Class DrawClusterGram

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.ScrollPane
                    |
                    +--DrawClusterGram

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.event.ItemListener, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.io.Serializable, java.awt.event.WindowListener

class DrawClusterGram

extends java.awt.ScrollPane

implements java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener

This class creates and displays a ClusterGram canvas window. It contains a scrollable ClusterGram canvas of ordered genes in a popup window. When performing clustering, it is updated by the PopupRegistry when the current gene, Filter.workingCL, or other state values change. If hierarchical clustering is used, it uses dendrogram data structures in HierClustNode - otherwise data may be] passed an ordered GeneList (i.e. mList[]).

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: 2002/10/14 20:46:12 $ $Revision: $

Author:

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

See Also:

MAExplorer Home, ClusterGenes, ClusterGramCanvas, HierClustNode, Serialized Form

Inner classes inherited from class java.awt.ScrollPane

java.awt.ScrollPane.AccessibleAWTScrollPane, java.awt.ScrollPane.PeerFixer

Inner classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Inner classes inherited from class java.awt.Component

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

Field Summary

(package private) ClusterGramCanvas	cgC Clustergram canvas
private int	curCGmid current mid of selected ClusterGram row
private int	curCGrow current selected row of ClusterGram
private java.awt.Button	custGramReport popup Report
private java.awt.Checkbox	dGramCheckBox toggle drawing the dendrogram
(package private) boolean	drawDendroGramFlag set if draw dendrogram as well
(package private) java.awt.Graphics	gGif draw status at top of Gif image
(package private) ShowExprProfilesPopup	hierClustersExprProfPopup exists if create EP plot subset popup
private boolean	keepFlagsOnClosing mode of operation used in creating thiswindow for use in closing the window
private MAExplorer	mae link to global instance
(package private) int	N_EP_GENES default # of genes to display in EP list
private int	nCols # of columns in clustergram
private int	nEPgenes # of genes to display in popup EP plot
private int	nGenes # genes in orderedCL
private int	nRows # of rows in clustergram
private GeneList	orderedCL GeneList being used
(package private) int	plotMode plot mode
private java.awt.Button	saveAsGIF Save display as GIF file
private java.awt.Button	showEPsubset show expression profiles for nEPgenes at current ClusterGram position curCGrow
private java.awt.Button	showHPnames show list of Samples
(package private) ShowPlotPopup	spp Parent popup window instance
(package private) StatusCanvas	statusCanvas status canvas
(package private) int	statusCanvasHeight height size of status canvas
private java.lang.String	title title for window
private java.awt.Panel	titlePanel titlePanel of parent
private HierClustNode	tree cluster tree
private java.awt.Button	zoomDgramButton zoom in on dendrogram

Fields inherited from class java.awt.ScrollPane

base, hAdjustable, nameCounter, scrollbarDisplayPolicy, SCROLLBARS_ALWAYS, SCROLLBARS_AS_NEEDED, SCROLLBARS_NEVER, serialVersionUID, vAdjustable

Fields inherited from class java.awt.Container

component, containerListener, containerSerializedDataVersion, dbg, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads

Fields inherited from class java.awt.Component

accessibleContext, actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, 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)

DrawClusterGram(MAExplorer mae, ShowPlotPopup spp, java.awt.Panel titlePanel, HierClustNode tree, GeneList orderedCL, java.lang.String title, int plotMode, boolean keepFlagsOnClosing) DrawClusterGram() - Create popup grid of ClusterGram plots.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
(package private) void	addButtonsToParent(ShowPlotPopup spp, java.awt.Panel p, java.awt.Font bFont) addButtonsToParent() - add buttons for this plot to parents's panel
(package private) void	close() close() - close this popup and reset flags if keepFlagsOnClosing is false
(package private) void	drawScaleMapAndVerticalLabels(java.awt.Graphics gGif) drawScaleMapAndVerticalLabels() - draw scale map & vert lbls i in the title panel status area
java.awt.Dimension	getMinimumSize() getMinimumSize() - get the minimum preferred size
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
void	itemStateChanged(java.awt.event.ItemEvent e)
void	mouseClicked(java.awt.event.MouseEvent e)
void	mouseDragged(java.awt.event.MouseEvent e)
void	mouseEntered(java.awt.event.MouseEvent e)
void	mouseExited(java.awt.event.MouseEvent e)
void	mouseMoved(java.awt.event.MouseEvent e) mouseMoved() - process mouse event
void	mousePressed(java.awt.event.MouseEvent e) Pass all mouse events down to the Canvas.
void	mouseReleased(java.awt.event.MouseEvent e) mouseReleased() - Pass all mouse events down to the Canvas.
void	paint() paint() - redraw clustergram
(package private) void	updateCGplot(GeneList orderedCL, HierClustNode tree) updateCGplot() - update ClusterGram plots using new GeneList.
(package private) void	updateCurGene(int mid) updateCurGene()- update the current gene in the ClusterGram
void	windowActivated(java.awt.event.WindowEvent e)
void	windowClosed(java.awt.event.WindowEvent e)
void	windowClosing(java.awt.event.WindowEvent e) windowClosing() - closing down the window, get rid of the frame.
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.awt.ScrollPane

