Class EventMenu

java.lang.Object
  |
  +--EventMenu
All Implemented Interfaces:
java.io.FilenameFilter

class EventMenu
extends java.lang.Object
implements java.io.FilenameFilter

Event handler class to process menubar Menu selection and menu checkbox events. It contains various other methods used to support the interpretation of these events and support the data structures. Some of these methods will ensure radio-button behavior of the ganged checkbox menu items. It updates global state flags and invokes various methods to perform the operation.

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: 2003/07/15 20:31:01 $ $Revision: 1.53 $
Author:
P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD
See Also:
MAExplorer Home, MenuBarFrame

Field Summary
private static Condition cdList
          link to global Condition instance
private static Config cfg
          link to global Config instance
private static Filter fc
          link to global Filter instance
private static GeneClass gct
          link to global GeneClass instance
private static MAExplorer mae
          link to global MAExplorer instance
private static MenuBarFrame mbf
          link to global MenuBarFrame instance
private static java.lang.String newDir
          new project directory if any if not null
private static GeneBitSet normCLbitSet
          link to global instanceof normalization GeneBitSet
private static java.awt.CheckboxMenuItem oldItem
          previous array display mode
private static MaHybridSample oldMS
          save old value of MaHybridSample mae.ms
private static PopupCondChooser oldPCC
          old PopupCondChooser to be closed if open up a new one without closing the first.
private static int oldPlotMode
          save old value of mae.plotModeImage
private static PopupOrderedCondChooser oldPOCC
          old PopupOrderedCondChooser to be closed if open up a new one without closing the first.
private static java.lang.String promptDir
          last prompted directory for popup dialog
private static java.lang.String promptExt
          for FilenameFilter file extension for popup dialog
private static java.lang.String promptFile
          last prompted file for popup dialog
private static java.lang.String promptProject
          last prompted project for popup dialog
private static PopupRegistry pur
          link to global PopupRegistry instance
(package private) static ShowStringPopup rloPopup
          RLO report popup if it exists
private static StateScrollers stateScr
          link to global StateScrollers instance
private static boolean useArgListFlag
          processing by eval method not GUI.
private static Util util
          link to global Util instance
private static GeneBitSet wkCLbitSet
          link to global instance of working GeneBitSet
private static GeneList workingCL
          link to global instance of working GeneList
 
Constructor Summary
(package private) EventMenu(MAExplorer mae)
          EventMenu() - constructor for event menu instance
 
