Class ExprProfileScrollPane

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

All Implemented Interfaces:

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

class ExprProfileScrollPane

extends java.awt.Panel

implements java.awt.event.AdjustmentListener

This creates and displays a scrollable pane list of individual expression profile graphic plots. It will be shown as a Grid of ExprProfilePanel's plots in popup window. Selecting a particular ExprProfilePanel will set the current gene and call 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: 1.7 $

Author:

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

See Also:

MAExplorer Home, ExprProfilePanel, 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 [0:nGenes-1] "#Master_ID"
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 grid of ExprProfilePanel's
private ExprProfilePanel[]	epplList Expr Profs [nGridElements]
private GeneList	exprProfileCL GeneList being used
private boolean	hasMeanPlotsFlag if hpDataXXX[] exists
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 MAExplorer	mae link to global MAExplorer instance
private float	maxHPdataMn max of hpDataMnA[][] data
private static int	MIN_COLS minimum # of columns for the grid
private static int	MIN_ROWS minimum # of rows for the grid
private int	mNbr .mList[mNbr] in database to display
(package private) int	N_EP_GENES
private int	nCols # of columns in the Grid
private int	nEPgenes # genes to display in popup EP plot
private int	nGenes # genes in exprProfileCL
private int	nGridElements i.e.
private int	nHP_E # of HPS in an Expr Profile
private int	nMnGenes # of averaged genes ~ nGenes
private int	nPoints nGenes*nHP_E
private int	nRows # of rows in the Grid
(package private) int	plotStyleMode plot style mode: 0=line, 1=circle, 2=curve
private int[]	propList [nGenes*nHP_E] EP overlay props
private int	sbSize width of scroll bar control
private ShowExprProfilesPopup	sepp Parent window
private boolean	showErrBarsFlag pass through to EP panel
private java.lang.String	title title for entire EP.
private java.awt.Scrollbar	vs vertical scroll bar
private float[]	xList [nGenes*nHP_E] EP overlay coords
private float[]	yList [nGenes*nHP_E] EP overlay coords
(package private) int	zoomBarsMag 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)

ExprProfileScrollPane(MAExplorer mae, ShowExprProfilesPopup sepp, GeneList exprProfileCL, java.lang.String title, int preferredPanelWidth, boolean showKmeansDataFlag) ExprProfileScrollPane() - Create a popup grid of ExprProfile plots.

Method Summary

void	adjustmentValueChanged(java.awt.event.AdjustmentEvent e) adjustmentValueChanged() - handle scroll events and cause repaint.
void	paint(java.awt.Graphics g) paint() - redraw plots near selected Row.
private void	setCurGene(int mid) setCurGene() - set current gene if mid is not -1
(package private) void	setEPcanvasDrawingOptions(boolean showErrBarsFlag, int zoomBarsMag, int plotStyleMode) setEPcanvasDrawingOptions() - set err-bar & zoom status and then repaint.
(package private) void	setPlotEPmeansData(int nMnGenes, int[] hpDataNbrA, float[][] hpDataMnA, float[][] hpDataSDA, boolean doMeanPlotsFlag) setPlotEPmeansData() - set EP to plot means for each panel
private void	setScrollBarPos(int cNumber) setScrollBarPos() - set the scroll barPosition for this panel.
private void	showGeneOfInterest(int mid, int mouseKeyMods) showGeneOfInterest() - show quant and genomic data if click on a point in plot
(package private) void	updateCurGene(int mid) updateCurGene()- update the current gene in the EP plot list.
(package private) void	updateData(GeneList exprProfileCL, java.lang.String title) updateData() - update expression profile scroller with new gene data.
private void	updateEPtitles() updateEPtitles() - generate array of titles for drawing in expression profile plots

