Class MenuBarFrame

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Window
                    |
                    +--java.awt.Frame
                          |
                          +--MenuBarFrame
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.event.ActionListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.event.ItemListener, java.awt.event.KeyListener, java.awt.MenuContainer, java.io.Serializable, java.awt.event.WindowListener

class MenuBarFrame
extends java.awt.Frame
implements java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.event.KeyListener

The class builds the MAExplorer GUI including a menu bar in a new Frame. We have to use a new Frame so we can get a MenuBar for the standalone GUI. It also has the Action (MenuItem) and Item (CheckBoxMenuItem) event listeners for the menu and passes the event commands back to the @see EventMenu classe to handle.

The builtin checkbox menu items are given (currently) individual variables. We track all all menu entries in order to be able to invoke commands from the program (in addition to user interaction with the GUI): 1. Menu Items are tracked in (menuActionLabelList[0:nCmds-1], and menuActionCmdList[0:nCmds-1]). 2.Checkbox menu items are tracked in (chkBoxMenuLabelList[0:nCBcmds-1] and chkBoxMenuItemList[0:nCBcmds-1])

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: 2003/07/18 17:27:37 $ $Revision: 1.44 $
Author:
P. Lemkin (NCI), J. Evans(CIT), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD
See Also:
MAExplorer Home, EventMenu, 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.Menu analysisMenu
          "Analysis" menu
(package private)  java.lang.String aTitle
          i.e.
private  Config cfg
          link to global Config instance
(package private) static java.awt.CheckboxMenuItem[] chkBoxMenuItemList
          [MAX_CHKBOX_CMDS] list of checkboxItem cmds menu items corresponding to names
(package private) static java.lang.String[] chkBoxMenuLabelList
          [MAX_CHKBOX_CMDS] list of checkboxItem cmds menu labels
(package private)  java.awt.Menu clusterMenu
          "Cluster" menu
(package private)  java.awt.Button curGeneTextButton
          enter cur.
(package private)  java.awt.Frame dialogFrame
          dialog frame created but not displayed until needed
(package private)  java.awt.Menu editMenu
          "Edit" menu
(package private)  ExprProfilePopup exprProfilePopup
          command pops it up
(package private)  java.awt.Menu fileMenu
          "File" menu
(package private)  java.awt.Menu filterMenu
          "Filter" menu
(package private)  java.awt.Menu geneClassMenu
          "GeneClass" menu
(package private)  PopupGeneGuesser gnMidGuesser
          create when needed
(package private)  boolean hasStopButtonFlag
          set if stopButton has "STOP!" label
(package private)  java.awt.Menu helpMenu
          "Help" menu
(package private)  java.awt.Label HP_Xlabel
          GUI label for current HP-X
(package private)  java.awt.Label HP_Ylabel
          GUI label for current HP-Y
(package private)  java.awt.Panel HPlabelPanel
          holds HP-X & -Y labels, STOP button
(package private)  boolean hpMenuChooserIsPoppedUp
          if chooser was popped up
(package private)  PopupHPmenuGuesser hpMenuGuesser
          HP menu guesser: create when needed
(package private)  boolean hpMenuGuesserIsPoppedUp
          if guesser was popped up
(package private)  java.lang.String hpMenuToUpdateFromChooser
          Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
(package private)  java.lang.String hpMenuToUpdateFromGuesser
          Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"
private  MAExplorer mae
          link to global instance
(package private)  boolean masterIDguesserIsPoppedUp
          if guesser was popped up
(package private) static int MAX_CHKBOX_CMDS
          max number of menu checkbox items allowed
(package private) static int MAX_CMDS
          max number of menu items allowed
(package private) static int MAX_MENU_STUBS
           
