canvas and display the colored green/red similarity table in a popup window.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/07/07 21:40:41 $ $Revision: 1.9 $

Author:

P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home, DrawClusterGram, HierClustNode, Serialized Form

Inner classes inherited from class java.awt.Canvas

java.awt.Canvas.AccessibleAWTCanvas

Inner classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock

Field Summary

private boolean	addKmeansDataFlag flag: if cdg.plotMode==mae.PLOT_KMEANS_CLUSTERGRAM)
private int	botEdge
private int	boxHeight size of a data box in the clustergram
private int	boxWidth bottom edge of box array
private int[]	boxX ULHC event hlr [0:nCols-1]
private int[]	boxY ULHC event hlr [0:nRows-1]
private java.lang.String[]	colLabel opt.
private DrawClusterGram	dcg parent class
private float[]	dGramDistL [0:nObj-2] log dist.
private float[]	dGramDistR [0:nObj-2] log dist.
private float[]	dGramDistS [0:nObj-2] log dist.
private float[]	dGramEnumOrder [0:nObj-2] enumeration order
private float[]	dGramEOleft [0:nObj-2] left child enum order
private float[]	dGramEOright [0:nObj-2] right child enum order
private int[]	dGramLeftNNbr [0:nObj-2] Left Node Number
private int[]	dGramNodeNbr [0:nObj-2] Node Number
private int[]	dGramRightNNbr [0:nObj-2] Right Node Number
private int	dGramX1 left horizontal size of dendrogram region
private int	dGramX2 right horizontal size of dendrogram region
(package private) int	dGramZoomMag zoom in on dendrogram - set by DrawClusterGram checkbox
private boolean	didDataSetupFlag flag: set by setupData() if successful
private boolean	drawIntoImageFlag set if draw clustergram to GIF file
private java.lang.String	featuresStr current gene feature data
private java.awt.FontMetrics	fm font metrics for font
private java.awt.Font	font drawing font
private int	fontHeight
private int	fontLeading
private int	fontWidth
(package private) boolean	foundObjFlag found object row when clicked on it
private java.lang.String	genomicDataStr current gene genomic data
private int	guardRows # of extra rows so cover the viewport
(package private) int	iDataV col to norm by in [0:nDataV-1]
private boolean	isBoxSelectedFlag set by event handler mouse on click
private int	leftEdge left edge of box array
private int	leftLabel left edge of Left label
(package private) static MAExplorer	mae link to global MAExplorer instance
(package private) static int	MAX_COLORS maximum colors used - Dark green to dark red
private float	maxDgramDist max of dGramDistS[]
(package private) static int	MIN_CANVAS_HEIGHT default canvas height
(package private) static int	MIN_CANVAS_WIDTH default canvas width
private int	mouseModifiers set by event handler mouse coords on click
private int	nCols # of columns i.e.
private int	nRows # of rows i.e.
private float[][]	objDataV [0:maxGenes-1][0:nCols-1] normalized data for each object
private java.lang.String	oGifFileName GIF output file if used
private GeneList	orderedCL gene list for rows
(package private) int	preferredHeight preferred height size of entire canvas
(package private) int	preferredWidth preferred width size of entire canvas
private java.awt.Color[]	ratioColor used for color mapping
private float[]	ratioRange used for color mapping
private int	rightEdge right edge of box array
private java.lang.String[]	rowLabel row labels (Master_ID + MasterGeneName)
private int[]	rowMID row MID index
private int	scaleMapX position of scale map X
private int	scaleMapY position of scale map Y
(package private) int	selCol selected column set by event handler mouse on click
private float	selDist distance selected by clicking on dendrogram
(package private) int	selMID set by event handler on click
(package private) int	selRow selected row set by event handler mouse on click
private boolean	shortWidthFlag flag: plot narrower boxes
(package private) int	statVertOffset offset of status canvas if drawing it at top of GIF image canvas, else 0
private int	topEdge top edge of box array
private HierClustNode	tree hierarchical cluster tree
private boolean	useColNbrFlag flag: 1, 2, 3, ...
private boolean	useFullHPStageNameFlag flag: use full HP stage name for COL name
private int	vertLabelX vertical label ULHC
private int	vertLabelY1 top y for vert label
private int	vertLabelY2 bottom y for vert label
private int	xCursor x cursor set by event handler mouse coords on click
private int	yCursor y cursor set by event handler mouse coords on click