Method Summary
 boolean accept(java.io.File dir, java.lang.String name)
          accept() - filter used to test if file should be in directory list.
(package private) static boolean changeDefSample(int sn, boolean rmvCmd)
          changeDefSample() - switch to new msList[i] hybridized sample list
(package private)  void changeProjDir(java.lang.String pName, java.lang.String pDir)
          changeProjDir() - change the project name and path.
(package private)  void cleanup()
          cleanup() - cleanup global static allocated variables in this class.
(package private) static boolean clearClusterDisplayState(java.awt.CheckboxMenuItem item)
          clearClusterDisplayState() - clear cluster display checkbox state.
static boolean handleActions(java.awt.event.ActionEvent e)
          handleActions() - handle menu item events (stateless command).
static void handleCheckboxStateChanged(java.awt.event.ItemEvent e)
          handleCheckboxStateChanged() - handle check box item state changed events.
static void handleItemStateChanged(java.awt.event.ItemEvent e)
          handleItemStateChanged() - handle checkbox menu item state changed events.
(package private) static boolean invokeMenuEntryByName(java.lang.String cmd, int forceStateFlag)
          invokeMenuEntryByName() - process the menu command by name.
(package private) static boolean invokeMenuEntryByName(java.lang.String cmd, int forceStateFlag, java.lang.String[] argList)
          invokeMenuEntryByName() - process the menu command by name with extra argList.
(package private) static boolean notAvailableYet()
          notAvailableYet() - print "Not available yet".
static void openNewMaeDB(java.lang.String optDefDir, java.lang.String optFileName)
          openNewMaeDB() - open new .mae file DB browser & select file.
private static void openNewWebDB(java.lang.String optURL)
          openNewWebDB() - open new Web database after closing the old one
(package private) static boolean processActionEventByName(java.lang.String actCmd, java.lang.String[] argList)
          processActionEventByName() - process Menu item events only...
(package private) static boolean processCheckboxMenuItemStateChangedByitem(java.awt.CheckboxMenuItem item, java.lang.String itemName)
          processCheckboxMenuItemStateChangedByitem() - process CheckboxMenuItem state changed events by item.
(package private) static boolean processCheckboxStateChangedByItem(java.awt.Checkbox cbItem, java.lang.String cbItemName)
          processCheckboxStateChangedByItem() - handle checkbox menu item state changed events.
(package private) static boolean processRLO(java.lang.String actCmd)
          processRLO() - process the "RLO:RscriptName" actions to invoke the R script
(package private) static boolean processSetHP(java.lang.String actCmd)
          processSetHP() - process the "HP_xxx:sample" actions to modify the HP-X, HP-Y, and HP-E lists and current sample.
(package private) static java.lang.String promptFileName(java.lang.String msg, java.lang.String useDir, java.lang.String initialFile, java.lang.String subDir, java.lang.String fileExt, boolean saveMode, boolean useFileDialog)
          promptFileName() - dialog prompt for file name.
private static void promptSaveAsMaeDB(boolean alwaysSaveFlag, boolean saveAllsamplesFlag)
          promptSaveAsMaeDB() - prompt SaveAs current .mae DB Optionally:
(package private) static boolean setClusterDisplayState(java.awt.CheckboxMenuItem item, boolean defaultFlag)
          setClusterDisplayState() - set the cluster display checkbox state.
private static void setCVmodeState(java.awt.CheckboxMenuItem item)
          setCVmodeState() - set theCV mode checkbox state.
private static void setCy3Cy5RatioRangeState(java.awt.CheckboxMenuItem item)
          setCy3Cy5RatioRangeState() - set the Cy3/Cy5 Ratio Range checkbox state.
private static void setDetValueSpotModeState(java.awt.CheckboxMenuItem item)
          setDetValueSpotModeState() - set the Spot detection value data mode checkbox state.
private static void setEditState(java.awt.CheckboxMenuItem item)
          setEditState() - set the edit checkbox state.
private static void setGoodSpotModeState(java.awt.CheckboxMenuItem item)
          setGoodSpotModeState() - set the Good Spot data mode checkbox state.
(package private) static void setIntensityCompareModeSlider(int newCompareMode)
          setIntensityCompareModeSlider() - set intensity compare mode Percent SI slider
private static void setIntensityRangeState(java.awt.CheckboxMenuItem item)
          setIntensityRangeState() - set the Intensity Range checkbox state.
private static boolean setNormalizationState(java.awt.CheckboxMenuItem item, java.lang.String methodName)
          setNormalizationState() - set the normalization checkbox state.
(package private) static void setNormalizationStateFromPlugin(java.lang.String normMethodName)
          setNormalizationStateFromPlugin() - set normalization state from MAEPlugin
(package private) static void setPlotState(java.awt.CheckboxMenuItem item)
          setPlotState() - set the Plot checkbox state.
private static void setPosQuantModeState(java.awt.CheckboxMenuItem item)
          setPosQuantModeState() - set the Postive Quant data mode checkbox state.
private static void setRatioRangeState(java.awt.CheckboxMenuItem item)
          setRatioRangeState() - set the Ratio Range checkbox state.
private static void setReportFontSizeState(java.awt.CheckboxMenuItem item)
          setReportFontSizeState() - set the Report Font Size checkbox state.
private static void setReportFormatState(java.awt.CheckboxMenuItem item)
          setReportFormatState() - set the Report Format checkbox state.
private static void setSIcompareModeState(java.awt.CheckboxMenuItem item)
          setSIcompareModeState() - set the spot intensity compare mode checkbox state.
private static void setSImodeState(java.awt.CheckboxMenuItem item)
          setSImodeState() - set the spot intensity mode checkbox state.
private static void setSIrangeState(java.awt.CheckboxMenuItem item)
          setSIrangeState() - set the spot intensity Range checkbox state.
(package private) static boolean setViewerDisplayState(java.awt.CheckboxMenuItem item, java.lang.String genomicDB)
          setViewerDisplayState() - set the viewer display checkbox state.
(package private) static void setZscoreNormalizationState()
          setZscoreNormalizationState() - set Zscore normalization state and adjust sliders if required.
(package private) static void showCurrentRplots()
          showCurrentRplots() - show plots generated if any with last R eval.
 