(package private) static java.awt.MenuBar mbar
          menu bar
(package private)  java.awt.Font mediumFontLbl
          current global medium font
(package private) static java.lang.String[] menuActionCmdList
          [MAX_CMDS] list of menuItem (short-form) commands for event handler
(package private) static java.lang.String[] menuActionLabelList
          [MAX_CMDS] list of menuItem commands labels
(package private)  java.awt.CheckboxMenuItem miCLHCMavgPGMALnk
          Menu: (Analysis | Cluster | Hierarchical) use average-arithmetic linkage for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLHCMavgPGMCLnk
          Menu: (Analysis | Cluster | Hierarchical) average-centroid linkage for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLHCMnextMinLnk
          Menu: (Analysis | Cluster | Hierarchical) next-min for linkage hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLHCMunWtAvg
          Menu: (Analysis | Cluster | Hierarchical) unweighted/weighted average for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLHCMuseClusterDistCache
          Menu: (Analysis | Cluster | Hierarchical) use Cluster dist-dist cache matrix for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLHCMuseShortClusterDistCache
          Menu: (Analysis | Cluster | Hierarchical) use 16-bit short vs 32-bit float for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLMdispKmeansNodes
          Menu: (Analysis | Cluster) cluster by K-means
(package private)  java.awt.CheckboxMenuItem miCLMfindSimGenesDisp
          Menu: (Analysis | Cluster) cluster by finding similar genes
(package private)  java.awt.CheckboxMenuItem miCLMhierClusterDisp
          Menu: (Analysis | Cluster) cluster by hierarchical clustering
(package private)  java.awt.CheckboxMenuItem miCLMnormHP
          Menu: (Analysis | Cluster | Hierarchical) normalize EP by HP sample for hier.clustering
(package private)  java.awt.CheckboxMenuItem miCLMsimGeneCountsDisp
          Menu: (Analysis | Cluster) cluster by finding similar gene counts
(package private)  java.awt.CheckboxMenuItem miCLMuseCorrCoeffDist
          Menu: (Analysis | Cluster) cluster using correlation coefficient else Euclidean distance
(package private)  java.awt.CheckboxMenuItem miCLMuseLSQmagNorm
          Menu: (Analysis | Cluster | hierarchical ) cluster using LSQ magnitude normalization else ...
(package private)  java.awt.CheckboxMenuItem miCLMuseMedianKmeans
          Menu: (Analysis | Cluster | cluster by K-means) cluster using K-medians else use K-means
(package private)  java.awt.CheckboxMenuItem miEMautoScrollerPopup
          Menu: (Edit | User Edited Gene List') [DEPRICATED]
(package private)  java.awt.CheckboxMenuItem miEMclusterWorkingCL
          Menu: (Edit | Preferences) Cluster Filtered Genes, else all genes
(package private)  java.awt.CheckboxMenuItem miEMeditAdd
          Menu: (Edit | User Edited Gene List') add gene to 'Edited Gene List'
(package private)  java.awt.CheckboxMenuItem miEMeditNop
          Menu: (Edit | User Edited Gene List') don't edit 'Edited Gene List'
(package private)  java.awt.CheckboxMenuItem miEMeditRmv
          Menu: (Edit | User Edited Gene List') delete gene to 'Edited Gene List'
(package private)  java.awt.CheckboxMenuItem miEMshowEditedGenes
          Menu: (Edit | User Edited Gene List') Show 'Edited Gene List'
(package private)  java.awt.CheckboxMenuItem miFEMenableFIOcache
          Menu: (Edit | Preferences) enable using cache for Web database
(package private)  java.awt.CheckboxMenuItem miFEMuseWebDB
          Menu: (Edit | Preferences) access data from Web database
(package private)  java.awt.CheckboxMenuItem miFRM_EGLfilter
          Menu: (Analysis | Filter) Filter by EGL gene membership
(package private)  java.awt.CheckboxMenuItem miFRMclusterHP_Efilter
          Menu: (Analysis | Filter) Filter by Cluster test
(package private)  java.awt.CheckboxMenuItem miFRMcvModeE
          Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMcvModeMS
          Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMcvModeXANDYsets
          Menu: (Analysis | Filter | CV threshold sliders) test current HP-X and HP-Y 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMcvModeXORYsets
          Menu: (Analysis | Filter | CV threshold sliders) test current HP-X or HP-Y 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMcvModeXset
          Menu: (Analysis | Filter | CV threshold sliders) test current HP-X 'set' samples
(package private)  java.awt.CheckboxMenuItem miFRMcvModeXY
          Menu: (Analysis | Filter | CV threshold sliders) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMcvModeYset
          Menu: (Analysis | Filter | CV threshold sliders) test current HP-Y 'set' samples
(package private)  java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngIn
          Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) in range
(package private)  java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngOut
          Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) outside of range
(package private)  java.awt.CheckboxMenuItem miFRMdetValueSpotModeE
          Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-E 'list' samples
(package private)  java.awt.CheckboxMenuItem miFRMdetValueSpotModeMS
          Menu: (Analysis | Filter | use Spot Detection Valuedata) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMdetValueSpotModeXANDYsets
          Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y 'set' samples
(package private)  java.awt.CheckboxMenuItem miFRMdetValueSpotModeXY
          Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y samples
(package private)  java.awt.CheckboxMenuItem miFRMfTestOCLFilter
          Menu: (Analysis | Filter) Filter by cur.
(package private)  java.awt.CheckboxMenuItem miFRMgeneClassMbrFilter
          Menu: (Analysis | Filter) Filter by GeneClass membership
(package private)  java.awt.CheckboxMenuItem miFRMgoodGeneListFilter
          Menu: (Analysis | Filter) Filter by good genes membership
(package private)  java.awt.CheckboxMenuItem miFRMgoodSpotModeE
          Menu: (Analysis | Filter | use Good Spot data) test current HP-E 'list' samples
(package private)  java.awt.CheckboxMenuItem miFRMgoodSpotModeMS
          Menu: (Analysis | Filter | use Good Spot data) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMgoodSpotModeXANDYsets
          Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y 'set' samples
(package private)  java.awt.CheckboxMenuItem miFRMgoodSpotModeXORYsets
          Menu: (Analysis | Filter | use Good Spot data)
(package private)  java.awt.CheckboxMenuItem miFRMgoodSpotModeXY
          Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y samples
(package private)  java.awt.CheckboxMenuItem miFRMgrayRngIn
          Menu: (Analysis | Filter | by intensity range test) within range
(package private)  java.awt.CheckboxMenuItem miFRMgrayRngOut
          Menu: (Analysis | Filter | by intensity range test) outside range
(package private)  java.awt.CheckboxMenuItem miFRMhighXYratioFilter
          Menu: (Analysis | Filter) Filter by high ratio range test
(package private)  java.awt.CheckboxMenuItem miFRMhistIntensRngFilter
          Menu: (Analysis | Filter) Filter by intensity histogram bin
(package private)  java.awt.CheckboxMenuItem miFRMhistRatioRngFilter
          Menu: (Analysis | Filter) Filter by ratio histogram bin
(package private)  java.awt.CheckboxMenuItem miFRMksTestXYsetsFilter
          Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' KS-Test
(package private)  java.awt.CheckboxMenuItem miFRMlowXYratioFilter
          Menu: (Analysis | Filter) Filter by low ratio range test
(package private)  java.awt.CheckboxMenuItem miFRMOnlyGenesWithNonZeroDensityFlag
          Menu: (Analysis | Filter | use only genes with non-zero intensity)
(package private)  java.awt.CheckboxMenuItem miFRMposQuantModeE
          Menu: (Analysis | Filter | use positive quantified data) test current HP-E 'list' samples
(package private)  java.awt.CheckboxMenuItem miFRMposQuantModeMS
          Menu: (Analysis | Filter | use positive quantified data) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMposQuantModeXY
          Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y samples
(package private)  java.awt.CheckboxMenuItem miFRMposQuantModeXYsets
          Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y 'set' samples
(package private)  java.awt.CheckboxMenuItem miFRMratioRngIn
          Menu: (Analysis | Filter | by ratio range test) in range
(package private)  java.awt.CheckboxMenuItem miFRMratioRngOut
          Menu: (Analysis | Filter | Filter by ratio range test) outside of range
(package private)  java.awt.CheckboxMenuItem miFRMreplicateGenesFilter
          Menu: (Analysis | Filter) Filter by replicate genes membership
(package private)  java.awt.CheckboxMenuItem miFRMspotCVfilter
          Menu: (Analysis | Filter) Filter by spot CV test
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModeALL
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ALL selected samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModeANY
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ANY selected samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_LEAST
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT LEAST (n) selected samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_MOST
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT MOST (n) selected samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModePRODUCT
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have PRODUCT selected samples less than threshold
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensCompareModeSUM
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have SUM selected samples less than threshold
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeE
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-E 'list' samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeMS
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP sample
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeXANDYsets
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeXORYsets
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X or HP-Y 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeXsets
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeXY
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensModeYsets
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-Y 'sets' samples
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensRngIn
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) within range test
(package private)  java.awt.CheckboxMenuItem miFRMspotIntensRngOut
          Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) outside range test
(package private)  java.awt.CheckboxMenuItem miFRMthrCy3Cy5Ratio
          Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) enabled
(package private)  java.awt.CheckboxMenuItem miFRMthrGray
          Menu: (Analysis | Filter | by intensity range test) enabled
(package private)  java.awt.CheckboxMenuItem miFRMthrRatio
          Menu: (Analysis | Filter | by ratio range test) enabled
(package private)  java.awt.CheckboxMenuItem miFRMthrSpotIntens
          Menu: (Analysis | Filter | Filter by spot intensity [SI1:SI2] sliders) Filter by spot intensity range test
(package private)  java.awt.CheckboxMenuItem miFRMtTestXYfilter
          Menu: (Analysis | Filter) Filter by HP-X and HP-Y F1+F2 t-Test
(package private)  java.awt.CheckboxMenuItem miFRMtTestXYsetsFilter
          Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' t-Test
(package private)  java.awt.CheckboxMenuItem miFRMuseCVmeanElseMax
          Menu: (Analysis | Filter | CV threshold sliders) use the CV mean else the CV max in computation
(package private)  java.awt.CheckboxMenuItem miFRMuseDetValueSpotDataFlag
          Menu: (Analysis | Filter | use Spot Detection Value data)
(package private)  java.awt.CheckboxMenuItem miFRMuseDiffFilter
          Menu: (Analysis | Filter) Filter by difference test
(package private)  java.awt.CheckboxMenuItem miFRMuseGeneSetFilter
          Menu: (Analysis | Filter) Filter by user gene set membership
(package private)  java.awt.CheckboxMenuItem miFRMuseGoodSpotDataFlag
          Menu: (Analysis | Filter | use Good Spot data)
(package private)  java.awt.CheckboxMenuItem miFRMusePosQuantDataFlag
          Menu: (Analysis | Filter | use positive quantified data)
(package private)  java.awt.CheckboxMenuItem miHPMuseHPxySets
          Menu: (Samples) use HP-X and HP-Y 'sets' of multiple samples else use individual HP-X and HP-Y samples.
(package private)  java.awt.CheckboxMenuItem miNRMbkgrdCorr
          (Analysis | Normalization) use background correction
(package private)  java.awt.CheckboxMenuItem miNRMCalDNAnorm
          (Analysis | Normalization | Calibration DNA genes)
(package private)  java.awt.CheckboxMenuItem miNRMgeneSetNorm
          (Analysis | Normalization | User defined gene set genes)
(package private)  java.awt.CheckboxMenuItem miNRMgoodSpotsStats
          (Analysis | Normalization) use per-sample Good Spots data for global array statistics
(package private)  java.awt.CheckboxMenuItem miNRMhousekeepNorm
          (Analysis | Normalization | Housekeeping genes)
(package private)  java.awt.CheckboxMenuItem miNRMlogMedianNorm
          (Analysis | Normalization | Normalize by logMedian )
(package private)  java.awt.CheckboxMenuItem miNRMmedianNorm
          (Analysis | Normalization | Median)
(package private)  java.awt.CheckboxMenuItem miNRMnoNorm
          (Analysis | Normalization } No normalization)
(package private)  java.awt.CheckboxMenuItem miNRMratioMedianCorrection
          (Analysis | Normalization) use ratio median correction for the Cy3 and Cy5 channels
(package private)  java.awt.CheckboxMenuItem miNRMscaleToMaxIntens
          (Analysis | Normalization | Normalize to maximum intensity (65K)
(package private)  java.awt.CheckboxMenuItem miNRMtestGenericNormPlugin
          only if mae.DBUG_GENERIC_NORM_PLUGIN is set, then (Analysis | Normalization | Test Generic Norm Plugin)
(package private)  java.awt.CheckboxMenuItem miNRMZscoreMeanAbsDevLogNorm
          (Analysis | Normalization | Normalize by Zscore of log (AbsDev) )
(package private)  java.awt.CheckboxMenuItem miNRMZscoreMeanStdDevLogNorm
          (Analysis | Normalization | Normalize by Zscore of log (StdDev) )
(package private)  java.awt.CheckboxMenuItem miNRMZscoreNorm
          (Analysis | Normalization | Zscore )
(package private)  java.awt.CheckboxMenuItem miPEPlistType
          (Analysis | Plot | Expression Profile) Menu Expression Profile list type (overlay or grid).
(package private)  java.awt.CheckboxMenuItem miPLGMuseSPLUSasComputingEngine
          Menu: (Plugins | Use S-PLUS, else R, as computing engine [CB])
(package private)  java.awt.CheckboxMenuItem miPLGMuseTimeStampReports
          Menu: (Plugins | Save SRLO reports in time-stampled folder [CB])
(package private)  java.awt.CheckboxMenuItem miPMdualXYpseudoImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor dual HP-X and HP-Y as Field 1 and Field 2 grids
(package private)  java.awt.CheckboxMenuItem miPMflickerXY
          Menu:(Analysis | Plot | Show Microarray) use Flicker of HP-X and HP-Y samples in intensity mode
(package private)  java.awt.CheckboxMenuItem miPMlowRangeZoom
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor low range zoom
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoF1F2Img
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Cy3/Cy5 ratio or Zdiff
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoHP_EP_CV_valueImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-EP 'list' CV-value
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoHP_F1F2_RYGImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_pValueImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor (HP-X,HP-Y) 'sets' p-value
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_RYGImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(X)-Yellow-Green(Y) HP-X/Y ratio or Zdiff
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoHP_XYImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-X/Y ratio or Zdiff
(package private)  java.awt.CheckboxMenuItem miPMplotPseudoImg
          Menu:(Analysis | Plot | Show Microarray) use Pseudograyscale intensity
(package private)  java.awt.CheckboxMenuItem miPRtblFontSize10pt
          Menu: (Analysis | Report) font size is 10 pt
(package private)  java.awt.CheckboxMenuItem miPRtblFontSize12pt
          Menu: (Analysis | Report) font size is 12 pt
(package private)  java.awt.CheckboxMenuItem miPRtblFontSize8pt
          Menu: (Analysis | Report) font size is 8 pt
(package private)  java.awt.CheckboxMenuItem miTMtblFmtAddEPdata
          Menu: (Analysis | Report) add Expr-Profile data to Table
(package private)  java.awt.CheckboxMenuItem miTMtblFmtAddHP_XYsetStat
          Menu: (Analysis | Report) add HP-XY set statistics data to Table
(package private)  java.awt.CheckboxMenuItem miTMtblFmtAddOCLstatistics
          Menu: (Analysis | Report) add OCL statistics data to Table
(package private)  java.awt.CheckboxMenuItem miTMtblFmtClickable
          Menu: (Analysis | Report) use Dynamic clickable table format
(package private)  java.awt.CheckboxMenuItem miTMtblFmtTabDelim
          Menu: (Analysis | Report) use Tab-Delimited table format
(package private)  java.awt.CheckboxMenuItem miTMtblFmtUseRawEPdata
          Menu: (Analysis | Report) use raw Expr-Profile data in Table
(package private)  java.awt.CheckboxMenuItem miTMtblFontSize10pt
          Menu: (Analysis | Report) font size is 10 pt
(package private)  java.awt.CheckboxMenuItem miTMtblFontSize12pt
          Menu: (Analysis | Report) font size is 12 pt
(package private)  java.awt.CheckboxMenuItem miTMtblFontSize8pt
          Menu: (Analysis | Report) font size is 8 pt
(package private)  java.awt.CheckboxMenuItem miVMdbESTviewer
          Menu:(View) enable popup GenBank browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMGang
          Menu:(View) show gang scrolling for duplicated grids of spots
(package private)  java.awt.CheckboxMenuItem miVMgenBankViewer
          Menu:(View) enable popup GenBank browser for new current gene
(package private)  java.awt.CheckboxMenuItem[] miVMgenomicViewer
          sGenomicMenu[cfg.nGenomicMenus] menu items as determined from Config DB
(package private)  java.awt.CheckboxMenuItem miVMlocusLinkViewer
          Menu:(View) enable popup LocusLink gene browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMmAdbViewer
          Menu:(View) enable popup mAdb gene browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMmedMinerViewer
          Menu:(View) enable popup MedMiner browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMomimViewer
          Menu:(View) enable popup OMIM browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMpirViewer
          Menu:(View) enable popup PIRs browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMPresentView
          Menu:(View) enable Presentation view that increases font sizes
(package private)  java.awt.CheckboxMenuItem miVMshowEditedGenes
          Menu:(View) show EGL genes
(package private)  java.awt.CheckboxMenuItem miVMshowFilteredSpots
          Menu:(View) show Filtered genes and spots
(package private)  java.awt.CheckboxMenuItem miVMshowHistoryLog
          Menu:(View) enable popup command history log
(package private)  java.awt.CheckboxMenuItem miVMshowMsgLog
          Menu:(View) enable popup message history log
(package private)  java.awt.CheckboxMenuItem miVMswissProtViewer
          Menu:(View) enable popup SwissProt browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMuniGeneViewer
          Menu:(View) enable popup UniGene browser for new current gene
(package private)  java.awt.CheckboxMenuItem miVMuseDichromasy
          Menu:(View) enable Dichromasy colors that may be useful for some colorblind researchers instead of default color schemes.
(package private)  java.awt.CheckboxMenuItem miVMuseMouseOver
          Menu:(View) enable mouse-over information for mouse over selected genes
(package private)  java.awt.Checkbox mouseOverCheckBox
          Show Mouse-over info
(package private) static int nCBcmds
          # of menu CheckBoxMenuItem item cmds [0:nCBcmds-1]
(package private) static int nCmds
          # of menu item commands [0:nCmds-1]
(package private)  int nMenuStubs
          # of menu stubs in the list
(package private)  java.awt.Menu normMenu
          "Normalization" menu
(package private)  int nRLOs
          # of RLO entries in the menu
(package private)  PopupBinOprDialogQuery pBOdq
          holds popup BinOpr dialog query
(package private)  PopupDialogQuery pdq
          holds popup dialog query
(package private)  java.awt.Menu plotMenu
          "Plot" menu
(package private)  java.awt.Menu pluginsMenu
          "Plugins" menu
(package private)  PopupProjDirGuesser projDirGuesser
          Project Guesser: create when needed
(package private)  boolean projDirGuesserIsPoppedUp
          if guesser was popped up
(package private)  java.lang.String projDirToUpdateFromGuesser
          prj dir result set in event handler
(package private)  java.awt.Panel ps
          holds above chkboxes & scrollbar panels
(package private)  java.awt.Label reportLabel
          report label must be global variable
(package private)  java.awt.Menu reportMenu
          "Report" menu
(package private)  java.lang.String[] rloMenuNames
          RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
(package private)  java.lang.String[] rloRscriptNames
          RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree
(package private)  java.awt.Menu rloSmnu
          Menu stub to add/modify R(Plugin | RLO methods (submenu)) menu items
(package private)  java.awt.Menu sampleMenu
          "Sample" command menu
(package private)  java.awt.Font smallFontLbl
          current global small font
(package private)  java.awt.Button stopButton
          If hasStopButtonFlag is set (i.e.
(package private)  java.lang.String stopLblName
          either "STOP!" or " "
(package private)  java.awt.Menu[] stubMenus
          list of Menu Stubs in Menu tree
(package private)  java.lang.String[] stubNames
          list of Names of Stubs in Menu tree
(package private)  java.lang.String title
          title for frame
(package private)  java.awt.Font useFontLbl
          current global font to use font
(package private)  java.awt.Menu viewMenu
          "View" menu
(package private)  int x0
          ULHC X of MenuBarFrame window
(package private)  int y0
          ULHC X of MenuBarFrame window
 
