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 and Djamel Medjahed (SAIC-Frederick). 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.

Version:

$Date: 2002/10/14 20:17:17 $ $Revision: $

Author:

P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD

See Also:

ProtPlot Home

This work was derived from prpxplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://prpxplorer.sourceforge.org/, ExprProfilePanel, 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 float	bestIntens intensity if mouse event
private int	bestMid gene clone ID if mouse event
private int	bestProtein gene if mouse event
private int	bestSample Sample if mouse event
private java.lang.String[]	cTitle [0:nProteins-1] "#MasterProtein_ID"
private ExprProfile[]	epOverlayList list of overlay expr.
private java.awt.Panel	epPanel holds grid of ExprProfilePanel's
private ExprProfilePanel[]	epplList Expr Profs [nGridElements]
private int[]	mEPprotList List of mPids being used for EP panel
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_PROTEINS
private int	nCols # of columns in the Grid
private int	nEPproteins # genes to display in popup EP plot
private int	nGridElements i.e.
private int	nHP_E # of HPS in an Expr Profile
private int	nPoints nProteins*nHP_E
private int	nProteins # genes in exprProfileCL
private int	nRows # of rows in the Grid
(package private) int	plotStyleMode plot style mode: 0=line, 1=circle, 2=curve
private ProtPlot	prp link to global ProtPlot instance
private int	sbSize width of scroll bar control
private ShowExprProfilesPopup	sepp Parent window
private java.lang.String	title title for entire EP.
private UtilPRP	util
private java.awt.Scrollbar	vs vertical scroll bar
private float[]	xList [nProteins*nHP_E] EP overlay coords
private float[]	yList [nProteins*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(ProtPlot prp, ShowExprProfilesPopup sepp, java.lang.String title, int[] mEPprotList, int nProteins, int preferredPanelWidth) 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	setCurProtein(int mPid) setCurProtein() - set current protein if mPid is not -1
(package private) void	setEPcanvasDrawingOptions(int zoomBarsMag, int plotStyleMode) setEPcanvasDrawingOptions() - set err-bar & zoom status and then repaint.
private void	setScrollBarPos(int cNumber) setScrollBarPos() - set the scroll barPosition for this panel.
(package private) void	updateCurProtein(int mPid) updateCurProtein()- update the current protein in the EP plot list.
(package private) void	updateData(int[] mEPprotList, int nProteins, java.lang.String title) updateData() - update expression profile scroller with new protein 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

prp

private ProtPlot prp

link to global ProtPlot instance

util

private UtilPRP util

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

mEPprotList

private int[] mEPprotList

List of mPids being used for EP panel

nProteins

private int nProteins

# genes in exprProfileCL

N_EP_PROTEINS

final int N_EP_PROTEINS

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

nEPproteins

private int nEPproteins

# 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:nProteins-1] "#MasterProtein_ID"

nHP_E

private int nHP_E

# of HPS in an Expr Profile

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

[nProteins*nHP_E] EP overlay coords

yList

private float[] yList

[nProteins*nHP_E] EP overlay coords

nPoints

private int nPoints

nProteins*nHP_E

bestProtein

private int bestProtein

gene if mouse event

bestSample

private int bestSample

Sample 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(ProtPlot prp,
                      ShowExprProfilesPopup sepp,
                      java.lang.String title,
                      int[] mEPprotList,
                      int nProteins,
                      int preferredPanelWidth)

ExprProfileScrollPane() - Create a popup grid of ExprProfile plots. Display proteins in the specified mPidList[]

Parameters:

prp - is ProtPlot instance

sepp - is the ShowExprProfilesPopup Parent

title - of window

mEPprotList - is an array of mPids to use

nProteins - is the size of mPidList[0:nProteins-1] to

preferredPanelWidth - is the set by parent Frame if not 0

See Also:

ExprProfilePanel, Util#showMsg, updateData(int[], int, java.lang.String)

Method Detail

updateEPtitles

private void updateEPtitles()

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

updateData

void updateData(int[] mEPprotList,
                int nProteins,
                java.lang.String title)

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

Parameters:

mEPprotList - is the new list of mPid proteins to scroll

nProteins - is the number of proteins to scroll

title - is the title for the canvas label

See Also:

updateEPtitles(), Component.repaint()

setEPcanvasDrawingOptions

void setEPcanvasDrawingOptions(int zoomBarsMag,
                               int plotStyleMode)

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

Parameters:

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

plotStyleMode - (line, circle, curve)

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, ExprProfilePanel.updateData(int, java.lang.String, boolean)

updateCurProtein

void updateCurProtein(int mPid)

updateCurProtein()- update the current protein in the EP plot list.

Parameters:

mPid - is the new Master Protein ID of the current protein

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()

setCurProtein

private void setCurProtein(int mPid)

setCurProtein() - set current protein if mPid is not -1

Parameters:

mPid - is the new Master Protein ID of the current protein