Class ShowExprProfilesPopup

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--ShowExprProfilesPopup

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.io.Serializable, java.awt.event.WindowListener

class ShowExprProfilesPopup

extends java.awt.Frame

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

The class pops up a window to display a list of expression profiles for the data filtered genes.

 There are two ways to display the list of genes: 
    (1) a scrollable list of Expression Profile plots, 
    (2) an overlay expression profile plot.
 

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 21:40:40 $ $Revision: 1.7 $

Author:

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

See Also:

MAExplorer Home, Serialized Form

Inner classes inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Inner classes inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

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) java.awt.Button	closeButton
(package private) ExprProfileOverlay	epov Overlay EP plots
(package private) java.awt.ScrollPane	epPane Scrollable panel
(package private) ExprProfileScrollPane	epsp scrollable panel of ExprProfilePanel's
(package private) java.awt.Label	epspStatusLabel
(package private) int	frameHeight this frame size computed
(package private) int	frameWidth this frame size computed
(package private) java.awt.Panel	gp Grid panel
(package private) boolean	hasMeanPlotsFlag Flag indicating that mean values should be plotted
(package private) float[][]	hpDataMnA opt.
(package private) int[]	hpDataNbrA opt.
(package private) float[][]	hpDataSDA opt.S.D.
(package private) MAExplorer	mae
(package private) GeneList	mlToUse Master GeneList being used
(package private) java.awt.Checkbox	mouseOverCheckBox
(package private) int	nGenes # of genes in expression profile
(package private) int	nMnGenes # of mean nodes
(package private) java.awt.Button	plotStyleButton
(package private) int	plotStyleMode Mode for plotting points in the expr profile where: 0=(bar) line, 1=circle, 2=curve
(package private) java.lang.String	popupName link to global instance
(package private) int	popupPropertyBits ARG: for PopupRegistry
(package private) java.awt.Button	saveAsButton
(package private) java.awt.Button	showEGLButton
(package private) boolean	showEGLlinesFlag
(package private) java.awt.Checkbox	showErrBarsCheckBox
(package private) boolean	showErrBarsFlag Flag allowing the plotting of error bars
(package private) java.awt.Button	showFilteredLinesButton
(package private) boolean	showFilteredLinesFlag
(package private) java.lang.String	title ARG: for PopupRegistry
(package private) java.awt.Button	zoomBarsButton
(package private) int	zoomBarsMag data magnification 1X, 2X, 5X, 10X, 20X

Fields inherited from class java.awt.Frame

base, CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, frameSerializedDataVersion, HAND_CURSOR, icon, ICONIFIED, mbManagement, menuBar, MOVE_CURSOR, N_RESIZE_CURSOR, nameCounter, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, ownedWindows, resizable, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, serialVersionUID, state, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR, weakThis

Fields inherited from class java.awt.Window

active, dbg, focusMgr, inputContext, inputContextLock, OPENED, ownedWindowList, showWithParent, warningString, windowListener, windowSerializedDataVersion

Fields inherited from class java.awt.Container

component, containerListener, containerSerializedDataVersion, 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)

ShowExprProfilesPopup(MAExplorer mae, GeneList mlToUse, int[] hpDataNbrA, float[][] hpDataMnA, float[][] hpDataSDA, int nMnGenes, boolean hasMeanPlotsFlag, java.lang.String title, java.lang.String popupName, int popupPropertyBits, boolean useEPoverlayFlag, boolean useLargeFrameFlag, boolean showKmeansDataFlag) ShowExprProfilesPopup() - Constructor.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
(package private) void	close(boolean keepFlags) close() - close this popup and reset flags if needed
java.awt.Dimension	getPreferredSize() getPreferredSize() - get the preferred size
void	itemStateChanged(java.awt.event.ItemEvent e)
void	paint(java.awt.Graphics g) paint() - repaint by causes the ExprProfileScrollPane to repaint.
(package private) void	setPlotEPclusterMeansData(boolean doMeanPlotsFlag) setPlotEPclusterMeansData() - set expression profile to plot Cluster means data
(package private) void	updateCurGene(int mid) updateCurGene() - update expression profile plot list if current gene changed and this type of string report requires it.
(package private) void	updateEPplots(GeneList mlToUse) updateEPplots() - update expression profile plots using new GeneList.
(package private) void	updateFilter(GeneList ml) updateFilter() - update expression profile plots using new GeneList ml.
(package private) void	updateLabels() updateLabels() - update string report if labels changed and this type of plot requires it.
(package private) void	updateSlider() updateSlider() - update expression profile plot list if Slider changed and Filter.workingCL is the current EP list.
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.Frame

