Class MAExplorer

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--java.awt.Panel
                    |
                    +--java.applet.Applet
                          |
                          +--MAExplorer
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.lang.Runnable, java.io.Serializable

public class MAExplorer
extends java.applet.Applet
implements java.lang.Runnable

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

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:
$Date: 2003/07/23 19:19:32 $ $Revision: 1.127 $
Author:
P. Lemkin (NCI), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD
See Also:
MAExplorer Home, Gene, GeneClass, GeneGeneDist, GeneList, GipoTable, GetParams, MaeJavaAPI, MaHybridSample, MaInfoTable, Maps, MenuBarFrame, PopupRegistry, SampleSets, SamplesTable, ScrollableImageCanvas, SpotData, SpotFeatures, StageNames, StateScrollers, Statistics, UserState, Util, Serialized Form

Inner classes inherited from class java.applet.Applet
java.applet.Applet.AccessibleApplet
 
Inner classes inherited from class java.awt.Panel
java.awt.Panel.AccessibleAWTPanel
 
Inner classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Inner classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock
 
Field Summary
(package private)  boolean abortFlag
          Flag: set true by the STOP button.
(package private)  boolean addExprProfileFlag
          set for EP ratios in gene REPORTS
(package private)  boolean addHP_XYstatFlag
          set for HP_XY statistics in gene REPORTS
(package private)  boolean addOCLstatFlag
          set for OCL statics statistics in gene REPORTS
(package private)  boolean allowNegQuantDataFlag
          PARAM "allowNegQuantDataFlag"
(package private)  java.applet.Applet applet
          "this" applet instance for MAExplorer main class
(package private)  boolean autoStateScrPopupFlag
          Auto state-scroller popup windown assoc w/Filters
(package private)  boolean bkgdCorrectFlag
          calc: I'= Intensity - background
(package private) static java.lang.String browserTitle
          browser title
(package private)  java.lang.String cacheDir
          Standalone /Cache directory for saving data downloaded for array Web server.
(package private)  boolean cacheFIOflag
          Flag: if enabled, it first checks the /Cache directory for all http:// codebase files and if not in the cache, it saves the file in the cache after reading it from the Web.
(package private) static boolean CANVAS_WRAPAROUND_BUG
          if debugging CANVAS_WRAPAROUND_BUG
(package private) static int canvasHSize
          PARAM "CanvasHorSize"
(package private) static int canvasVSize
          PARAM "CanvasVertSize"
(package private)  GeneGeneDist ccd
          Global instance of Gene-Gene distances
(package private)  CompositeDatabase cdb
          Global instance of composite database object
(package private)  Condition cdList
          Global instance of condition list tables
(package private)  Config cfg
          Global instance of Configuration and state variables including top level file, URL configs, etc.
(package private)  ConfigTable cfgDB
          Global instance of configuration data from MaExplorerConfig.txt file
(package private)  java.lang.String classNameX
          "HP-X 'set'" name for msListX[] HPs
(package private)  java.lang.String classNameY
          "HP-Y 'set'" name for msListY[] HPs
(package private)  ClusterGenes clg
          Global instance of Cluster Genes object
(package private)  GeneList clLst
          Global instance of GeneList contains gene (clone) list tables
(package private)  ClusterSamples clstrSamp
          Global instance of ClusterSamples class
(package private)  boolean clusterHP_EfilterFlag
          filter genes by cluster HP-E
(package private)  boolean clusterOnFilteredCLflag
          cluster on Filtered/All genes
(package private) static java.lang.String codeBase
          full codebase path for /mae/ on MAE svr
(package private) static int COMPARE_ALL
          range-compare mode: spot intensity of samples - ALL samples must comply
(package private) static int COMPARE_ANY
          range-compare mode: spot intensity of samples - ANY samples must comply
(package private) static int COMPARE_AT_LEAST
          range-compare mode: spot intensity of samples - AT LEAST n samples must comply
(package private) static int COMPARE_AT_MOST
          range-compare mode: spot intensity of samples - AT MOST n samples must comply
(package private) static int COMPARE_PRODUCT