Methods inherited from class java.lang.Object
, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait
 

Field Detail

mae

private static MAExplorer mae
link to global MAExplorer instance

mbf

private static MenuBarFrame mbf
link to global MenuBarFrame instance

fc

private static Filter fc
link to global Filter instance

gct

private static GeneClass gct
link to global GeneClass instance

cdList

private static Condition cdList
link to global Condition instance

cfg

private static Config cfg
link to global Config instance

pur

private static PopupRegistry pur
link to global PopupRegistry instance

stateScr

private static StateScrollers stateScr
link to global StateScrollers instance

util

private static Util util
link to global Util instance

newDir

private static java.lang.String newDir
new project directory if any if not null

promptFile

private static java.lang.String promptFile
last prompted file for popup dialog

promptDir

private static java.lang.String promptDir
last prompted directory for popup dialog

promptProject

private static java.lang.String promptProject
last prompted project for popup dialog

promptExt

private static java.lang.String promptExt
for FilenameFilter file extension for popup dialog

workingCL

private static GeneList workingCL
link to global instance of working GeneList

normCLbitSet

private static GeneBitSet normCLbitSet
link to global instanceof normalization GeneBitSet

wkCLbitSet

private static GeneBitSet wkCLbitSet
link to global instance of working GeneBitSet

oldPlotMode

private static int oldPlotMode
save old value of mae.plotModeImage

oldMS

private static MaHybridSample oldMS
save old value of MaHybridSample mae.ms

oldItem

private static java.awt.CheckboxMenuItem oldItem
previous array display mode

useArgListFlag

private static boolean useArgListFlag
processing by eval method not GUI. Use the argList supplied by eval

oldPCC

private static PopupCondChooser oldPCC
old PopupCondChooser to be closed if open up a new one without closing the first.

oldPOCC

private static PopupOrderedCondChooser oldPOCC
old PopupOrderedCondChooser to be closed if open up a new one without closing the first.

rloPopup

static ShowStringPopup rloPopup
RLO report popup if it exists
Constructor Detail

EventMenu

EventMenu(MAExplorer mae)
EventMenu() - constructor for event menu instance
Parameters:
mae - is the MAExplorer instance
Method Detail

setPlotState

static void setPlotState(java.awt.CheckboxMenuItem item)
setPlotState() - set the Plot checkbox state. NOTE may force the plotMode from outside. EG. to pseduo image if no original or vice versa.
Parameters:
item - is a CheckboxMenuItem item for this radio group

setEditState

private static void setEditState(java.awt.CheckboxMenuItem item)
setEditState() - set the edit checkbox state.
Parameters:
item - is a CheckboxMenuItem item for this radio group

setSIrangeState

private static void setSIrangeState(java.awt.CheckboxMenuItem item)
setSIrangeState() - set the spot intensity Range checkbox state. Also revalidate the selected genes since the state is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setIntensityRangeState

private static void setIntensityRangeState(java.awt.CheckboxMenuItem item)
setIntensityRangeState() - set the Intensity Range checkbox state. Also revalidate the selected genes since the state is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setRatioRangeState

private static void setRatioRangeState(java.awt.CheckboxMenuItem item)
setRatioRangeState() - set the Ratio Range checkbox state. Also revalidate the selected genes since the state is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setCy3Cy5RatioRangeState

