Class ExprProfileOverlay

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Panel
                    |
                    +--ExprProfileOverlay

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.AdjustmentListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

class ExprProfileOverlay

extends java.awt.Panel

implements java.awt.event.AdjustmentListener

This class displays a scrollable expression profile overlay. It extends the Draw2Dplot class and consists of an overlay plot of the expression profiles of genes in the specifimed gene list. Selecting a particular profile sets the current gene and calls the PopupRegistry to update other windows.

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: 1.8 $

Author:

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

See Also:

MAExplorer Home, ExprProfile, ShowPlotPopup, Serialized Form

Inner classes inherited from class java.awt.Panel

java.awt.Panel.AccessibleAWTPanel

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

private Gene	bestGene gene if mouse event
private int	bestHP HP if mouse event
private float	bestIntens intensity if mouse event
private int	bestMid gene clone ID if mouse event
private java.lang.String[]	cTitle titles [0:nGenes-1] "#Master_ID"
(package private) Draw2Dplot	d2dp draw 2D overlay of EP plots
private boolean	doMeanPlotsFlag if plot means and SD
private ExprProfile[]	epOverlayList list of overlay expr.
private GeneList	epOvrLayCL special [nGenes*nHP_E] CL
private java.awt.Panel	epPanel holds g2D overlay plot
private ExprProfilePanel[]	epplList Expr Profs [nGridElements]
private GeneList	exprProfileCL GeneList being used
private boolean	hasMeanPlotsFlag if hpDataXXX[] exists
private float	hLB lower HP sample # to display
private float[][]	hpDataMnA mean[0:nMnGenes-1][0:nHP_E-1]
private int[]	hpDataNbrA # of samples for hpDataXXX[n][]
private float[][]	hpDataSDA S.D.[0:nMnGenes-1][0:nHP_E-1]
private java.awt.Scrollbar	hsL lower bound horizontal scroll bar
private java.awt.Scrollbar	hsU upper bound horizontal scroll bar
private float	hUB upper HP sample # to display
private MAExplorer	mae links to global MAExplorer instance
private int[]	mapPointToMid [nGenes*nHP_E] mid mapping
private float	maxHPdataMn max of hpDataMnA[][] data
private int	maxHsteps # of steps for hsL hsU
private int	maxVsteps # of steps for vsL vsU
private int	mNbr .mList[mNbr] in database to display
private int	nGenes # genes in exprProfileCL
private int	nHP_E # of HPS in an Expr Profile
private int	nMnGenes # of averaged genes ~ nGenes
private int	nPoints nGenes*nHP_E
(package private) int	plotStyleMode plot style mode: 0=line, 1=circle, 2=curve
private int	prevBestMID save previous MID found with mouse
private int[]	propList [nGenes*nHP_E] EP overlay props
private int	sbSize width of scroll bar control
(package private) ShowExprProfilesPopup	sepp Parent window
private boolean	showErrBarsFlag pass through to EP panel
private java.lang.String	title title for entire EP.
private float	vLB lower expression value to display
private java.awt.Scrollbar	vsL lower bound vertical scroll bar
private java.awt.Scrollbar	vsU upper bound vertical scroll bar
private float	vUB upper expression value to display
private float[]	xList [nGenes*nHP_E] EP overlay X coords
private float[]	yList [nGenes*nHP_E] EP overlay Y coords
(package private) int	zoomBarsMag zoom factor: 1X, 2X, 5X, 10X pass through to EP panel

Fields inherited from class java.awt.Panel

base, nameCounter, serialVersionUID

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)

ExprProfileOverlay(MAExplorer mae, ShowExprProfilesPopup sepp, GeneList exprProfileCL, java.lang.String title, int preferredPanelWidth, boolean showKmeansDataFlag) ExprProfileOverlay() - Create popup overlay plot of ExprProfiles.

Method Summary

void	adjustmentValueChanged(java.awt.event.AdjustmentEvent e) adjustmentValueChanged() - handle scroll events and cause a repaint.
(package private) boolean	drawGifFile(java.lang.String oGifFileName) drawGifFile() - draw plot into Gif image file if in standalone mode.
void	mouseHandler(int x, int y, int mouseKeyMods, boolean setCurGeneFlag) mouseHandler() - interact with current 2D plot if a graphic plot.
void	paint(java.awt.Graphics g) paint() - redraw plots near selected row.
private void	setCurGene(int mid) setCurGene() - set current gene from mid if it is not -1.
(package private) void	setEPcanvasDrawingOptions(boolean showErrBarsFlag, int zoomBarsMag, int plotStyleMode) setEPcanvasDrawingOptions() - set err-bar and zoom status and then repaint.
(package private) void	setPlotEPmeansData(int nMnGenes, int[] hpDataNbrA, float[][] hpDataMnA, float[][] hpDataSDA, boolean doMeanPlotsFlag) setPlotEPmeansData() - set expression profile to plot mean data for each panel
private void	showGeneMsgsAndPlot() showGeneMsgsAndPlot() - show quant genomic data messages in MSG and in plot
private void	showGeneOfInterest(int mid, int mouseKeyMods, boolean setCurGeneFlag) showGeneOfInterest() - show quant and genomic data if click on point in plot
(package private) void	updateCurGene(int mid) updateCurGene() - update the current gene in the expression profile plot list
(package private) void	updateData(GeneList exprProfileCL, java.lang.String title) updateData() - update exprression profile scroller with new gene data.