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) MenuBarFrame(MAExplorer mae)
          MnuBarFrame() - constructor used with the Applet.
(package private) MenuBarFrame(MAExplorer mae, java.lang.String title, int x0, int y0)
          MenuBarFrame() - constructor for main GUI window and menubar.
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent e)
          actionPerformed() - handle action events for Buttons and menu commands.
(package private)  int addMenuBar()
          addMenuBar() - add menubar with menus to the frame
private  void addMenuStubToMenuStubList(java.lang.String name, java.awt.Menu menuStub)
          addMenuStubToMenuStubList() - add menu position to Menu Stub List.
(package private)  void addRLOsubmenuTree()
          addRLOsubmenuTree() - add RLO R scripts submenu tree to rloSmnu if RLOs exist.
(package private)  void addSetHP_XYEsubmenuTree(java.awt.Menu subMenu, java.lang.String hpPostfixStr)
          addSetHP_XYEsubmenuTree() - add HP sample submenu tree to submenu if submenus exist.
(package private)  void buildMenuGUI(int x0, int y0, int width, int height)
          buildMenuGUI() - build the GUI with pop up menus
(package private)  void callAllStartupPlugins()
          callAllStartupPlugins() - call all Plugins initialized at Startup.
(package private)  void createDialogQueryFrames()
          createDialogQueryFrames() - create all popup dialog frames
(package private)  void enableMenus(java.lang.String opr)
          enableMenus() - enable/disable all menus, checkboxes, typein fields etc.
private  java.awt.Menu findMenuStubByName(java.lang.String name)
          findMenuStubByName() - find menu stub associated with name in Menu Stub List.
private  void insertPluginMenuEntries()
          insertPluginMenuEntries() - insert Plugin menus if any at proper stubs.
 void itemStateChanged(java.awt.event.ItemEvent e)
          itemStateChanged() - handle item state changed events.
 void keyPressed(java.awt.event.KeyEvent e)
          keyPressed() - get key Pressed event - look for ESCAPE key to set STOP flag
 void keyReleased(java.awt.event.KeyEvent e)
          keyReleased() - get key Released event
 void keyTyped(java.awt.event.KeyEvent e)
          keyTyped() - get key typed event - look for ESCAPE key to set STOP flag
private  java.awt.CheckboxMenuItem makeChkBoxMenuItem(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut, boolean value)
          makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list.
private  void makeMenuItem(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut)
          makeMenuItem() - make menuItem entry in menu list.
private  java.awt.Menu makeSubMenu(java.awt.Menu pm, java.lang.String sLabel, java.lang.String sCmd, int shortcut)
          makeSubMenu() - make submenu entry in menu list.
(package private)  void redoMenuBar()
          redoMenuBar() - redo the menubar if restarted a new database with different entries.
(package private)  void setHP_XYlabels()
          setHP_XYlabels() - set the GUI HP-X: and HP-Y: labels as singles or multiple (Class names)
(package private)  void setSTOPbuttonState(boolean flag, boolean isEnabledFlag)
          setSTOPbuttonState() - enable/disable STOP button & clear abortFlag.
 void windowActivated(java.awt.event.WindowEvent e)
           