private static void setCy3Cy5RatioRangeState(java.awt.CheckboxMenuItem item)
setCy3Cy5RatioRangeState() - set the Cy3/Cy5 Ratio Range checkbox state. Also revalidate the selected genes since the state is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setSImodeState

private static void setSImodeState(java.awt.CheckboxMenuItem item)
setSImodeState() - set the spot intensity mode checkbox state. Also revalidate the selected genes if CV mode checking is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setSIcompareModeState

private static void setSIcompareModeState(java.awt.CheckboxMenuItem item)
setSIcompareModeState() - set the spot intensity compare mode checkbox state. Also revalidate the selected genes since the state is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList(), StateScrollers.regenerateScrollers(boolean)

setCVmodeState

private static void setCVmodeState(java.awt.CheckboxMenuItem item)
setCVmodeState() - set theCV mode checkbox state. Also revalidate the selected genes if CV data checking is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setPosQuantModeState

private static void setPosQuantModeState(java.awt.CheckboxMenuItem item)
setPosQuantModeState() - set the Postive Quant data mode checkbox state. Also revalidate the selected genes if Positive Quant data checking is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setGoodSpotModeState

private static void setGoodSpotModeState(java.awt.CheckboxMenuItem item)
setGoodSpotModeState() - set the Good Spot data mode checkbox state. Also revalidate the selected genes if the mode data checking is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setDetValueSpotModeState

private static void setDetValueSpotModeState(java.awt.CheckboxMenuItem item)
setDetValueSpotModeState() - set the Spot detection value data mode checkbox state. Also revalidate the selected genes if the mode data checking is changed.
Parameters:
item - is a CheckboxMenuItem item for this radio group
See Also:
Filter.computeWorkingGeneList()

setReportFormatState

private static void setReportFormatState(java.awt.CheckboxMenuItem item)
setReportFormatState() - set the Report Format checkbox state.
Parameters:
item - is a CheckboxMenuItem item for this radio group

setReportFontSizeState

private static void setReportFontSizeState(java.awt.CheckboxMenuItem item)
setReportFontSizeState() - set the Report Font Size checkbox state.
Parameters:
item - is a CheckboxMenuItem item for this radio group

setViewerDisplayState

static boolean setViewerDisplayState(java.awt.CheckboxMenuItem item,
                                     java.lang.String genomicDB)
setViewerDisplayState() - set the viewer display checkbox state.
Parameters:
item - is a CheckboxMenuItem item for this radio group
genomicDB - is name of the genomic DB for use in msg
See Also:
Util.saveCmdHistory(java.lang.String)

setClusterDisplayState

static boolean setClusterDisplayState(java.awt.CheckboxMenuItem item,
                                      boolean defaultFlag)
setClusterDisplayState() - set the cluster display checkbox state. NOTE: it first clears ALL clustering flags and checkboxes. Also revalidate the cluster method state by calling removePreviousClusterMethod() to close down the current cluster method if it is active. The checkbox is toggled and if if false, it returns the default flag.
Parameters:
item - is the checkbox menu item to set if not null.
defaultFlag - is value to set if checkbox was not selected.
Returns:
the (value of the checkbox OR the defaultFlag value).
See Also:
ClusterGenes.removePreviousClusterMethod(int)

clearClusterDisplayState

static boolean clearClusterDisplayState(java.awt.CheckboxMenuItem item)
clearClusterDisplayState() - clear cluster display checkbox state.
Parameters:
item - is the cluster checkbox menu item to set if not null.
Returns:
true if succeed

setIntensityCompareModeSlider

static void setIntensityCompareModeSlider(int newCompareMode)
setIntensityCompareModeSlider() - set intensity compare mode Percent SI slider
Parameters:
newCompareMode -  

setZscoreNormalizationState

static void setZscoreNormalizationState()
setZscoreNormalizationState() - set Zscore normalization state and adjust sliders if required.