Fields inherited from class java.awt.Canvas

base, nameCounter, serialVersionUID

Fields inherited from class java.awt.Component

accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dbg, dropTarget, enabled, eventMask, focusListener, focusListenerK, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

(package private)

ClusterGramCanvas(MAExplorer mae, DrawClusterGram dcg, GeneList orderedCL, HierClustNode tree) ClusterGramCanvas() - Constructor to display expresion profile in canvas

Method Summary

private void	copyGenesInSubtreeToEGL() copyGenesInSubtreeToEGL() - Copy terminal genes in dendrogram subtree to E.G.L for box that was selected at (selRow,selCol) such that terminal genes LEQ selDist GT 0.0F and dcg.drawDendroGramFlag.
private void	drawDendrogram(java.awt.Graphics g, int r1, int r2) drawDendrogram() - draw dendrogram from row r1 to r2.
(package private) boolean	drawGifFile(java.lang.String oGifFileName) drawGifFile() - draw clustergram into Gif image file if in stand-alone mode.
private void	drawRow(java.awt.Graphics g, int r, float[] dataV) drawRow() - draw row of boxes, left & right label, save the coords.
(package private) void	drawScaleMap(java.awt.Graphics g) drawScaleMap() - draw the X/Y color scale map.
private void	drawSelectedHP(java.awt.Graphics g, int r1, int r2) drawSelectedHP() - draw selected box as white circle if the selected row is within [r1:r2].
(package private) void	drawVerticalLabels(java.awt.Graphics g) drawVerticalLabels() - Draw the vertical labels of samples
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
void	paint(java.awt.Graphics g) paint() - draw ClusterGram [r1:r2] from scroller percentage and canvas height.
private boolean	selectObject(int xC, int yC) selectObject() - test mouse cursor to select row or box if within any box
(package private) void	setBoxSizes(java.awt.Graphics g) setBoxSizes() - set box sizes based on font metrics.
(package private) void	setCurrentGene(int xCursor, int yCursor, int mouseModifiers, boolean changeCurGeneFlag) setCurrentGene() - set current gene from (xCursor,yCursor) in ClusterGram.
(package private) void	setEGLtoSubTreeGenes(int[] subtreeNbrs) setEGLtoSubTreeGenes() - Copy genes to E.G.L.
private java.awt.Color	setRatioColor(float ratio, int n) setRatioColor() - map data ratio to color (used to color a box).
private void	setupData() setupData() - setup additional data arrays for ClusterGram
(package private) void	showGeneMsgsAndPlot(int mid, int selRow) showGeneMsgsAndPlot() - show quant & genomic data messages in MSG & in plot
private void	unpackTreeDgramLists(HierClustNode tree) unpackTreeDgramLists() - extract dGram arrays for drawing dendrograms
(package private) void	updateCurGene(int mid) updateCurGene() - set current gene by MID from PopupRegistry
(package private) boolean	updateData(GeneList orderedCL, HierClustNode tree) updateData() - update expression profile with new gene data

Methods inherited from class java.awt.Canvas

, addNotify, constructComponentName, getAccessibleContext, postsOldMouseEvents

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkGD, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createChildHierarchyEvents, createHierarchyEvents, createImage, createImage, deliverEvent, disable, disableEvents, dispatchEvent, dispatchEventImpl, doLayout, enable, enable, enableEvents, enableInputMethods, eventEnabled, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getAlignmentX, getAlignmentY, getBackground, getBounds, getBounds, getColorModel, getComponentAt, getComponentAt, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getListeners, getLocale, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getMaximumSize, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkit, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, initIDs, inside, invalidate, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, layout, lightweightPaint, lightweightPrint, list, list, list, list, list, locate, location, lostFocus, minimumSize, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, numListening, paintAll, paintHeavyweightComponents, paramString, postEvent, preferredSize, prepareImage, prepareImage, print, printAll, printHeavyweightComponents, processComponentEvent, processEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, readObject, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, resetGC, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFont, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, show, size, toString, transferFocus, update, validate, writeObject

