Class MAExplorer

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Panel
                    |
                    +--java.applet.Applet
                          |
                          +--MAExplorer

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.lang.Runnable, java.io.Serializable

public class MAExplorer

extends java.applet.Applet

implements java.lang.Runnable

MicroArray Explorer main() class. See the MAExplorer Reference Manual for the details.

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: 2003/07/23 19:19:32 $ $Revision: 1.127 $

Author:

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

See Also:

MAExplorer Home, Gene, GeneClass, GeneGeneDist, GeneList, GipoTable, GetParams, MaeJavaAPI, MaHybridSample, MaInfoTable, Maps, MenuBarFrame, PopupRegistry, SampleSets, SamplesTable, ScrollableImageCanvas, SpotData, SpotFeatures, StageNames, StateScrollers, Statistics, UserState, Util, Serialized Form

Inner classes inherited from class java.applet.Applet

java.applet.Applet.AccessibleApplet

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

Field Summary

static int	MAX_COND_PARAM maximum number of Condition parameters
static MaeJavaAPI	mja Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

MAExplorer()

Method Summary

void	destroy() destroy() - destroy this class
void	init() init() - allocate,clear state, read PARAMs, build GUI and start things off.
static void	main(java.lang.String[] args) main() - for MAExplorer started by standalone application.
void	paint(java.awt.Graphics g) paint() - generate viewable scrollable pseudoarray image with overlays.
void	run() run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change.
void	start() start() - (re)create GUI if needed, read PARAMs & start run thread.
void	stop() stop() - stop the thread.
void	update(java.awt.Graphics g) update() - redraw graphics

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, layout, list, list, locate, minimumSize, paintComponents, paramString, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, removeNotify, setFont, setLayout, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen, getName, getParent, getPeer, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isFocusTraversable, isLightweight, isOpaque, 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, reshape, 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, wait, wait, wait

Field Detail

MAX_COND_PARAM

public static final int MAX_COND_PARAM

maximum number of Condition parameters

mja

public static MaeJavaAPI mja

Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins

Constructor Detail

MAExplorer

public MAExplorer()

Method Detail

main

public static void main(java.lang.String[] args)

main() - for MAExplorer started by standalone application.

Parameters:

args - is the command line arg list

init

public void init()

init() - allocate,clear state, read PARAMs, build GUI and start things off. Clear state, read PARAMs, build GUI and start things off. This code can be called repeatedly to restart MAExplorer on a difference saCodeBase.

Overrides:

init in class java.applet.Applet

See Also:

Component.repaint(), CompositeDatabase, CompositeDatabase#recalcNorms, CompositeDatabase#setOBJtoGID, Config#getStateParamValues, Config#setupFullpathFilenames, Config#setupPathBase, Condition, DrawPseudoImage, EditedGeneList, EventMenu, EventMenu#setPlotState, Filter, Filter#computeWorkingGeneList, FileIO, Gene, GeneClass, GeneClass#assignGeneNames2StaticGeneList, GeneClass#setCurrentGeneClassName, GeneClass#setupSpecialGeneLists, GeneClass#updateStdGenePartitions, GeneGeneDist, GeneList, GetParams, GipoTable, GipoTable#copyGBCTdataToStaticGeneDB, GipoTable#copyGeneNamesTableFile, GridCoords, MaeJavaAPI, MaeJavaAPI#initStateAndMJAchildren, Maps, MaInfoTable, MenuBarFrame, MenuBarFrame#callAllStartupPlugins, MenuBarFrame#enableMenus, MenuBarFrame#redoMenuBar, Frame.setTitle(java.lang.String), PopupRegistry, SamplesTable, SampleSets, SamplesTable#readListOfSampleNames, Component.repaint(), StageNames, StageNames#getMenuTreeFromSamplesTable, SpotData, SpotFeatures, Statistics, SimpleTable.freeTable(), UserState, Util, Util#chkDirFinalSeparator, Util#getRatioStr, Util#popupDryrotMsgsAndQuit, Util#popupViewer, Util#showMsg, Util#showMsg2, Util#showMsg3, #doAnyLoginsRequired, #clearDynamicState, #destroy2, #destroyStaticState, Applet.getParameter(java.lang.String), #readListOfSampleDataFiles, Component.repaint(), #resetDefaultstate

start

public void start()

start() - (re)create GUI if needed, read PARAMs & start run thread.

Overrides:

start in class java.applet.Applet

stop

public void stop()

stop() - stop the thread.

Overrides:

stop in class java.applet.Applet

run

public void run()

run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change. [2] Check to see if need to garbage collect

Specified by:

run in interface java.lang.Runnable

See Also:

FileIO#logMsgln, PopupRegistry#checkStringPopupTimeouts, Component.repaint(), Util#sleepMsec, destroy(), stop()

paint

public void paint(java.awt.Graphics g)

paint() - generate viewable scrollable pseudoarray image with overlays.

Overrides:

paint in class java.awt.Container

Parameters:

g - is graphics context

See Also:

ArrayScroller#syncScrollerAccess

update

public void update(java.awt.Graphics g)

update() - redraw graphics

Overrides:

update in class java.awt.Container

Parameters:

g - is graphics context

destroy

public void destroy()

destroy() - destroy this class

Overrides:

destroy in class java.applet.Applet

See Also:

#destroy2