setNormalizationStateFromPlugin

static void setNormalizationStateFromPlugin(java.lang.String normMethodName)
setNormalizationStateFromPlugin() - set normalization state from MAEPlugin
Parameters:
normMethodName - to be specified
See Also:
setNormalizationState(java.awt.CheckboxMenuItem, java.lang.String)

setNormalizationState

private static boolean setNormalizationState(java.awt.CheckboxMenuItem item,
                                             java.lang.String methodName)
setNormalizationState() - set the normalization checkbox state. and toggle the checkbox item in the menu. Also set flag that made change in the state.
Parameters:
item - is a CheckboxMenuItem item for this radio group
methodName - is name of new normalization method
See Also:
MaeJavaAPI.getNormalizationState(), MaeJavaAPI.setNormalizationState(boolean), Util.saveCmdHistory(java.lang.String)

changeDefSample

static boolean changeDefSample(int sn,
                               boolean rmvCmd)
changeDefSample() - switch to new msList[i] hybridized sample list
Parameters:
sn - is the index in the snxxx[] list
rmvCmd - remove sample else add sample
Returns:
true if succeed
See Also:
ArrayScroller.syncScrollerAccess(), MaHybridSample, Util.showMsg3(java.lang.String)

processRLO

static boolean processRLO(java.lang.String actCmd)
processRLO() - process the "RLO:RscriptName" actions to invoke the R script
Parameters:
actCmd - is the action command to process
Returns:
true if succeed
See Also:
#makeMenuItem, #makeSubMenu

showCurrentRplots

static void showCurrentRplots()
showCurrentRplots() - show plots generated if any with last R eval. If there were not plots generated with the last Eval, then it is a no-op. Just say so in the msg area
See Also:
MJAReval#getCurrentRLO, MJAReval.getOutputDataFileNames(), MJAReval.getOutputDataTypes(), MJAReval.getReportBasePath(), MJAUtil#displayPDF, MJAUtil#displayURL, #appendReport, #showGuiMsg

processSetHP

static boolean processSetHP(java.lang.String actCmd)
processSetHP() - process the "HP_xxx:sample" actions to modify the HP-X, HP-Y, and HP-E lists and current sample. Where xxx is either '', 'X+', 'X-', 'Y+', 'Y-', 'E+', 'E-'.
Parameters:
actCmd - is the action command to process
Returns:
true if succeed
See Also:
Filter.computeWorkingGeneList(), HPxyData.setupDataStruct(boolean), MenuBarFrame.setHP_XYlabels(), Component.repaint(), SampleSets.addHPtoXset(MaHybridSample), SampleSets.addHPtoYset(MaHybridSample), SampleSets.addHPtoElist(MaHybridSample), SampleSets.rmvHPfromXset(MaHybridSample), SampleSets.rmvHPfromYset(MaHybridSample), SampleSets.rmvHPfromElist(MaHybridSample), Util.showMsg(java.lang.String), Util.saveCmdHistory(java.lang.String), changeDefSample(int, boolean)

accept

public boolean accept(java.io.File dir,
                      java.lang.String name)
accept() - filter used to test if file should be in directory list. NOTE: implements method for io.FilenameFilter.accept() Checks if the file extension is promptExt
Specified by:
accept in interface java.io.FilenameFilter
Parameters:
dir - is the file directory
name - is the name of the file
Returns:
true if accept it

promptFileName

static java.lang.String promptFileName(java.lang.String msg,
                                       java.lang.String useDir,
                                       java.lang.String initialFile,
                                       java.lang.String subDir,
                                       java.lang.String fileExt,
                                       boolean saveMode,
                                       boolean useFileDialog)
promptFileName() - dialog prompt for file name. If useFileDialog is set use FileDialog else dialogQuery. Set promptFile, and promptDir.
Parameters:
msg - is the prompt msg
useDir - is the opt. dir to use
initialFile - is the opt. initial file
subDir - is theopt. subdir to use
fileExt - is the file extension
saveMode - is the mode. Save if true else open
useFileDialog - if true else query dialog
Returns:
the file name.
See Also:
PopupDialogQuery.dialogQuery(java.lang.String, int)

notAvailableYet

static boolean notAvailableYet()
notAvailableYet() - print "Not available yet". Used as a placeholder for future functionality.
Returns:
true
See Also:
Util.showMsg(java.lang.String)