Methods inherited from class java.lang.Object

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

Field Detail

mae

static MAExplorer mae

link to global MAExplorer instance

MIN_CANVAS_WIDTH

static final int MIN_CANVAS_WIDTH

default canvas width

MIN_CANVAS_HEIGHT

static final int MIN_CANVAS_HEIGHT

default canvas height

MAX_COLORS

static final int MAX_COLORS

maximum colors used - Dark green to dark red

preferredHeight

int preferredHeight

preferred height size of entire canvas

preferredWidth

int preferredWidth

preferred width size of entire canvas

statVertOffset

int statVertOffset

offset of status canvas if drawing it at top of GIF image canvas, else 0

tree

private HierClustNode tree

hierarchical cluster tree

dcg

private DrawClusterGram dcg

parent class

objDataV

private float[][] objDataV

[0:maxGenes-1][0:nCols-1] normalized data for each object

maxDgramDist

private float maxDgramDist

max of dGramDistS[]

dGramDistS

private float[] dGramDistS

[0:nObj-2] log dist. between children

dGramDistR

private float[] dGramDistR

[0:nObj-2] log dist. between Right's children

dGramDistL

private float[] dGramDistL

[0:nObj-2] log dist. between Left's children

dGramEnumOrder

private float[] dGramEnumOrder

[0:nObj-2] enumeration order

dGramEOright

private float[] dGramEOright

[0:nObj-2] right child enum order

dGramEOleft

private float[] dGramEOleft

[0:nObj-2] left child enum order

dGramNodeNbr

private int[] dGramNodeNbr

[0:nObj-2] Node Number

dGramRightNNbr

private int[] dGramRightNNbr

[0:nObj-2] Right Node Number

dGramLeftNNbr

private int[] dGramLeftNNbr

[0:nObj-2] Left Node Number

ratioColor

private java.awt.Color[] ratioColor

used for color mapping

ratioRange

private float[] ratioRange

used for color mapping

shortWidthFlag

private boolean shortWidthFlag

flag: plot narrower boxes

addKmeansDataFlag

private boolean addKmeansDataFlag

flag: if cdg.plotMode==mae.PLOT_KMEANS_CLUSTERGRAM)

useColNbrFlag

private boolean useColNbrFlag

flag: 1, 2, 3, ... for COL name

useFullHPStageNameFlag

private boolean useFullHPStageNameFlag

flag: use full HP stage name for COL name

didDataSetupFlag

private boolean didDataSetupFlag

flag: set by setupData() if successful

foundObjFlag

boolean foundObjFlag

found object row when clicked on it

dGramZoomMag

int dGramZoomMag

zoom in on dendrogram - set by DrawClusterGram checkbox

font

private java.awt.Font font

drawing font

fm

private java.awt.FontMetrics fm

font metrics for font

fontHeight

private int fontHeight

fontWidth

private int fontWidth

fontLeading

private int fontLeading

guardRows

private int guardRows

# of extra rows so cover the viewport

nRows

private int nRows

# of rows i.e. genes

nCols

private int nCols

# of columns i.e. HPs

orderedCL

private GeneList orderedCL

gene list for rows

dGramX1

private int dGramX1

left horizontal size of dendrogram region

dGramX2

private int dGramX2

right horizontal size of dendrogram region

scaleMapX

private int scaleMapX

position of scale map X

scaleMapY

private int scaleMapY

position of scale map Y

vertLabelX

private int vertLabelX

vertical label ULHC

vertLabelY1

private int vertLabelY1

top y for vert label

vertLabelY2

private int vertLabelY2

bottom y for vert label

leftLabel

private int leftLabel

left edge of Left label

leftEdge

private int leftEdge

left edge of box array

rightEdge

private int rightEdge

right edge of box array

topEdge

private int topEdge

top edge of box array

botEdge

private int botEdge

boxWidth

private int boxWidth

bottom edge of box array

boxHeight

private int boxHeight

size of a data box in the clustergram

isBoxSelectedFlag

private boolean isBoxSelectedFlag

set by event handler mouse on click

selRow

int selRow

selected row set by event handler mouse on click

selCol

int selCol

selected column set by event handler mouse on click

iDataV

int iDataV

col to norm by in [0:nDataV-1]

mouseModifiers

private int mouseModifiers

set by event handler mouse coords on click

xCursor

private int xCursor

x cursor set by event handler mouse coords on click

yCursor

private int yCursor

y cursor set by event handler mouse coords on click

selMID

int selMID

set by event handler on click

selDist

private float selDist

distance selected by clicking on dendrogram

featuresStr

private java.lang.String featuresStr

current gene feature data

genomicDataStr

private java.lang.String genomicDataStr

current gene genomic data

boxX

private int[] boxX

ULHC event hlr [0:nCols-1]

boxY

private int[] boxY

ULHC event hlr [0:nRows-1]

colLabel

private java.lang.String[] colLabel

opt. column labels

rowLabel

private java.lang.String[] rowLabel

row labels (Master_ID + MasterGeneName)

rowMID

private int[] rowMID

row MID index

drawIntoImageFlag

private boolean drawIntoImageFlag

set if draw clustergram to GIF file

oGifFileName

private java.lang.String oGifFileName

GIF output file if used

Constructor Detail

ClusterGramCanvas

ClusterGramCanvas(MAExplorer mae,
                  DrawClusterGram dcg,
                  GeneList orderedCL,
                  HierClustNode tree)