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

link to global MAExplorer instance

MIN_ROWS

private static final int MIN_ROWS

minimum # of rows for the grid

MIN_COLS

private static final int MIN_COLS

minimum # of columns for the grid

sepp

private 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

N_EP_GENES

final int N_EP_GENES

sbSize

private int sbSize

width of scroll bar control

nGridElements

private int nGridElements

i.e. nRows*nCols

nRows

private int nRows

# of rows in the Grid

nCols

private int nCols

# of columns in the Grid

mNbr

private int mNbr

.mList[mNbr] in database to display

nEPgenes

private int nEPgenes

# genes to display in popup EP plot

epOverlayList

private ExprProfile[] epOverlayList

list of overlay expr. profiles

epplList

private ExprProfilePanel[] epplList

Expr Profs [nGridElements]

cTitle

private java.lang.String[] cTitle

[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

1X, 2X, 5X, 10X pass through to EP panel

epPanel

private java.awt.Panel epPanel

holds grid of ExprProfilePanel's

vs

private java.awt.Scrollbar vs

vertical scroll bar

xList

private float[] xList

[nGenes*nHP_E] EP overlay coords

yList

private float[] yList

[nGenes*nHP_E] EP overlay coords

nPoints

private int nPoints

nGenes*nHP_E

propList

private int[] propList

[nGenes*nHP_E] EP overlay props

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

ExprProfileScrollPane

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

ExprProfileScrollPane() - Create a popup grid of ExprProfile plots. Set the Filter.workingCL if the specified list is null.

Parameters:

mae - is MAExplorer instance

sepp - is the ShowExprProfilesPopup Parent

exprProfileCL - is the gene list to use

title - of window

preferredPanelWidth - is the set by parent Frame if not 0

showKmeansDataFlag - is the report Kmeans data else just CloneID and name

See Also:

ExprProfilePanel, Util.showMsg(java.lang.String), updateData(GeneList, java.lang.String)

Method Detail

updateEPtitles

private void updateEPtitles()

updateEPtitles() - generate array of titles for drawing in expression profile plots

updateData

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

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

Parameters:

exprProfileCL - is the new list of genes

title - is the title for the canvas label

See Also:

updateEPtitles(), Component.repaint()

setEPcanvasDrawingOptions

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

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

Parameters:

showErrBarsFlag - is used if their is duplicate data

zoomBarsMag - magnification factor (1,2,5,10,20) for expression data

plotStyleMode - (line, circle, curve)

See Also:

Component.repaint()

setPlotEPmeansData

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

setPlotEPmeansData() - set EP to plot means for each panel

Parameters:

nMnGenes - is the # of averaged genes

hpDataNbrA - is the # samples hpDataXXX[n][]

hpDataMnA - is the mean[0:nMnGenes-1][0:nHP_E-1] expression data

hpDataSDA - is the S.D.[0:nMnGenes-1][0:nHP_E-1] expression data

doMeanPlotsFlag - if plot the mean data

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:

ExprProfilePanel.setPlotEPmeansData(int, int, float, float[], float[], boolean), ExprProfilePanel.updateData(int, java.lang.String, boolean)

updateCurGene

void updateCurGene(int mid)

updateCurGene()- update the current gene in the EP plot list.

Parameters:

mid - is the new Master Gene ID of the current gene

See Also:

Component.repaint()

setScrollBarPos

private void setScrollBarPos(int cNumber)

setScrollBarPos() - set the scroll barPosition for this panel. The arguments are in the range of allowable values otherwise it is a no-op.

Parameters:

cNumber - is data range to be mapped to scroller range

adjustmentValueChanged

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

adjustmentValueChanged() - handle scroll events and cause repaint.

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

Parameters:

e - is scroller adjustment event

See Also:

Component.repaint()

setCurGene

private void setCurGene(int mid)

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

Parameters:

mid - is the new Master Gene ID of the current gene

See Also:

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

showGeneOfInterest

private void showGeneOfInterest(int mid,
                                int mouseKeyMods)

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

Parameters:

mid - is the new Master Gene ID of the current gene

mouseKeyMods - is SHIFT or CONTROL key modifiers if not 0

See Also:

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