changeProjDir

void changeProjDir(java.lang.String pName,
                   java.lang.String pDir)
changeProjDir() - change the project name and path. Called by PopupProjDirGuesser "Done" event handler After user exits the popup window.
Parameters:
pName - is the name of the project directory
pdir - is the project directory
See Also:
PopupProjDirGuesser.done(java.lang.String), Util.saveCmdHistory(java.lang.String), Util.showMsg(java.lang.String), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), openNewMaeDB(java.lang.String, java.lang.String), openNewWebDB(java.lang.String)

promptSaveAsMaeDB

private static void promptSaveAsMaeDB(boolean alwaysSaveFlag,
                                      boolean saveAllsamplesFlag)
promptSaveAsMaeDB() - prompt SaveAs current .mae DB Optionally:
  1. prompt if should save
  2. prompt for SaveAs name.
Parameters:
alwaysSaveFlag - always save and don't prompt first
saveAllsamplesFlag - save all samples, else just save the samples in the HP-X, HP-Y 'sets' and HP-E 'list'
See Also:
PopupDialogQuery.dialogQuery(java.lang.String, int), UserState.writeMAEstartupFile(java.lang.String, java.lang.String, boolean)

openNewMaeDB

public static void openNewMaeDB(java.lang.String optDefDir,
                                java.lang.String optFileName)
openNewMaeDB() - open new .mae file DB browser & select file. If mae.defStartupFile.equals(mae.MAE_STARTUP_FILE) then look in MAEprojects.txt for the last "Active-Project" entry. Look in (mae.defDir, mae.defStartupFile) for the file.
Parameters:
dbMAEdir - - full path of the new database MAE/ 'project' directory. E.g. "C:/user/test/MAE/" (with appropriate delimiters for the OS you are using).
maeFilename - - name of the .mae startup file to be started E.g. "Start.mae"
See Also:
MAExplorer.start(), MAExplorer.init(), MAExplorer.stop(), SimpleTable.lookupFieldIdx(java.lang.String), UserState.readMAEstartupFile(java.lang.String, java.lang.String), Util.showMsg(java.lang.String), promptSaveAsMaeDB(boolean, boolean), promptFileName(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean)

openNewWebDB

private static void openNewWebDB(java.lang.String optURL)
openNewWebDB() - open new Web database after closing the old one
Parameters:
optURL - - optional URL to use
See Also:
PopupDialogQuery.dialogQuery(java.lang.String, int), MenuBarFrame.enableMenus(java.lang.String), Component.repaint(), MAExplorer.start(), MAExplorer.init(), MAExplorer.stop(), notAvailableYet()

invokeMenuEntryByName

static boolean invokeMenuEntryByName(java.lang.String cmd,
                                     int forceStateFlag)
invokeMenuEntryByName() - process the menu command by name. This is designed to drive event processing from either client-server, scripts or MAEPlugins.
Parameters:
cmd - to be evaluated (exact spelling)
forceStateFlag - (optional) is set to 1 for true, 0 for false if force a checkbox state otherwise the checkbox state is toggled.
Returns:
true if suceed, false if can't find command in command list
See Also:
processActionEventByName(java.lang.String, java.lang.String[]), processCheckboxMenuItemStateChangedByitem(java.awt.CheckboxMenuItem, java.lang.String), processCheckboxStateChangedByItem(java.awt.Checkbox, java.lang.String)

invokeMenuEntryByName

static boolean invokeMenuEntryByName(java.lang.String cmd,
                                     int forceStateFlag,
                                     java.lang.String[] argList)
invokeMenuEntryByName() - process the menu command by name with extra argList. This is designed to drive event processing from either client-server, scripts or MAEPlugins.
Parameters:
cmd - to be evaluated (exact spelling)
forceStateFlag - (optional) is set to 1 for true, 0 for false if force a checkbox state otherwise the checkbox state is toggled.
argList - is an optional (if not null) arglist that can be used to supply arguments to various commands (eg. file names or database names etc).
Returns:
true if suceed, false if can't find command in command list
See Also:
processActionEventByName(java.lang.String, java.lang.String[]), processCheckboxMenuItemStateChangedByitem(java.awt.CheckboxMenuItem, java.lang.String), processCheckboxStateChangedByItem(java.awt.Checkbox, java.lang.String)