, addNotify, addToFrameList, constructComponentName, finalize, getAccessibleContext, getCursorType, getFrames, getIconImage, getMenuBar, getState, getTitle, initIDs, isResizable, paramString, postProcessKeyEvent, readObject, remove, removeFromFrameList, removeNotify, setCursor, setIconImage, setMenuBar, setResizable, setState, setTitle, writeObject

Methods inherited from class java.awt.Window

addOwnedWindow, addWindowListener, adjustListeningChildren, applyResourceBundle, applyResourceBundle, connectOwnedWindow, dispatchEventImpl, dispose, eventEnabled, getFocusOwner, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getOwnedWindows, getOwner, getToolkit, getWarningString, hide, isActive, isShowing, nextFocus, ownedInit, pack, postEvent, postWindowEvent, preProcessKeyEvent, processEvent, processWindowEvent, removeOwnedWindow, removeWindowListener, resetGC, setCursor, setFocusOwner, setWarningString, show, toBack, toFront, transferFocus

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventToSelf, doLayout, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getMaximumSize, getMinimumSize, getMouseEventTarget, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paintComponents, paintHeavyweightComponents, postsOldMouseEvents, preferredSize, print, printComponents, printHeavyweightComponents, processContainerEvent, proxyEnableEvents, proxyRequestFocus, remove, remove, removeAll, removeContainerListener, setFont, setLayout, update, validate, validateTree

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, getHeight, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

mae

MAExplorer mae

popupName

java.lang.String popupName

link to global instance

popupPropertyBits

int popupPropertyBits

ARG: for PopupRegistry

title

java.lang.String title

ARG: for PopupRegistry

epov

ExprProfileOverlay epov

Overlay EP plots

epsp

ExprProfileScrollPane epsp

scrollable panel of ExprProfilePanel's

epPane

java.awt.ScrollPane epPane

Scrollable panel

gp

java.awt.Panel gp

Grid panel

mlToUse

GeneList mlToUse

Master GeneList being used

nGenes

int nGenes

# of genes in expression profile

frameWidth

int frameWidth

this frame size computed

frameHeight

int frameHeight

this frame size computed

epspStatusLabel

java.awt.Label epspStatusLabel

mouseOverCheckBox

java.awt.Checkbox mouseOverCheckBox

showErrBarsCheckBox

java.awt.Checkbox showErrBarsCheckBox

closeButton

java.awt.Button closeButton

plotStyleButton

java.awt.Button plotStyleButton

zoomBarsButton

java.awt.Button zoomBarsButton

showEGLButton

java.awt.Button showEGLButton

showFilteredLinesButton

java.awt.Button showFilteredLinesButton

saveAsButton

java.awt.Button saveAsButton

showErrBarsFlag

boolean showErrBarsFlag

Flag allowing the plotting of error bars

hasMeanPlotsFlag

boolean hasMeanPlotsFlag

Flag indicating that mean values should be plotted

plotStyleMode

int plotStyleMode

Mode for plotting points in the expr profile where: 0=(bar) line, 1=circle, 2=curve

zoomBarsMag

int zoomBarsMag

data magnification 1X, 2X, 5X, 10X, 20X

hpDataNbrA

int[] hpDataNbrA

opt. # data @ each gene avg

hpDataMnA

float[][] hpDataMnA

opt. Mean data @ each HP sample

hpDataSDA

float[][] hpDataSDA

opt.S.D. @ each HP sample

nMnGenes

int nMnGenes

# of mean nodes

showEGLlinesFlag

boolean showEGLlinesFlag

showFilteredLinesFlag

boolean showFilteredLinesFlag

Constructor Detail

ShowExprProfilesPopup

ShowExprProfilesPopup(MAExplorer mae,
                      GeneList mlToUse,
                      int[] hpDataNbrA,
                      float[][] hpDataMnA,
                      float[][] hpDataSDA,
                      int nMnGenes,
                      boolean hasMeanPlotsFlag,
                      java.lang.String title,
                      java.lang.String popupName,
                      int popupPropertyBits,
                      boolean useEPoverlayFlag,
                      boolean useLargeFrameFlag,
                      boolean showKmeansDataFlag)

ShowExprProfilesPopup() - Constructor. Create popup grid of expression profile plots. Set the Filter.workingCL if the specified list is null.