, addImpl, addNotify, calculateChildSize, constructComponentName, doLayout, getAccessibleContext, getHAdjustable, getHScrollbarHeight, getScrollbarDisplayPolicy, getScrollPosition, getVAdjustable, getViewportSize, getVScrollbarWidth, initIDs, layout, paramString, printComponents, setLayout, setScrollPosition, setScrollPosition

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, adjustListeningChildren, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventImpl, dispatchEventToSelf, eventEnabled, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getListeners, getMaximumSize, getMouseEventTarget, getWindow, insets, invalidate, invalidateTree, isAncestorOf, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, nextFocus, numListening, paint, paintComponents, paintHeavyweightComponents, postProcessKeyEvent, postsOldMouseEvents, preferredSize, preProcessKeyEvent, print, printHeavyweightComponents, processContainerEvent, processEvent, proxyEnableEvents, proxyRequestFocus, readObject, remove, remove, removeAll, removeContainerListener, removeNotify, setFocusOwner, setFont, transferFocus, update, validate, validateTree, writeObject

Methods inherited from class java.awt.Component

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

Methods inherited from class java.lang.Object

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

Field Detail

mae

private MAExplorer mae

link to global instance

spp

ShowPlotPopup spp

Parent popup window instance

tree

private HierClustNode tree

cluster tree

title

private java.lang.String title

title for window

titlePanel

private java.awt.Panel titlePanel

titlePanel of parent

cgC

ClusterGramCanvas cgC

Clustergram canvas

orderedCL

private GeneList orderedCL

GeneList being used

nGenes

private int nGenes

# genes in orderedCL

N_EP_GENES

final int N_EP_GENES

default # of genes to display in EP list

plotMode

int plotMode

plot mode

nRows

private int nRows

# of rows in clustergram

nCols

private int nCols

# of columns in clustergram

curCGrow

private int curCGrow

current selected row of ClusterGram

curCGmid

private int curCGmid

current mid of selected ClusterGram row

nEPgenes

private int nEPgenes

# of genes to display in popup EP plot

statusCanvasHeight

int statusCanvasHeight

height size of status canvas

drawDendroGramFlag

boolean drawDendroGramFlag

set if draw dendrogram as well

keepFlagsOnClosing

private boolean keepFlagsOnClosing

mode of operation used in creating thiswindow for use in closing the window

statusCanvas

StatusCanvas statusCanvas

status canvas

gGif

java.awt.Graphics gGif

draw status at top of Gif image

dGramCheckBox

private java.awt.Checkbox dGramCheckBox

toggle drawing the dendrogram

saveAsGIF

private java.awt.Button saveAsGIF

Save display as GIF file

custGramReport

private java.awt.Button custGramReport

popup Report

zoomDgramButton

private java.awt.Button zoomDgramButton

zoom in on dendrogram

showHPnames

private java.awt.Button showHPnames

show list of Samples

showEPsubset

private java.awt.Button showEPsubset

show expression profiles for nEPgenes at current ClusterGram position curCGrow

hierClustersExprProfPopup

ShowExprProfilesPopup hierClustersExprProfPopup

exists if create EP plot subset popup

Constructor Detail

DrawClusterGram

DrawClusterGram(MAExplorer mae,
                ShowPlotPopup spp,
                java.awt.Panel titlePanel,
                HierClustNode tree,
                GeneList orderedCL,
                java.lang.String title,
                int plotMode,
                boolean keepFlagsOnClosing)

DrawClusterGram() - Create popup grid of ClusterGram plots. Set the mae.fc.workingCL if the specified list is null.