Methods inherited from class java.awt.Panel

, addNotify, constructComponentName, getAccessibleContext

Methods inherited from class java.awt.Container

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

links to global MAExplorer instance

sepp

ShowExprProfilesPopup sepp

Parent window

title

private java.lang.String title

title for entire EP. panel

exprProfileCL

private GeneList exprProfileCL

GeneList being used

nGenes

private int nGenes

# genes in exprProfileCL

sbSize

private int sbSize

width of scroll bar control

prevBestMID

private int prevBestMID

save previous MID found with mouse

mNbr

private int mNbr

.mList[mNbr] in database to display

epOverlayList

private ExprProfile[] epOverlayList

list of overlay expr. profiles

d2dp

Draw2Dplot d2dp

draw 2D overlay of EP plots

epplList

private ExprProfilePanel[] epplList

Expr Profs [nGridElements]

cTitle

private java.lang.String[] cTitle

titles [0:nGenes-1] "#Master_ID"

nHP_E

private int nHP_E

# of HPS in an Expr Profile

nMnGenes

private int nMnGenes

# of averaged genes ~ nGenes

hpDataNbrA

private int[] hpDataNbrA

# of samples for hpDataXXX[n][]

maxHPdataMn

private float maxHPdataMn

max of hpDataMnA[][] data

hpDataMnA

private float[][] hpDataMnA

mean[0:nMnGenes-1][0:nHP_E-1]

hpDataSDA

private float[][] hpDataSDA

S.D.[0:nMnGenes-1][0:nHP_E-1]

showErrBarsFlag

private boolean showErrBarsFlag

pass through to EP panel

doMeanPlotsFlag

private boolean doMeanPlotsFlag

if plot means and SD

hasMeanPlotsFlag

private boolean hasMeanPlotsFlag

if hpDataXXX[] exists

plotStyleMode

int plotStyleMode

plot style mode: 0=line, 1=circle, 2=curve

zoomBarsMag

int zoomBarsMag

zoom factor: 1X, 2X, 5X, 10X pass through to EP panel

epPanel

private java.awt.Panel epPanel

holds g2D overlay plot

hsL

private java.awt.Scrollbar hsL

lower bound horizontal scroll bar

hsU

private java.awt.Scrollbar hsU

upper bound horizontal scroll bar

vsL

private java.awt.Scrollbar vsL

lower bound vertical scroll bar

vsU

private java.awt.Scrollbar vsU

upper bound vertical scroll bar

maxHsteps

private int maxHsteps

# of steps for hsL hsU

maxVsteps

private int maxVsteps

# of steps for vsL vsU

hLB

private float hLB

lower HP sample # to display

hUB

private float hUB

upper HP sample # to display

vLB

private float vLB

lower expression value to display

vUB

private float vUB

upper expression value to display

xList

private float[] xList

[nGenes*nHP_E] EP overlay X coords

yList

private float[] yList

[nGenes*nHP_E] EP overlay Y coords

nPoints

private int nPoints

nGenes*nHP_E

propList

private int[] propList

[nGenes*nHP_E] EP overlay props

mapPointToMid

private int[] mapPointToMid

[nGenes*nHP_E] mid mapping

epOvrLayCL

private GeneList epOvrLayCL

special [nGenes*nHP_E] CL

bestGene

private Gene bestGene

gene if mouse event

bestHP

private int bestHP

HP if mouse event

bestMid

private int bestMid

gene clone ID if mouse event

bestIntens

private float bestIntens

intensity if mouse event

Constructor Detail

ExprProfileOverlay

ExprProfileOverlay(MAExplorer mae,
                   ShowExprProfilesPopup sepp,
                   GeneList exprProfileCL,
                   java.lang.String title,
                   int preferredPanelWidth,
                   boolean showKmeansDataFlag)

ExprProfileOverlay() - Create popup overlay plot of ExprProfiles. Set the Filter.workingCL if the specified list is null.