 void windowClosed(java.awt.event.WindowEvent e)
           
 void windowClosing(java.awt.event.WindowEvent e)
          windowClosing() - close the window
 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, getPreferredSize, getWindow, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, numListening, paint, 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

private MAExplorer mae
link to global instance

cfg

private Config cfg
link to global Config instance

title

java.lang.String title
title for frame

mbar

static java.awt.MenuBar mbar
menu bar

MAX_CMDS

static final int MAX_CMDS
max number of menu items allowed

MAX_CHKBOX_CMDS

static final int MAX_CHKBOX_CMDS
max number of menu checkbox items allowed

nCmds

static int nCmds
# of menu item commands [0:nCmds-1]

menuActionLabelList

static java.lang.String[] menuActionLabelList
[MAX_CMDS] list of menuItem commands labels

menuActionCmdList

static java.lang.String[] menuActionCmdList
[MAX_CMDS] list of menuItem (short-form) commands for event handler

nCBcmds

static int nCBcmds
# of menu CheckBoxMenuItem item cmds [0:nCBcmds-1]

chkBoxMenuLabelList

static java.lang.String[] chkBoxMenuLabelList
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu labels

chkBoxMenuItemList

static java.awt.CheckboxMenuItem[] chkBoxMenuItemList
[MAX_CHKBOX_CMDS] list of checkboxItem cmds menu items corresponding to names

MAX_MENU_STUBS

static final int MAX_MENU_STUBS

nMenuStubs

int nMenuStubs
# of menu stubs in the list

stubNames

java.lang.String[] stubNames
list of Names of Stubs in Menu tree

stubMenus

java.awt.Menu[] stubMenus
list of Menu Stubs in Menu tree

rloSmnu

java.awt.Menu rloSmnu
Menu stub to add/modify R(Plugin | RLO methods (submenu)) menu items

nRLOs

int nRLOs
# of RLO entries in the menu

rloMenuNames

java.lang.String[] rloMenuNames
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree

rloRscriptNames

java.lang.String[] rloRscriptNames
RLO menu names [0:nRLOs-1] in Plugin | RLO methods) menu tree

aTitle

java.lang.String aTitle
i.e. mae.browserTitle

x0

int x0
ULHC X of MenuBarFrame window

y0

int y0
ULHC X of MenuBarFrame window

reportLabel

java.awt.Label reportLabel
report label must be global variable

smallFontLbl

java.awt.Font smallFontLbl
current global small font

mediumFontLbl

java.awt.Font mediumFontLbl
current global medium font

useFontLbl

java.awt.Font useFontLbl
current global font to use font

exprProfilePopup

ExprProfilePopup exprProfilePopup
command pops it up

dialogFrame

java.awt.Frame dialogFrame
dialog frame created but not displayed until needed

pdq

PopupDialogQuery pdq
holds popup dialog query

pBOdq

PopupBinOprDialogQuery pBOdq
holds popup BinOpr dialog query

HPlabelPanel

java.awt.Panel HPlabelPanel
holds HP-X & -Y labels, STOP button

ps

java.awt.Panel ps
holds above chkboxes & scrollbar panels

stopButton

java.awt.Button stopButton
If hasStopButtonFlag is set (i.e. button exists, then set if want to abort a computation. The event handler sets the mae.abortFlag

mouseOverCheckBox

java.awt.Checkbox mouseOverCheckBox
Show Mouse-over info

curGeneTextButton

java.awt.Button curGeneTextButton
enter cur. gene name in popup guesser

masterIDguesserIsPoppedUp

boolean masterIDguesserIsPoppedUp
if guesser was popped up

gnMidGuesser

PopupGeneGuesser gnMidGuesser
create when needed

hasStopButtonFlag

boolean hasStopButtonFlag
set if stopButton has "STOP!" label

hpMenuChooserIsPoppedUp

boolean hpMenuChooserIsPoppedUp
if chooser was popped up

hpMenuGuesserIsPoppedUp

boolean hpMenuGuesserIsPoppedUp
if guesser was popped up

stopLblName

java.lang.String stopLblName
either "STOP!" or " "

hpMenuToUpdateFromGuesser

java.lang.String hpMenuToUpdateFromGuesser
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"

hpMenuToUpdateFromChooser

java.lang.String hpMenuToUpdateFromChooser
Set in event handler to one of: ":HP" ":HP_X" ":HP_Y" ":HP_X+" ":HP_X-" ":HP_Y+" ":HP_Y-" ":HP_E+" ":HP_E-"

hpMenuGuesser

PopupHPmenuGuesser hpMenuGuesser
HP menu guesser: create when needed

projDirGuesser

PopupProjDirGuesser projDirGuesser
Project Guesser: create when needed

projDirGuesserIsPoppedUp

boolean projDirGuesserIsPoppedUp
if guesser was popped up

projDirToUpdateFromGuesser

java.lang.String projDirToUpdateFromGuesser
prj dir result set in event handler

analysisMenu

java.awt.Menu analysisMenu
"Analysis" menu

fileMenu

java.awt.Menu fileMenu
"File" menu

sampleMenu

java.awt.Menu sampleMenu
"Sample" command menu

geneClassMenu

java.awt.Menu geneClassMenu
"GeneClass" menu

normMenu

java.awt.Menu normMenu
"Normalization" menu

editMenu

java.awt.Menu editMenu
"Edit" menu

filterMenu

java.awt.Menu filterMenu
"Filter" menu

viewMenu

java.awt.Menu viewMenu
"View" menu

plotMenu

java.awt.Menu plotMenu
"Plot" menu

clusterMenu

java.awt.Menu clusterMenu
"Cluster" menu

reportMenu

java.awt.Menu reportMenu
"Report" menu

pluginsMenu

java.awt.Menu pluginsMenu
"Plugins" menu

helpMenu

java.awt.Menu helpMenu
"Help" menu

miFEMuseWebDB

java.awt.CheckboxMenuItem miFEMuseWebDB
Menu: (Edit | Preferences) access data from Web database

miFEMenableFIOcache

java.awt.CheckboxMenuItem miFEMenableFIOcache
Menu: (Edit | Preferences) enable using cache for Web database

miHPMuseHPxySets

java.awt.CheckboxMenuItem miHPMuseHPxySets
Menu: (Samples) use HP-X and HP-Y 'sets' of multiple samples else use individual HP-X and HP-Y samples.