Parameters:

mae - is the MAExplorer instance

spp - is the ShowPlotPopup instance

titlePanel - is where to put extra stuff

tree - is the HierClustNode cluster tree

orderedCL - is thegene list to use

title - for window

plotMode - is the specific plot mode to implement

keepFlagsOnClosing - to save flags on closing

See Also:

ClusterGramCanvas, Filter.showNbrFilteredGenes(), StatusCanvas, Util.showMsg(java.lang.String), Component.repaint()

Method Detail

addButtonsToParent

void addButtonsToParent(ShowPlotPopup spp,
                        java.awt.Panel p,
                        java.awt.Font bFont)

addButtonsToParent() - add buttons for this plot to parents's panel

Parameters:

spp - is the ShowPlotPopup instance

p - is panel where to put extra stuff

bFont - is font to use

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Container

Returns:

window size

getMinimumSize

public java.awt.Dimension getMinimumSize()

getMinimumSize() - get the minimum preferred size

Overrides:

getMinimumSize in class java.awt.Container

Returns:

window size

paint

public void paint()

paint() - redraw clustergram

Parameters:

g - is graphics context

See Also:

Component.repaint(), updateCGplot(GeneList, HierClustNode)

updateCurGene

void updateCurGene(int mid)

updateCurGene()- update the current gene in the ClusterGram

Parameters:

mid - is the Master Gene Index if not -1

See Also:

ClusterGramCanvas.updateCurGene(int), Component.repaint()

updateCGplot

void updateCGplot(GeneList orderedCL,
                  HierClustNode tree)

updateCGplot() - update ClusterGram plots using new GeneList. Set the mae.fc.workingCL if the specified list is null.

Parameters:

orderedCL - is thegene list to use

tree - is the HierClustNode cluster tree

See Also:

ClusterGramCanvas.updateData(GeneList, HierClustNode)

close

void close()

close() - close this popup and reset flags if keepFlagsOnClosing is false

See Also:

EventMenu.setClusterDisplayState(java.awt.CheckboxMenuItem, boolean)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

actionPerformed() - Handle button clicks

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - is button pressed event

See Also:

ClusterGramCanvas.drawGifFile(java.lang.String), Component.repaint(), EventMenu.promptFileName(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean), Component.repaint(), Report, SampleSets.showHP_E_assignmentsPopup(), ShowExprProfilesPopup, Util.rmvFinalSubDirectory(java.lang.String, java.lang.String, boolean), Util.nextZoomMag(int, int), Util.saveCmdHistory(java.lang.String), Component.repaint(), close()

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

windowClosing

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

windowClosing() - closing down the window, get rid of the frame.

Specified by:

windowClosing in interface java.awt.event.WindowListener

Parameters:

e - is window closing event

See Also:

Window.dispose()

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

Pass all mouse events down to the Canvas.

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

mouseReleased() - Pass all mouse events down to the Canvas.

Specified by:

mouseReleased in interface java.awt.event.MouseListener

Parameters:

e - is button released event

See Also:

ClusterGramCanvas.setCurrentGene(int, int, int, boolean)

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)

Specified by:

mouseExited in interface java.awt.event.MouseListener

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)

mouseMoved() - process mouse event

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

Parameters:

e - is button moved event

windowOpened

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

Specified by:

windowOpened in interface java.awt.event.WindowListener

windowActivated

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

Specified by:

windowActivated in interface java.awt.event.WindowListener

windowClosed

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

Specified by:

windowClosed in interface java.awt.event.WindowListener

windowDeactivated

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

Specified by:

windowDeactivated in interface java.awt.event.WindowListener

windowDeiconified

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

Specified by:

windowDeiconified in interface java.awt.event.WindowListener

windowIconified

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

Specified by:

windowIconified in interface java.awt.event.WindowListener

drawScaleMapAndVerticalLabels

void drawScaleMapAndVerticalLabels(java.awt.Graphics gGif)

drawScaleMapAndVerticalLabels() - draw scale map & vert lbls i in the title panel status area

Parameters:

gGif - is graphics context