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.

Version:

$Date: 2002/10/14 20:44:21 $ $Revision $

Author:

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

See Also:

ProtPlot 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) 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) int[]	mEPprotList Master Protein List being used for EP plots
(package private) int	nProteins # of genes in expression profile
(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
(package private) int	popupPropertyBits ARG: for PopupRegistry
(package private) ProtPlot	prp
(package private) boolean	showFilteredLinesFlag
(package private) java.lang.String	title ARG: for PopupRegistry
private UtilPRP	util link to global instance
(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(ProtPlot prp, int[] mEPprotList, int nProteins, java.lang.String title, boolean useLargeFrameFlag) ShowExprProfilesPopup() - Constructor.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) actionPerformed() - Handle button clicks
(package private) void	close() close() - close this popup
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	updateCurProtein(int mPid) updateCurProtein() - update expression profile plot list if current protein changed and this type of string report requires it.
(package private) void	updateEPplots(int[] mEPplotList, int nProteins) updateEPplots() - update expression profile plots using new GeneList.
(package private) void	updateFilter(int[] mEPprotList, int nProteins, java.lang.String title) updateFilter() - update expression profile plots using new protein list.
(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
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

prp

ProtPlot prp

util

private UtilPRP util

link to global instance

popupName

java.lang.String popupName

popupPropertyBits

int popupPropertyBits

ARG: for PopupRegistry

title

java.lang.String title

ARG: for PopupRegistry

epsp

ExprProfileScrollPane epsp

scrollable panel of ExprProfilePanel's

epPane

java.awt.ScrollPane epPane

Scrollable panel

gp

java.awt.Panel gp

Grid panel

mEPprotList

int[] mEPprotList

Master Protein List being used for EP plots

nProteins

int nProteins

# of genes in expression profile

frameWidth

int frameWidth

this frame size computed

frameHeight

int frameHeight

this frame size computed

epspStatusLabel

java.awt.Label epspStatusLabel

closeButton

java.awt.Button closeButton

plotStyleButton

java.awt.Button plotStyleButton

zoomBarsButton

java.awt.Button zoomBarsButton

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

showFilteredLinesFlag

boolean showFilteredLinesFlag

Constructor Detail

ShowExprProfilesPopup

ShowExprProfilesPopup(ProtPlot prp,
                      int[] mEPprotList,
                      int nProteins,
                      java.lang.String title,
                      boolean useLargeFrameFlag)

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

Parameters:

prp - is the ProtPlot instance

mEPprotList - is the mPid list instance to use in mEPprotList[0:nProteins-1]

nProteins - is the number of proteins to use.

title - of plot

useLargeFrameFlag - if need it for more samples

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:

ExprProfileOverlay#repaint, Component.repaint()

updateEPplots

void updateEPplots(int[] mEPplotList,
                   int nProteins)

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()

close() - close this popup

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

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

updateCurProtein

void updateCurProtein(int mPid)

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

Parameters:

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

updateFilter

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

updateFilter() - update expression profile plots using new protein list.

Parameters:

mEPprotList - is list of mPids to plot

nProteins - size of nEPprotList to use

updateSlider

void updateSlider()

updateSlider() - update expression profile plot list if Slider changed

updateLabels

void updateLabels()

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