miNRMhousekeepNorm

java.awt.CheckboxMenuItem miNRMhousekeepNorm
(Analysis | Normalization | Housekeeping genes)

miNRMgeneSetNorm

java.awt.CheckboxMenuItem miNRMgeneSetNorm
(Analysis | Normalization | User defined gene set genes)

miNRMCalDNAnorm

java.awt.CheckboxMenuItem miNRMCalDNAnorm
(Analysis | Normalization | Calibration DNA genes)

miNRMZscoreNorm

java.awt.CheckboxMenuItem miNRMZscoreNorm
(Analysis | Normalization | Zscore )

miNRMmedianNorm

java.awt.CheckboxMenuItem miNRMmedianNorm
(Analysis | Normalization | Median)

miNRMlogMedianNorm

java.awt.CheckboxMenuItem miNRMlogMedianNorm
(Analysis | Normalization | Normalize by logMedian )

miNRMZscoreMeanStdDevLogNorm

java.awt.CheckboxMenuItem miNRMZscoreMeanStdDevLogNorm
(Analysis | Normalization | Normalize by Zscore of log (StdDev) )

miNRMZscoreMeanAbsDevLogNorm

java.awt.CheckboxMenuItem miNRMZscoreMeanAbsDevLogNorm
(Analysis | Normalization | Normalize by Zscore of log (AbsDev) )

miNRMscaleToMaxIntens

java.awt.CheckboxMenuItem miNRMscaleToMaxIntens
(Analysis | Normalization | Normalize to maximum intensity (65K)

miNRMnoNorm

java.awt.CheckboxMenuItem miNRMnoNorm
(Analysis | Normalization } No normalization)

miNRMtestGenericNormPlugin

java.awt.CheckboxMenuItem miNRMtestGenericNormPlugin
only if mae.DBUG_GENERIC_NORM_PLUGIN is set, then (Analysis | Normalization | Test Generic Norm Plugin)

miNRMgoodSpotsStats

java.awt.CheckboxMenuItem miNRMgoodSpotsStats
(Analysis | Normalization) use per-sample Good Spots data for global array statistics

miNRMbkgrdCorr

java.awt.CheckboxMenuItem miNRMbkgrdCorr
(Analysis | Normalization) use background correction

miNRMratioMedianCorrection

java.awt.CheckboxMenuItem miNRMratioMedianCorrection
(Analysis | Normalization) use ratio median correction for the Cy3 and Cy5 channels

miEMshowEditedGenes

java.awt.CheckboxMenuItem miEMshowEditedGenes
Menu: (Edit | User Edited Gene List') Show 'Edited Gene List'

miEMeditNop

java.awt.CheckboxMenuItem miEMeditNop
Menu: (Edit | User Edited Gene List') don't edit 'Edited Gene List'

miEMeditAdd

java.awt.CheckboxMenuItem miEMeditAdd
Menu: (Edit | User Edited Gene List') add gene to 'Edited Gene List'

miEMeditRmv

java.awt.CheckboxMenuItem miEMeditRmv
Menu: (Edit | User Edited Gene List') delete gene to 'Edited Gene List'

miEMautoScrollerPopup

java.awt.CheckboxMenuItem miEMautoScrollerPopup
Menu: (Edit | User Edited Gene List') [DEPRICATED]

miEMclusterWorkingCL

java.awt.CheckboxMenuItem miEMclusterWorkingCL
Menu: (Edit | Preferences) Cluster Filtered Genes, else all genes

miVMshowEditedGenes

java.awt.CheckboxMenuItem miVMshowEditedGenes
Menu:(View) show EGL genes

miVMshowFilteredSpots

java.awt.CheckboxMenuItem miVMshowFilteredSpots
Menu:(View) show Filtered genes and spots

miVMPresentView

java.awt.CheckboxMenuItem miVMPresentView
Menu:(View) enable Presentation view that increases font sizes

miVMGang

java.awt.CheckboxMenuItem miVMGang
Menu:(View) show gang scrolling for duplicated grids of spots

miVMuseMouseOver

java.awt.CheckboxMenuItem miVMuseMouseOver
Menu:(View) enable mouse-over information for mouse over selected genes

miVMgenBankViewer

java.awt.CheckboxMenuItem miVMgenBankViewer
Menu:(View) enable popup GenBank browser for new current gene

miVMdbESTviewer

java.awt.CheckboxMenuItem miVMdbESTviewer
Menu:(View) enable popup GenBank browser for new current gene

miVMuniGeneViewer

java.awt.CheckboxMenuItem miVMuniGeneViewer
Menu:(View) enable popup UniGene browser for new current gene

miVMomimViewer

java.awt.CheckboxMenuItem miVMomimViewer
Menu:(View) enable popup OMIM browser for new current gene

miVMmAdbViewer

java.awt.CheckboxMenuItem miVMmAdbViewer
Menu:(View) enable popup mAdb gene browser for new current gene

miVMlocusLinkViewer

java.awt.CheckboxMenuItem miVMlocusLinkViewer
Menu:(View) enable popup LocusLink gene browser for new current gene

miVMmedMinerViewer

java.awt.CheckboxMenuItem miVMmedMinerViewer
Menu:(View) enable popup MedMiner browser for new current gene

miVMswissProtViewer

java.awt.CheckboxMenuItem miVMswissProtViewer
Menu:(View) enable popup SwissProt browser for new current gene

miVMpirViewer

java.awt.CheckboxMenuItem miVMpirViewer
Menu:(View) enable popup PIRs browser for new current gene

miVMuseDichromasy

java.awt.CheckboxMenuItem miVMuseDichromasy
Menu:(View) enable Dichromasy colors that may be useful for some colorblind researchers instead of default color schemes.

miVMshowMsgLog

java.awt.CheckboxMenuItem miVMshowMsgLog
Menu:(View) enable popup message history log

miVMshowHistoryLog

java.awt.CheckboxMenuItem miVMshowHistoryLog
Menu:(View) enable popup command history log

miVMgenomicViewer

java.awt.CheckboxMenuItem[] miVMgenomicViewer
sGenomicMenu[cfg.nGenomicMenus] menu items as determined from Config DB

miFRMgeneClassMbrFilter

java.awt.CheckboxMenuItem miFRMgeneClassMbrFilter
Menu: (Analysis | Filter) Filter by GeneClass membership

miFRMuseGeneSetFilter

java.awt.CheckboxMenuItem miFRMuseGeneSetFilter
Menu: (Analysis | Filter) Filter by user gene set membership

miFRMgoodGeneListFilter

java.awt.CheckboxMenuItem miFRMgoodGeneListFilter
Menu: (Analysis | Filter) Filter by good genes membership

miFRMreplicateGenesFilter

java.awt.CheckboxMenuItem miFRMreplicateGenesFilter
Menu: (Analysis | Filter) Filter by replicate genes membership

miFRMhistRatioRngFilter

java.awt.CheckboxMenuItem miFRMhistRatioRngFilter
Menu: (Analysis | Filter) Filter by ratio histogram bin

miFRMhistIntensRngFilter

java.awt.CheckboxMenuItem miFRMhistIntensRngFilter
Menu: (Analysis | Filter) Filter by intensity histogram bin

miFRM_EGLfilter

java.awt.CheckboxMenuItem miFRM_EGLfilter
Menu: (Analysis | Filter) Filter by EGL gene membership

miFRMspotCVfilter

java.awt.CheckboxMenuItem miFRMspotCVfilter
Menu: (Analysis | Filter) Filter by spot CV test

miFRMclusterHP_Efilter

java.awt.CheckboxMenuItem miFRMclusterHP_Efilter
Menu: (Analysis | Filter) Filter by Cluster test

miFRMuseDiffFilter

java.awt.CheckboxMenuItem miFRMuseDiffFilter
Menu: (Analysis | Filter) Filter by difference test

miFRMtTestXYfilter

java.awt.CheckboxMenuItem miFRMtTestXYfilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y F1+F2 t-Test

miFRMtTestXYsetsFilter

java.awt.CheckboxMenuItem miFRMtTestXYsetsFilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' t-Test

miFRMksTestXYsetsFilter

java.awt.CheckboxMenuItem miFRMksTestXYsetsFilter
Menu: (Analysis | Filter) Filter by HP-X and HP-Y 'sets' KS-Test

miFRMfTestOCLFilter

java.awt.CheckboxMenuItem miFRMfTestOCLFilter
Menu: (Analysis | Filter) Filter by cur. OCL F-Test)

miFRMhighXYratioFilter

java.awt.CheckboxMenuItem miFRMhighXYratioFilter
Menu: (Analysis | Filter) Filter by high ratio range test

miFRMlowXYratioFilter

java.awt.CheckboxMenuItem miFRMlowXYratioFilter
Menu: (Analysis | Filter) Filter by low ratio range test