ClusterGramCanvas() - Constructor to display expresion profile in canvas

Parameters:

mae - is the instance of MAExplorer

dcg - is the parent window

orderedCL - is the gene list for rows

tree - is the hierarchical cluster tree

See Also:

unpackTreeDgramLists(HierClustNode), updateData(GeneList, HierClustNode)

Method Detail

drawGifFile

boolean drawGifFile(java.lang.String oGifFileName)

drawGifFile() - draw clustergram into Gif image file if in stand-alone mode. This sets it up and lets paint() to the heavy lifting... *

Parameters:

oGifFileName - is the name of the GIF output file.

Returns:

false if unable to generate the image file.

See Also:

Component.repaint()

updateData

boolean updateData(GeneList orderedCL,
                   HierClustNode tree)

updateData() - update expression profile with new gene data

Parameters:

orderedCL - is the ordered gene list for rows

tree - hierarchical cluster tree

Returns:

true if succeed

See Also:

GeneList, HierClustNode, Component.repaint(), setupData(), unpackTreeDgramLists(HierClustNode)

unpackTreeDgramLists

private void unpackTreeDgramLists(HierClustNode tree)

unpackTreeDgramLists() - extract dGram arrays for drawing dendrograms

Parameters:

tree - hierarchical cluster tree

See Also:

HierClustNode

setupData

private void setupData()

setupData() - setup additional data arrays for ClusterGram

See Also:

Gene.isGeneProperty(int), GeneList, Util.cvtValueToStars(float, float, int, boolean)

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Component

Returns:

size of the window

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Overrides:

getMinimumSize in class java.awt.Component

Returns:

size of the window

selectObject

private boolean selectObject(int xC,
                             int yC)

selectObject() - test mouse cursor to select row or box if within any box

Parameters:

xC - is the x coordinate selected in the window

yC - is the y coordinate selected in the window

Returns:

true if successful and set the appropriate values.

showGeneMsgsAndPlot

void showGeneMsgsAndPlot(int mid,
                         int selRow)

showGeneMsgsAndPlot() - show quant & genomic data messages in MSG & in plot

Parameters:

mid - is the master gene index

selRow - is the row selected if not -1

See Also:

MaHybridSample.getSpotDataStatic(int, boolean), SpotFeatures.getSpotFeatures(java.awt.Point, MaHybridSample), SpotFeatures.getSpotGenomicData(java.awt.Point, MaHybridSample), Util.cvf2s(float, int), Util.showFeatures(java.lang.String, java.lang.String), Util.showMsg(java.lang.String)

updateCurGene

void updateCurGene(int mid)

updateCurGene() - set current gene by MID from PopupRegistry

Parameters:

mid - is the master gene index

See Also:

ScrollPane.getScrollPosition(), ScrollPane.getViewportSize(), ScrollPane.setScrollPosition(int, int), showGeneMsgsAndPlot(int, int)

setCurrentGene

void setCurrentGene(int xCursor,
                    int yCursor,
                    int mouseModifiers,
                    boolean changeCurGeneFlag)

setCurrentGene() - set current gene from (xCursor,yCursor) in ClusterGram.

Parameters:

xCursor - of current gene

yCursor - of current gene

mouseModifiers - when selected the current gene

changeCurGeneFlag - is on if we should call the popup registry

See Also:

PopupRegistry.updateCurGene(int, int, java.lang.Object), Component.repaint(), selectObject(int, int), showGeneMsgsAndPlot(int, int)

setBoxSizes

void setBoxSizes(java.awt.Graphics g)

setBoxSizes() - set box sizes based on font metrics. If the dgc.drawDendroGramFlag is set, then add space to left of clustergram for the dendrogram to be drawn.

Parameters:

g - is graphics context

setRatioColor

private java.awt.Color setRatioColor(float ratio,
                                     int n)

setRatioColor() - map data ratio to color (used to color a box). Color is in (ratioMin : ratioMax]. i.e. ratioMin < ratio <= ratioMax for ratio <1.0 and ratioMin <= ratio < ratioMax for ratio >1.0

Parameters:

ratio - is the ratio to use in looking up the color

n - is the number of colors in map

drawRow

private void drawRow(java.awt.Graphics g,
                     int r,
                     float[] dataV)

drawRow() - draw row of boxes, left & right label, save the coords. Use this.font as the font size.