Parameters:

mae - is the MAExplorer instance

mlToUse - is the GeneList instance to use. If null, use fc.workingCL

hpDataNbrA - is the opt. # data @ each gene average

hpDataMnA - is the opt. Mean data @ each HP sample

hpDataSDA - is the opt.S.D. @ each HP sample

nMnGenes - is the # of mean nodes

hasMeanPlotsFlag - to compute the means for each sample

title - of plot

popupName - is the name for PopupRegistry

popupPropertyBits - are the property bits for PopupRegistry

useEPoverlayFlag - to display overlay 2Dplot else scrollable Grid of EPs

useLargeFrameFlag - if need it for more samples

showKmeansDataFlag - /* report Kmeans data else just CloneID and name

See Also:

ExprProfileOverlay, Component.repaint(), ExprProfileOverlay.setEPcanvasDrawingOptions(boolean, int, int), ExprProfileOverlay.setPlotEPmeansData(int, int[], float[][], float[][], boolean), ExprProfileOverlay.updateCurGene(int), ExprProfileScrollPane, Component.repaint(), ExprProfileScrollPane.setEPcanvasDrawingOptions(boolean, int, int), ExprProfileScrollPane.setPlotEPmeansData(int, int[], float[][], float[][], boolean), ExprProfileScrollPane.updateCurGene(int), Filter.showNbrFilteredGenes(), PopupRegistry.addPopupWindowToReg(ShowPlotPopup, java.lang.String, int), PopupRegistry.removePopupByKey(java.lang.String), Util.showMsg(java.lang.String), Util.showMsg3(java.lang.String)

Method Detail

getPreferredSize

public java.awt.Dimension getPreferredSize()

getPreferredSize() - get the preferred size

Overrides:

getPreferredSize in class java.awt.Container

Returns:

preferred size as a Dimension instance

paint

public void paint(java.awt.Graphics g)

paint() - repaint by causes the ExprProfileScrollPane to repaint.

Overrides:

paint in class java.awt.Container

Parameters:

g - is the Graphics instance

See Also:

Component.repaint(), Component.repaint()

setPlotEPclusterMeansData

void setPlotEPclusterMeansData(boolean doMeanPlotsFlag)

setPlotEPclusterMeansData() - set expression profile to plot Cluster means data

Parameters:

doMeanPlotsFlag - compute expression profile means else no-op

See Also:

ExprProfileOverlay.setPlotEPmeansData(int, int[], float[][], float[][], boolean), ExprProfileScrollPane.setPlotEPmeansData(int, int[], float[][], float[][], boolean)

updateEPplots

void updateEPplots(GeneList mlToUse)

updateEPplots() - update expression profile plots using new GeneList. Use the Filter.workingCL if the specified list is null.

Parameters:

mlToUse - if specified, else use fc.workingCL

close

void close(boolean keepFlags)

close() - close this popup and reset flags if needed

Parameters:

keepFlags - (ignored for now)

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 ActionEvent for buttons in control panel

See Also:

EventMenu.promptFileName(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean), ExprProfileOverlay.drawGifFile(java.lang.String), Component.repaint(), ExprProfileOverlay.setEPcanvasDrawingOptions(boolean, int, int), ExprProfileScrollPane.setEPcanvasDrawingOptions(boolean, int, int), SampleSets.showHP_E_assignmentsPopup(), Util.nextZoomMag(int, int), Util.rmvFinalSubDirectory(java.lang.String, java.lang.String, boolean), Util.saveCmdHistory(java.lang.String)

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

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

updateCurGene

void updateCurGene(int mid)

updateCurGene() - update expression profile plot list if current gene changed and this type of string report requires it.

Parameters:

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

See Also:

ExprProfileOverlay.updateCurGene(int), ExprProfileScrollPane.updateCurGene(int)

updateFilter

void updateFilter(GeneList ml)

updateFilter() - update expression profile plots using new GeneList ml. Use the Filter.workingCL if the specified list is null.

Parameters:

ml - is the gene list to update now that filter has changed.

See Also:

ExprProfileOverlay.updateData(GeneList, java.lang.String), ExprProfileScrollPane.updateData(GeneList, java.lang.String)

updateSlider

void updateSlider()

updateSlider() - update expression profile plot list if Slider changed and Filter.workingCL is the current EP list.

See Also:

ExprProfileOverlay.updateData(GeneList, java.lang.String), ExprProfileScrollPane.updateData(GeneList, java.lang.String)

updateLabels

void updateLabels()

updateLabels() - update string report if labels changed and this type of plot requires it.