miFRMthrSpotIntens

java.awt.CheckboxMenuItem miFRMthrSpotIntens
Menu: (Analysis | Filter | Filter by spot intensity [SI1:SI2] sliders) Filter by spot intensity range test

miFRMspotIntensRngIn

java.awt.CheckboxMenuItem miFRMspotIntensRngIn
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) within range test

miFRMspotIntensRngOut

java.awt.CheckboxMenuItem miFRMspotIntensRngOut
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) outside range test

miFRMspotIntensModeMS

java.awt.CheckboxMenuItem miFRMspotIntensModeMS
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP sample

miFRMspotIntensModeXY

java.awt.CheckboxMenuItem miFRMspotIntensModeXY
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y samples

miFRMspotIntensModeXsets

java.awt.CheckboxMenuItem miFRMspotIntensModeXsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X 'sets' samples

miFRMspotIntensModeYsets

java.awt.CheckboxMenuItem miFRMspotIntensModeYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-Y 'sets' samples

miFRMspotIntensModeXORYsets

java.awt.CheckboxMenuItem miFRMspotIntensModeXORYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X or HP-Y 'sets' samples

miFRMspotIntensModeXANDYsets

java.awt.CheckboxMenuItem miFRMspotIntensModeXANDYsets
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-X and HP-Y 'sets' samples

miFRMspotIntensModeE

java.awt.CheckboxMenuItem miFRMspotIntensModeE
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) test current HP-E 'list' samples

miFRMspotIntensCompareModeALL

java.awt.CheckboxMenuItem miFRMspotIntensCompareModeALL
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ALL selected samples

miFRMspotIntensCompareModeANY

java.awt.CheckboxMenuItem miFRMspotIntensCompareModeANY
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have ANY selected samples

miFRMspotIntensCompareModeAT_MOST

java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_MOST
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT MOST (n) selected samples

miFRMspotIntensCompareModeAT_LEAST

java.awt.CheckboxMenuItem miFRMspotIntensCompareModeAT_LEAST
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have AT LEAST (n) selected samples

miFRMspotIntensCompareModePRODUCT

java.awt.CheckboxMenuItem miFRMspotIntensCompareModePRODUCT
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have PRODUCT selected samples less than threshold

miFRMspotIntensCompareModeSUM

java.awt.CheckboxMenuItem miFRMspotIntensCompareModeSUM
Menu: (Analysis | Filter | spot intensity [SI1:SI2] sliders) must have SUM selected samples less than threshold

miFRMthrGray

java.awt.CheckboxMenuItem miFRMthrGray
Menu: (Analysis | Filter | by intensity range test) enabled

miFRMgrayRngIn

java.awt.CheckboxMenuItem miFRMgrayRngIn
Menu: (Analysis | Filter | by intensity range test) within range

miFRMgrayRngOut

java.awt.CheckboxMenuItem miFRMgrayRngOut
Menu: (Analysis | Filter | by intensity range test) outside range

miFRMthrRatio

java.awt.CheckboxMenuItem miFRMthrRatio
Menu: (Analysis | Filter | by ratio range test) enabled

miFRMratioRngIn

java.awt.CheckboxMenuItem miFRMratioRngIn
Menu: (Analysis | Filter | by ratio range test) in range

miFRMratioRngOut

java.awt.CheckboxMenuItem miFRMratioRngOut
Menu: (Analysis | Filter | Filter by ratio range test) outside of range

miFRMthrCy3Cy5Ratio

java.awt.CheckboxMenuItem miFRMthrCy3Cy5Ratio
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) enabled

miFRMCy3Cy5RatioRngIn

java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngIn
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) in range

miFRMCy3Cy5RatioRngOut

java.awt.CheckboxMenuItem miFRMCy3Cy5RatioRngOut
Menu: (Analysis | Filter | Filter by Cy3/Cy5 ratio range test) outside of range

miFRMcvModeMS

java.awt.CheckboxMenuItem miFRMcvModeMS
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample

miFRMcvModeXY

java.awt.CheckboxMenuItem miFRMcvModeXY
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample

miFRMcvModeXset

java.awt.CheckboxMenuItem miFRMcvModeXset
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X 'set' samples

miFRMcvModeYset

java.awt.CheckboxMenuItem miFRMcvModeYset
Menu: (Analysis | Filter | CV threshold sliders) test current HP-Y 'set' samples

miFRMcvModeXORYsets

java.awt.CheckboxMenuItem miFRMcvModeXORYsets
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X or HP-Y 'sets' samples

miFRMcvModeXANDYsets

java.awt.CheckboxMenuItem miFRMcvModeXANDYsets
Menu: (Analysis | Filter | CV threshold sliders) test current HP-X and HP-Y 'sets' samples

miFRMcvModeE

java.awt.CheckboxMenuItem miFRMcvModeE
Menu: (Analysis | Filter | CV threshold sliders) test current HP sample

miFRMuseCVmeanElseMax

java.awt.CheckboxMenuItem miFRMuseCVmeanElseMax
Menu: (Analysis | Filter | CV threshold sliders) use the CV mean else the CV max in computation

miFRMusePosQuantDataFlag

java.awt.CheckboxMenuItem miFRMusePosQuantDataFlag
Menu: (Analysis | Filter | use positive quantified data)

miFRMposQuantModeMS

java.awt.CheckboxMenuItem miFRMposQuantModeMS
Menu: (Analysis | Filter | use positive quantified data) test current HP sample

miFRMposQuantModeXY

java.awt.CheckboxMenuItem miFRMposQuantModeXY
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y samples

miFRMposQuantModeXYsets

java.awt.CheckboxMenuItem miFRMposQuantModeXYsets
Menu: (Analysis | Filter | use positive quantified data) test current HP-X and HP-Y 'set' samples

miFRMposQuantModeE

java.awt.CheckboxMenuItem miFRMposQuantModeE
Menu: (Analysis | Filter | use positive quantified data) test current HP-E 'list' samples

miFRMuseGoodSpotDataFlag

java.awt.CheckboxMenuItem miFRMuseGoodSpotDataFlag
Menu: (Analysis | Filter | use Good Spot data)

miFRMgoodSpotModeMS

java.awt.CheckboxMenuItem miFRMgoodSpotModeMS
Menu: (Analysis | Filter | use Good Spot data) test current HP sample

miFRMgoodSpotModeXY

java.awt.CheckboxMenuItem miFRMgoodSpotModeXY
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y samples

miFRMgoodSpotModeXORYsets

java.awt.CheckboxMenuItem miFRMgoodSpotModeXORYsets
Menu: (Analysis | Filter | use Good Spot data)

miFRMgoodSpotModeXANDYsets

java.awt.CheckboxMenuItem miFRMgoodSpotModeXANDYsets
Menu: (Analysis | Filter | use Good Spot data) test current HP-X and HP-Y 'set' samples

miFRMgoodSpotModeE

java.awt.CheckboxMenuItem miFRMgoodSpotModeE
Menu: (Analysis | Filter | use Good Spot data) test current HP-E 'list' samples

miFRMuseDetValueSpotDataFlag

java.awt.CheckboxMenuItem miFRMuseDetValueSpotDataFlag
Menu: (Analysis | Filter | use Spot Detection Value data)

miFRMOnlyGenesWithNonZeroDensityFlag

java.awt.CheckboxMenuItem miFRMOnlyGenesWithNonZeroDensityFlag
Menu: (Analysis | Filter | use only genes with non-zero intensity)

miFRMdetValueSpotModeMS

java.awt.CheckboxMenuItem miFRMdetValueSpotModeMS
Menu: (Analysis | Filter | use Spot Detection Valuedata) test current HP sample

miFRMdetValueSpotModeXY

java.awt.CheckboxMenuItem miFRMdetValueSpotModeXY
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y samples

miFRMdetValueSpotModeXANDYsets

java.awt.CheckboxMenuItem miFRMdetValueSpotModeXANDYsets
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-X and HP-Y 'set' samples

miFRMdetValueSpotModeE

java.awt.CheckboxMenuItem miFRMdetValueSpotModeE
Menu: (Analysis | Filter | use Spot Detection Value data) test current HP-E 'list' samples

miPMplotPseudoImg

java.awt.CheckboxMenuItem miPMplotPseudoImg
Menu:(Analysis | Plot | Show Microarray) use Pseudograyscale intensity

miPMplotPseudoHP_XY_RYGImg

java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_RYGImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(X)-Yellow-Green(Y) HP-X/Y ratio or Zdiff