Parameters:

mae - is the MAExplorer instance

sepp - is the ShowExprProfilesPopup Parent

GeneList - exprProfileCL is thege ne list to use

title - is the window title

preferredPanelWidth - is set by parent Frame if not 0

showKmeansDataFlag - to report Kmeans data else just Master_ID and name

See Also:

Draw2Dplot, ExprProfile, Util.showMsg(java.lang.String), updateData(GeneList, java.lang.String)

Method Detail

drawGifFile

boolean drawGifFile(java.lang.String oGifFileName)

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

Parameters:

oGifFileName - is the full path GIF output file

Returns:

false if unable to generate the image file.

See Also:

Component.repaint()

updateData

void updateData(GeneList exprProfileCL,
                java.lang.String title)

updateData() - update exprression profile scroller with new gene data. This will cause it to repaint as well.

Parameters:

exprProfileCL - is the new list of genes

title - for canvas label

See Also:

Component.repaint()

setEPcanvasDrawingOptions

void setEPcanvasDrawingOptions(boolean showErrBarsFlag,
                               int zoomBarsMag,
                               int plotStyleMode)

setEPcanvasDrawingOptions() - set err-bar and zoom status and then repaint.

Parameters:

showErrBarsFlag - to show error bars in the plot

zoomBarsMag - is the zoom magnification

plotStyleMode - is the style mode as line, circle, curve

See Also:

Component.repaint()

setPlotEPmeansData

void setPlotEPmeansData(int nMnGenes,
                        int[] hpDataNbrA,
                        float[][] hpDataMnA,
                        float[][] hpDataSDA,
                        boolean doMeanPlotsFlag)

setPlotEPmeansData() - set expression profile to plot mean data for each panel

Parameters:

nMnGenes - is the # of averaged genes

hpDataNbrA - is a list of the # samples hpDataXXX[n][]

hpDataMnA - is a list of the mean[0:nMnGenes-1][0:nHP_E-1] data

hpDataSDA - is a list ofthe S.D.[0:nMnGenes-1][0:nHP_E-1] data

doMeanPlotsFlag - if true

See Also:

Component.repaint()

paint

public void paint(java.awt.Graphics g)

paint() - redraw plots near selected row.

Overrides:

paint in class java.awt.Container

Parameters:

g - is graphics context

See Also:

Draw2Dplot.update2Dplot(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, int, int, double, double, double, double, double, double, boolean, boolean, float[], float[], int[], GeneList, int, int[]), GeneBitSet.setItem(int), GeneList, GeneList.clear()

updateCurGene

void updateCurGene(int mid)

updateCurGene() - update the current gene in the expression profile plot list

Parameters:

mid - is the Master Gene Index if not -1

See Also:

PopupRegistry

adjustmentValueChanged

public void adjustmentValueChanged(java.awt.event.AdjustmentEvent e)

adjustmentValueChanged() - handle scroll events and cause a repaint.

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

Parameters:

e - is scroller adjustment event

See Also:

Draw2Dplot.updateScrolledRegion(float, float, float, float), Component.repaint()

mouseHandler

public void mouseHandler(int x,
                         int y,
                         int mouseKeyMods,
                         boolean setCurGeneFlag)

mouseHandler() - interact with current 2D plot if a graphic plot. If get a hit, then display data for the gene. Note: because the plot lives in the ScrollerImageCanvas, there is only ONE plot so can't get into trouble with multiple plots.

Parameters:

x - is x coordinate at mouse event

y - is y coordinate at mouse event

mouseKeyMods - is keyboard status at mouse event

setCurGeneFlag - if true

See Also:

Draw2Dplot.set2DplotSubtitles(java.lang.String, java.lang.String, java.lang.String, java.lang.String), showGeneOfInterest(int, int, boolean), Component.repaint()

setCurGene

private void setCurGene(int mid)

setCurGene() - set current gene from mid if it is not -1.

Parameters:

mid - is the Master Gene Index if not -1

See Also:

CompositeDatabase.setObjCoordFromMID(int, java.lang.Object)

showGeneMsgsAndPlot

private void showGeneMsgsAndPlot()

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

See Also:

Draw2Dplot.set2DplotSubtitles(java.lang.String, java.lang.String, java.lang.String, java.lang.String), GridCoords.cvtGID2str(int, boolean), SpotFeatures.getSpotFeatures(java.awt.Point, MaHybridSample), SpotFeatures.getSpotGenomicData(java.awt.Point, MaHybridSample), Util.showMsg(java.lang.String), Util.showFeatures(java.lang.String, java.lang.String)

showGeneOfInterest

private void showGeneOfInterest(int mid,
                                int mouseKeyMods,
                                boolean setCurGeneFlag)

showGeneOfInterest() - show quant and genomic data if click on point in plot

Parameters:

mid - is the Master Gene Index if not -1

mouseKeyMods - is keyboard status at mouse press event

setCurGeneFlag - if true

See Also:

Component.repaint(), PopupRegistry.chkOtherCurGeneEffects(int, int), setCurGene(int), showGeneMsgsAndPlot(), Component.repaint()