Parameters:

g - is graphics context

r - is the row in the cluster gram

dataV - is the data vector

See Also:

GeneList.isMIDinGeneList(int), setRatioColor(float, int)

copyGenesInSubtreeToEGL

private void copyGenesInSubtreeToEGL()

copyGenesInSubtreeToEGL() - Copy terminal genes in dendrogram subtree to E.G.L for box that was selected at (selRow,selCol) such that terminal genes LEQ selDist GT 0.0F and dcg.drawDendroGramFlag. [TODO] - needs to be debugged. Not picking up correct subset of the tree.

See Also:

HierClustNode.findSubtreeOfNodeNbrs(int), setEGLtoSubTreeGenes(int[])

setEGLtoSubTreeGenes

void setEGLtoSubTreeGenes(int[] subtreeNbrs)

setEGLtoSubTreeGenes() - Copy genes to E.G.L. (Edited Gene List)

Parameters:

subtreeNbrs - is the list of genes to be copied to the E.G.L.

See Also:

EditedGeneList.addGeneToEditedCL(int)

drawSelectedHP

private void drawSelectedHP(java.awt.Graphics g,
                            int r1,
                            int r2)

drawSelectedHP() - draw selected box as white circle if the selected row is within [r1:r2].

Parameters:

g - is the graphic context

r1 - starting row that is visible

r2 - ending row that is visible

drawVerticalLabels

void drawVerticalLabels(java.awt.Graphics g)

drawVerticalLabels() - Draw the vertical labels of samples

Parameters:

g - is the graphic context

drawScaleMap

void drawScaleMap(java.awt.Graphics g)

drawScaleMap() - draw the X/Y color scale map.

  RED                 BLACK             GREEN
  <1/8X 1/6X 1/4X 1/2X  1X    2X  4X  6X  >8X

   Selected Row[#row] Master_ID (if Y selected)
   Selected Col[#col] Sample name (if X & Y selected)
   Normalization Col[#iDataV] Norm Sample name (if X selected)
    (if X selected)
    (if X selected)

Parameters:

g - is the graphic context

See Also:

Util.cvf2s(float, int)

drawDendrogram

private void drawDendrogram(java.awt.Graphics g,
                            int r1,
                            int r2)

drawDendrogram() - draw dendrogram from row r1 to r2.

 The spacing between terminal nodes is boxHeight.
 The region for drawing dendrogram is dGramX1 to dGramX2.
 The 'enum order' is the spacing on particular ordered rows
 and is fractional for non-terminal nodes.
 We used the ordered hierarchical cluster data for nodes in [r1:r2].
   dGramDist[0:nObj-1] distance between children.
   dGramDistR[0:nObj-1] distance between Right children.
   dGramDistL[0:nObj-1] distance between Left children.
   dGramEnumOrder[0:nObj-1] enumeration order.
   dGramEOright[0:nObj-1] right child enum order.
   dGramEOleft[0:nObj-1] left child enum order.
   dGramNodeNbr[0:nObj-1] - Node Number
   dGramEOrightNNbr[0:nObj-1] - Right Node Number
   dGramLeftNNbr[0:nObj-1] - Left Node Number

Parameters:

g - is the graphic context

r1 - starting row that is visible

r1 - ending row that is visible

paint

public void paint(java.awt.Graphics g)

paint() - draw ClusterGram [r1:r2] from scroller percentage and canvas height. Redraw only what is visible...

Overrides:

paint in class java.awt.Canvas

Parameters:

g - is the graphic context

See Also:

DrawClusterGram.drawScaleMapAndVerticalLabels(java.awt.Graphics), ScrollPane.getHScrollbarHeight(), ScrollPane.getVAdjustable(), ScrollPane.getViewportSize(), WriteGifEncoder, WriteGifEncoder.writeFile(java.lang.String), copyGenesInSubtreeToEGL(), drawDendrogram(java.awt.Graphics, int, int), drawRow(java.awt.Graphics, int, float[]), drawScaleMap(java.awt.Graphics), drawSelectedHP(java.awt.Graphics, int, int), drawVerticalLabels(java.awt.Graphics), Component.repaint(), setBoxSizes(java.awt.Graphics)