miPMplotPseudoHP_F1F2_RYGImg

java.awt.CheckboxMenuItem miPMplotPseudoHP_F1F2_RYGImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff

miPMplotPseudoHP_XYImg

java.awt.CheckboxMenuItem miPMplotPseudoHP_XYImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-X/Y ratio or Zdiff

miPMplotPseudoF1F2Img

java.awt.CheckboxMenuItem miPMplotPseudoF1F2Img
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor Cy3/Cy5 ratio or Zdiff

miPMplotPseudoHP_XY_pValueImg

java.awt.CheckboxMenuItem miPMplotPseudoHP_XY_pValueImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor (HP-X,HP-Y) 'sets' p-value

miPMplotPseudoHP_EP_CV_valueImg

java.awt.CheckboxMenuItem miPMplotPseudoHP_EP_CV_valueImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor HP-EP 'list' CV-value

miPMdualXYpseudoImg

java.awt.CheckboxMenuItem miPMdualXYpseudoImg
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor dual HP-X and HP-Y as Field 1 and Field 2 grids

miPMflickerXY

java.awt.CheckboxMenuItem miPMflickerXY
Menu:(Analysis | Plot | Show Microarray) use Flicker of HP-X and HP-Y samples in intensity mode

miPMlowRangeZoom

java.awt.CheckboxMenuItem miPMlowRangeZoom
Menu:(Analysis | Plot | Show Microarray) use Pseudocolor low range zoom

miPEPlistType

java.awt.CheckboxMenuItem miPEPlistType
(Analysis | Plot | Expression Profile) Menu Expression Profile list type (overlay or grid).

miCLMfindSimGenesDisp

java.awt.CheckboxMenuItem miCLMfindSimGenesDisp
Menu: (Analysis | Cluster) cluster by finding similar genes

miCLMsimGeneCountsDisp

java.awt.CheckboxMenuItem miCLMsimGeneCountsDisp
Menu: (Analysis | Cluster) cluster by finding similar gene counts

miCLMhierClusterDisp

java.awt.CheckboxMenuItem miCLMhierClusterDisp
Menu: (Analysis | Cluster) cluster by hierarchical clustering

miCLMdispKmeansNodes

java.awt.CheckboxMenuItem miCLMdispKmeansNodes
Menu: (Analysis | Cluster) cluster by K-means

miCLMuseMedianKmeans

java.awt.CheckboxMenuItem miCLMuseMedianKmeans
Menu: (Analysis | Cluster | cluster by K-means) cluster using K-medians else use K-means

miCLMuseCorrCoeffDist

java.awt.CheckboxMenuItem miCLMuseCorrCoeffDist
Menu: (Analysis | Cluster) cluster using correlation coefficient else Euclidean distance

miCLMuseLSQmagNorm

java.awt.CheckboxMenuItem miCLMuseLSQmagNorm
Menu: (Analysis | Cluster | hierarchical ) cluster using LSQ magnitude normalization else ...

miCLHCMavgPGMALnk

java.awt.CheckboxMenuItem miCLHCMavgPGMALnk
Menu: (Analysis | Cluster | Hierarchical) use average-arithmetic linkage for hier.clustering

miCLHCMavgPGMCLnk

java.awt.CheckboxMenuItem miCLHCMavgPGMCLnk
Menu: (Analysis | Cluster | Hierarchical) average-centroid linkage for hier.clustering

miCLHCMnextMinLnk

java.awt.CheckboxMenuItem miCLHCMnextMinLnk
Menu: (Analysis | Cluster | Hierarchical) next-min for linkage hier.clustering

miCLHCMunWtAvg

java.awt.CheckboxMenuItem miCLHCMunWtAvg
Menu: (Analysis | Cluster | Hierarchical) unweighted/weighted average for hier.clustering

miCLMnormHP

java.awt.CheckboxMenuItem miCLMnormHP
Menu: (Analysis | Cluster | Hierarchical) normalize EP by HP sample for hier.clustering

miCLHCMuseClusterDistCache

java.awt.CheckboxMenuItem miCLHCMuseClusterDistCache
Menu: (Analysis | Cluster | Hierarchical) use Cluster dist-dist cache matrix for hier.clustering

miCLHCMuseShortClusterDistCache

java.awt.CheckboxMenuItem miCLHCMuseShortClusterDistCache
Menu: (Analysis | Cluster | Hierarchical) use 16-bit short vs 32-bit float for hier.clustering

miTMtblFontSize8pt

java.awt.CheckboxMenuItem miTMtblFontSize8pt
Menu: (Analysis | Report) font size is 8 pt

miTMtblFontSize10pt

java.awt.CheckboxMenuItem miTMtblFontSize10pt
Menu: (Analysis | Report) font size is 10 pt

miTMtblFontSize12pt

java.awt.CheckboxMenuItem miTMtblFontSize12pt
Menu: (Analysis | Report) font size is 12 pt

miPRtblFontSize8pt

java.awt.CheckboxMenuItem miPRtblFontSize8pt
Menu: (Analysis | Report) font size is 8 pt

miPRtblFontSize10pt

java.awt.CheckboxMenuItem miPRtblFontSize10pt
Menu: (Analysis | Report) font size is 10 pt

miPRtblFontSize12pt

java.awt.CheckboxMenuItem miPRtblFontSize12pt
Menu: (Analysis | Report) font size is 12 pt

miTMtblFmtTabDelim

java.awt.CheckboxMenuItem miTMtblFmtTabDelim
Menu: (Analysis | Report) use Tab-Delimited table format

miTMtblFmtClickable

java.awt.CheckboxMenuItem miTMtblFmtClickable
Menu: (Analysis | Report) use Dynamic clickable table format

miTMtblFmtAddEPdata

java.awt.CheckboxMenuItem miTMtblFmtAddEPdata
Menu: (Analysis | Report) add Expr-Profile data to Table

miTMtblFmtUseRawEPdata

java.awt.CheckboxMenuItem miTMtblFmtUseRawEPdata
Menu: (Analysis | Report) use raw Expr-Profile data in Table

miTMtblFmtAddHP_XYsetStat

java.awt.CheckboxMenuItem miTMtblFmtAddHP_XYsetStat
Menu: (Analysis | Report) add HP-XY set statistics data to Table

miTMtblFmtAddOCLstatistics

java.awt.CheckboxMenuItem miTMtblFmtAddOCLstatistics
Menu: (Analysis | Report) add OCL statistics data to Table

miPLGMuseSPLUSasComputingEngine

java.awt.CheckboxMenuItem miPLGMuseSPLUSasComputingEngine
Menu: (Plugins | Use S-PLUS, else R, as computing engine [CB])

miPLGMuseTimeStampReports

java.awt.CheckboxMenuItem miPLGMuseTimeStampReports
Menu: (Plugins | Save SRLO reports in time-stampled folder [CB])

HP_Xlabel

java.awt.Label HP_Xlabel
GUI label for current HP-X

HP_Ylabel

java.awt.Label HP_Ylabel
GUI label for current HP-Y
Constructor Detail

MenuBarFrame

MenuBarFrame(MAExplorer mae,
             java.lang.String title,
             int x0,
             int y0)
MenuBarFrame() - constructor for main GUI window and menubar.
Parameters:
mae - is instance of MAExplorer
title - is the name of the frame
x0 - is ULHC X position of frame
y0 - is ULHC Y position of frame
See Also:
addMenuBar(), buildMenuGUI(int, int, int, int), insertPluginMenuEntries(), Frame.setTitle(java.lang.String)