handleActions

public static boolean handleActions(java.awt.event.ActionEvent e)
handleActions() - handle menu item events (stateless command). We split the code using @see #processActionEventByName for actCmd so you can invoke commands via a client-server plugin.
Parameters:
e - is menu item event
See Also:
processActionEventByName(java.lang.String, java.lang.String[])

handleCheckboxStateChanged

public static void handleCheckboxStateChanged(java.awt.event.ItemEvent e)
handleCheckboxStateChanged() - handle check box item state changed events. We split the code
Parameters:
e - is menu checkbox item event
See Also:
for (cbItem, cbName) so you can invoke commands via a client-server plugin., processCheckboxStateChangedByItem(java.awt.Checkbox, java.lang.String)

handleItemStateChanged

public static void handleItemStateChanged(java.awt.event.ItemEvent e)
handleItemStateChanged() - handle checkbox menu item state changed events. We split the code
See Also:
processCheckboxMenuItemStateChangedByitem(java.awt.CheckboxMenuItem, java.lang.String)

processActionEventByName

static boolean processActionEventByName(java.lang.String actCmd,
                                        java.lang.String[] argList)
processActionEventByName() - process Menu item events only... We split the code so you can invoke commands via a client-server plugin.
Parameters:
actCmd - is the menu item action command to process
argList - is an optional (if not null) arglist that can be used to supply arguments to various commands (eg. file names or database names etc).
Returns:
true if succeed.
See Also:
CompositeDatabase.recalcNorms(java.lang.String, boolean), Condition.addCondList(java.lang.String, MaHybridSample[], int, int), Condition.difference(Condition, Condition, java.lang.String), Condition.getCondListLength(), Condition.getConditionByName(java.lang.String), Condition.getHPlist(), Condition.intersection(Condition, Condition, java.lang.String), Condition.listCondLists(), Condition.rmvCondList(java.lang.String, boolean, boolean), Condition.renameCondList(java.lang.String, java.lang.String, boolean), Condition.updateListCondLists(), Condition.union(Condition, Condition, java.lang.String), ExprProfilePopup, Filter.computeWorkingGeneList(), GeneBitSet.assignCLtoUserBS(java.lang.String, GeneList), GeneBitSet.getGBSnames(), GeneBitSet.lookupGeneSetByName(java.lang.String, boolean), GeneBitSet.listGeneBitSets(java.lang.String), GeneBitSet.removeUserBS(java.lang.String), GeneBitSet.updateListGeneBitSets(), GeneBitSet.useGeneSetBS(GeneList, java.lang.String, java.lang.String), GeneClass.setCurrentGeneClassName(java.lang.String), GeneList.clear(), MAExplorer.logDRYROTerr(java.lang.String), MAExplorer.resetImageAndState(), Component.repaint(), Frame.setTitle(java.lang.String), PopupDialogQuery.dialogQuery(java.lang.String, int), PopupBinOprDialogQuery.dialogQuery(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String), PopupHPChooser, PopupHPmenuGuesser, PopupProjDirGuesser, PopupRegistry.updateFilter(GeneList), Report, SampleSets.showHP_XY_assignmentsPopup(), SampleSets.showHP_E_assignmentsPopup(), SampleSets.changeHPswapCy5Cy3Samples(), ScrollableImageCanvas.drawGifFile(java.lang.String), ShowExprProfilesPopup, ShowPlotPopup, StateScrollers.regenerateScrollers(boolean), Table, UserState.doLogin(java.lang.String, boolean), UserState.openState(java.lang.String), UserState.openOtherUserState(java.lang.String, java.lang.String), UserState.readUserGeneSet(java.lang.String, java.lang.String), UserState.saveStateFile(java.lang.String, java.lang.String, java.lang.String), UserState.shareUserState(java.lang.String, java.lang.String, java.lang.String), UserState.updateMAEprojectDB(java.lang.String, java.lang.String, java.lang.String, java.lang.String), UserState.writeMAEstartupFile(java.lang.String, java.lang.String, boolean), Util.popupViewer(java.net.URL, java.lang.String, java.lang.String), Util.rmvFinalSubDirectory(java.lang.String, java.lang.String, boolean), Util.saveCmdHistory(java.lang.String), Util.showMsg(java.lang.String), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), Util.showFeatures(java.lang.String, java.lang.String), Util.chkDirFinalSeparator(java.lang.String, java.lang.String), notAvailableYet(), openNewMaeDB(java.lang.String, java.lang.String), openNewWebDB(java.lang.String), promptFileName(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean), promptSaveAsMaeDB(boolean, boolean), processSetHP(java.lang.String)