MenuBarFrame

MenuBarFrame(MAExplorer mae)
MnuBarFrame() - constructor used with the Applet.
Parameters:
mae - is instance of MAExplorer
Method Detail

redoMenuBar

void redoMenuBar()
redoMenuBar() - redo the menubar if restarted a new database with different entries.
See Also:
addMenuBar(), insertPluginMenuEntries(), Frame.setTitle(java.lang.String)

addMenuStubToMenuStubList

private void addMenuStubToMenuStubList(java.lang.String name,
                                       java.awt.Menu menuStub)
addMenuStubToMenuStubList() - add menu position to Menu Stub List. This list can be used when loading plugins to associate the plugin with a particular menu stub in the menu tree.
The data for this is found in the Config DB as four paired numbered PARAM entries and is loaded when the Config DB is loaded:
    "PluginMenuName"+i.         E.g. "New sample report"
    "PluginMenuStubName"+i.     E.g. "Report:sample"
    "PluginClassFile"+i.        E.g. "NewReport.class"
    "PluginCallAtStartup"+i.    E.g. "TRUE"
Parameters:
name - is the name of the menu stub
menuStub - is the Menu stub associated with the name

findMenuStubByName

private java.awt.Menu findMenuStubByName(java.lang.String name)
findMenuStubByName() - find menu stub associated with name in Menu Stub List. The data for this is found in the Config DB as four paired numbered PARAM entries and is loaded when the Config DB is loaded:
    "PluginMenuName"+i.         E.g. "New sample report"
    "PluginMenuStubName"+i.     E.g. "Report:sample"
    "PluginClassFile"+i.        E.g. "NewReport.class"
    "PluginCallAtStartup"+i.    E.g. "TRUE"
Parameters:
name - is the name of the menu stub to look for
Returns:
Menu stub associated with the name

insertPluginMenuEntries

private void insertPluginMenuEntries()
insertPluginMenuEntries() - insert Plugin menus if any at proper stubs. Search the config sPluginXXX[] database for plugins to install in the menu and to load. Note: this is called AFTER the initial menu tree is built. The data for this is found in the Config DB as three paired numbered PARAM entries and is loaded when the Config DB is loaded:
    "PluginMenuName"+i.         E.g. "New sample report"
    "PluginMenuStubName"+i.     E.g. "Report:sample"
                         (from legal list of Menu stub names)
    "PluginClassFile"+i.        E.g. "NewReport.class"
    "PluginCallAtStartup"+i.    E.g. "InstallInMenu"
                                 (1 of: "InstallInMenu", "RunOnStartup", "NoInstall")
See Also:
findMenuStubByName(java.lang.String)

callAllStartupPlugins

void callAllStartupPlugins()
callAllStartupPlugins() - call all Plugins initialized at Startup. These are indicated by sPluginCallAtStartup[] being "TRUE". Search the config sPluginXXX[] database for Startup plugins to call. Note: these classes were previously installed. The data for this is found in the Config DB as four paired numbered PARAM entries and is loaded when the Config DB is loaded:
    "PluginMenuName"+i.         E.g. "New sample report"
    "PluginMenuStubName"+i.     E.g. "Report:sample"
    "PluginClassFile"+i.        E.g. "NewReport.class"
    "PluginCallAtStartup"+i.    E.g. "TRUE"

makeMenuItem

private void makeMenuItem(java.awt.Menu pm,
                          java.lang.String sLabel,
                          java.lang.String sCmd,
                          int shortcut)
makeMenuItem() - make menuItem entry in menu list. Setup action command and listener call back. If the command name is null, set the command name to label name. if shortCut is <0, then gray-out the item. i.e. not available and do not add to event handler.
Parameters:
pm - is the menu to install it
sLabel - is the visible label
sCmd - is the opt Cmd name (uses sLabel if null)
shortcut - is the opt short cut

makeSubMenu

private java.awt.Menu makeSubMenu(java.awt.Menu pm,
                                  java.lang.String sLabel,
                                  java.lang.String sCmd,
                                  int shortcut)
makeSubMenu() - make submenu entry in menu list. Setup action command and listener call back. If the command name is null, set the command name to label name.
Parameters:
pm - is the menu to install it
sLabel - is the visible label
sCmd - is the opt Cmd name (uses sLabel if null)
shortcut - is the opt short cut

makeChkBoxMenuItem

private java.awt.CheckboxMenuItem makeChkBoxMenuItem(java.awt.Menu pm,
                                                     java.lang.String sLabel,
                                                     java.lang.String sCmd,
                                                     int shortcut,
                                                     boolean value)
makeChkBoxMenuItem() - make CheckboxMenuItem entry in popup menu list. Setup action command and listener call back. If the command name is null, set the command name to label name. if shortCut is <0, then gray-out the item. i.e. not available and do not add to event handler.
Parameters:
pm - is the menu to install it
sLabel - is the visible label
sCmd - is the opt Cmd name (uses sLabel if null)
shortcut - is the opt short cut
value - is the initial value of the checkbox

addSetHP_XYEsubmenuTree

void addSetHP_XYEsubmenuTree(java.awt.Menu subMenu,
                             java.lang.String hpPostfixStr)
addSetHP_XYEsubmenuTree() - add HP sample submenu tree to submenu if submenus exist. The hpPostfixStr : "_X" or "_Y" or "_E" or ""
Parameters:
subMenu - to add to the tree
hpPostfixStr - command string to associate with the submenu entries.
See Also:
makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int), makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)

addRLOsubmenuTree

void addRLOsubmenuTree()
addRLOsubmenuTree() - add RLO R scripts submenu tree to rloSmnu if RLOs exist.
See Also:
makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int), makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)

addMenuBar

int addMenuBar()
addMenuBar() - add menubar with menus to the frame
Returns:
the number of menu and commands created
See Also:
MaeJavaAPI, MaeJavaAPI.setMenuHook(java.awt.Menu), addSetHP_XYEsubmenuTree(java.awt.Menu, java.lang.String), addMenuStubToMenuStubList(java.lang.String, java.awt.Menu), makeChkBoxMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int, boolean), makeMenuItem(java.awt.Menu, java.lang.String, java.lang.String, int), makeSubMenu(java.awt.Menu, java.lang.String, java.lang.String, int)

buildMenuGUI

void buildMenuGUI(int x0,
                  int y0,
                  int width,
                  int height)
buildMenuGUI() - build the GUI with pop up menus
Parameters:
x0 - is X ULHC position of window
y0 - is Y ULHC position of window
width - of window
height - of window
See Also:
ArrayScroller, StateScrollers, createDialogQueryFrames(), setSTOPbuttonState(boolean, boolean)

createDialogQueryFrames

void createDialogQueryFrames()
createDialogQueryFrames() - create all popup dialog frames
See Also:
PopupDialogQuery, PopupBinOprDialogQuery

setSTOPbuttonState

void setSTOPbuttonState(boolean flag,
                        boolean isEnabledFlag)
setSTOPbuttonState() - enable/disable STOP button & clear abortFlag. If either flag is true, then repaint the button or force it to appear. [TODO] need to make this handler a separate thread. Need to put all EventMenu processes on a separate thread so can abort it. For now, the button is disabled...
Parameters:
flag - to abort command process if true.
isEnabledFlag - sets stop label to "STOP!" else "RUNNING"
See Also:
Component.repaint()

setHP_XYlabels

void setHP_XYlabels()
setHP_XYlabels() - set the GUI HP-X: and HP-Y: labels as singles or multiple (Class names)
See Also:
SampleSets.setHPxyModStrings()

enableMenus

void enableMenus(java.lang.String opr)
enableMenus() - enable/disable all menus, checkboxes, typein fields etc.
Parameters:
opr - is "none", "all", or "basic"

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed() - handle action events for Buttons and menu commands.
Specified by:
actionPerformed in interface java.awt.event.ActionListener
Parameters:
e - is action event for buttons and menu commands
See Also:
EventMenu.handleActions(java.awt.event.ActionEvent), FileIO.logMsgln(java.lang.String), PopupGeneGuesser, setSTOPbuttonState(boolean, boolean)

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)
itemStateChanged() - handle item state changed events. NOTE: need to implement radio groups here since AWT only implements radio groups for Checkboxes, and ot for Checkbox MenuItems.
Specified by:
itemStateChanged in interface java.awt.event.ItemListener
Parameters:
e - is checkbox event Checkbox and menu checkbox commands
See Also:
EventMenu.handleItemStateChanged(java.awt.event.ItemEvent)

windowClosing

public void windowClosing(java.awt.event.WindowEvent e)
windowClosing() - close the window
Specified by:
windowClosing in interface java.awt.event.WindowListener
Parameters:
e - is window closing event
See Also:
MAExplorer.quit()

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

windowOpened

public void windowOpened(java.awt.event.WindowEvent e)
Specified by:
windowOpened in interface java.awt.event.WindowListener

keyPressed

public void keyPressed(java.awt.event.KeyEvent e)
keyPressed() - get key Pressed event - look for ESCAPE key to set STOP flag
Specified by:
keyPressed in interface java.awt.event.KeyListener
Parameters:
e - is key pressed event

keyReleased

public void keyReleased(java.awt.event.KeyEvent e)
keyReleased() - get key Released event
Specified by:
keyReleased in interface java.awt.event.KeyListener
Parameters:
e - is key released event

keyTyped

public void keyTyped(java.awt.event.KeyEvent e)
keyTyped() - get key typed event - look for ESCAPE key to set STOP flag
Specified by:
keyTyped in interface java.awt.event.KeyListener
Parameters:
e - is key typed event