processCheckboxStateChangedByItem

static boolean processCheckboxStateChangedByItem(java.awt.Checkbox cbItem,
                                                 java.lang.String cbItemName)
processCheckboxStateChangedByItem() - handle checkbox menu item state changed events. NOTE: need to implement radio groups here since AWT only implements radio groups for checkboxes, not for Checkbox MenuItems. We split the code so you can invoke commands via a client-server plugin.
Parameters:
item - is the check box item to process
itemName - is the associated name for debugging purposes
Returns:
true if succeed.
See Also:
Util.showMsg(java.lang.String), Util.showMsg2(java.lang.String), Util.showFeatures(java.lang.String, java.lang.String)

processCheckboxMenuItemStateChangedByitem

static boolean processCheckboxMenuItemStateChangedByitem(java.awt.CheckboxMenuItem item,
                                                         java.lang.String itemName)
processCheckboxMenuItemStateChangedByitem() - process CheckboxMenuItem state changed events by item. NOTE: need to implement radio groups here since AWT only implements radio groups for checkboxes, not for Checkbox MenuItems. We split the code so you can invoke commands via a client-server plugin.
Parameters:
item - is the check box menu item to process
itemName - is the associated name for debugging purpose
See Also:
ClusterGenes, CompositeDatabase.recalcNorms(java.lang.String, boolean), CompositeDatabase.recalcGlobalStats(boolean), Filter.computeWorkingGeneList(), HPxyData.setupDataStruct(boolean), MAExplorer.chkIfCache(), Component.repaint(), MenuBarFrame.setHP_XYlabels(), PopupRegistry.updateCurGene(int, int, java.lang.Object), PopupRegistry.updateFilter(GeneList), StateScrollers.regenerateScrollers(boolean), Table.lookupFieldIdxAndRemapFieldName(java.lang.String, java.lang.String), ShowStringPopup, Util.setLogMsgWindowVisible(boolean), Util.setLogHistoryWindowVisible(boolean), Util.showMsg(java.lang.String), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), Util.saveCmdHistory(java.lang.String), setClusterDisplayState(java.awt.CheckboxMenuItem, boolean), setCVmodeState(java.awt.CheckboxMenuItem), setCy3Cy5RatioRangeState(java.awt.CheckboxMenuItem), setEditState(java.awt.CheckboxMenuItem), setGoodSpotModeState(java.awt.CheckboxMenuItem), setIntensityRangeState(java.awt.CheckboxMenuItem), setNormalizationState(java.awt.CheckboxMenuItem, java.lang.String), setPlotState(java.awt.CheckboxMenuItem), setRatioRangeState(java.awt.CheckboxMenuItem), setReportFontSizeState(java.awt.CheckboxMenuItem), setReportFontSizeState(java.awt.CheckboxMenuItem), setSIrangeState(java.awt.CheckboxMenuItem), setSImodeState(java.awt.CheckboxMenuItem), setSIcompareModeState(java.awt.CheckboxMenuItem), setViewerDisplayState(java.awt.CheckboxMenuItem, java.lang.String)

cleanup

void cleanup()
cleanup() - cleanup global static allocated variables in this class. If statics are added later to this class, then set them to null here.