          range-compare mode: spot intensity of samples - PRODUCT of samples must comply
(package private) static int COMPARE_SUM
          range-compare mode: spot intensity of samples - SUM samples must comply
(package private)  java.lang.String configFile
          Default Configuration file: "MaExplorerConfig.txt"
(package private) static boolean CONSOLE_FLAG
          Debugging flag - Always TRUE
(package private)  float cr1
          PARAM "CR1" MIN_RATIO range (i.e.
(package private)  float cr2
          PARAM "CR2" MAX_RATIO range
(package private) static int curHP
          Current hybridized sample index for hps.msList[]
(package private) static int curHP_X
          Current HP-X sample index for hps.msList[]
(package private) static int curHP_Y
          Current HP-Y sample index for hps.msList[]
(package private) static java.lang.String curPrjName
          current project being requested
(package private)  int cvTestMode
          CV test mode: SS_MODE_xxxx
(package private) static java.lang.String date
          startup date
(package private)  boolean dbESTviewerFlag
          dbEST popup browser Mode
(package private) static java.lang.String dbID
          Unique Database ID ("DIDxxxxxx") - used as prefix for State/ files
(package private) static boolean DBUG_CV_DISPLAY_EPLIST
          if debugging display the CV of HP-EP samples as colors [0:1.0] lie for p-value display.
(package private) static boolean DBUG_GENERIC_NORM_PLUGIN
          [DEBUGGING] If debugging a plugin extending NormalizationPlugin, you may debug it in the MAExplorer core image by temporarily including in in the code.
(package private) static boolean DBUG_GENOMIC_URLS_FLAG
          debugging Genomic Menu/URLs
(package private) static boolean DBUG_HCN
          debugging HierClustNode lists
(package private) static boolean DBUG_LOGIN
          Debugging variablen - debugging CGI login locally
(package private) static boolean DBUG_MAERlibr_ZIP_UPDATE
          If debugging MAERlibr.zip file update.
(package private) static boolean DBUG_MEDMINER_FLAG
          debugging MedMiner Menu/URLs
(package private) static boolean DBUG_NORM_PLUGIN
          if debugging NormalizationPlugins using the PluginLoader
(package private) static boolean DBUG_QUALCHK_QUANT_FLAG
          debugging QualCheck
(package private) static boolean DBUG_SET_EGL_FROM_DENDROGRAM
          if debugging setting EGL set from subtree of HCN dendrogram
(package private) static boolean DBUG_STANDALONE
          debugging Stand-Alone code
(package private) static boolean DBUG_TEST_PLUGIN_FLAG
          Enable testing MAEPlugin from the intial menu without dynamic MAEPlugin loading of the class.
(package private) static boolean DBUG_TEST_R_OR_SPLUS_CHECKBOX
          Test the code to let the user switch between R or S-Plus as the statistics evaluation engine.
(package private) static boolean DEBUG
          General purpose debugging flag.
(package private) static java.lang.String DEF_BASESERVER
          Default microarray database server.
(package private) static java.lang.String defDir
          Default standalone directory (=null JWS hack)
(package private)  java.lang.String defSAprjName
          Standalone current project DB name
(package private) static java.lang.String defSAwebAddr
          Default standalone assoc.
(package private) static java.lang.String defStartupFile
          Default standalone .mae startup file
(package private)  int detValueSpotTestMode
          Spot (Detection Value) test mode: SS_MODE_xxxx
(package private)  boolean dieFlag
          Flag: call quit() if flag set to exit run().
(package private)  java.lang.String docCodeBase
          codebase where the documentation Reference Manual is kept
(package private)  boolean doGCflag
          Flag: run the Garbage Collector.
(package private) static int DRAW_BIN
          Plotting types - draw histogram bin
(package private) static int DRAW_BOX
          Plotting types - draw box symbol in scatter plot
(package private) static int DRAW_CIRCLE
          Plotting types - draw circle symbol in scatter plot
(package private) static int DRAW_PLUS
          Plotting types - draw plus symbol in scatter plot
(package private)  DryRotException dryRotExcept
          Global instance of DryRotException class
(package private)  java.lang.String dryrotLogStr
          List of dryrot messages if any occur.
(package private)  boolean dualXYpseudoPlotFlag
          Flag: plot mean HP-X in F1, HP-Y in F2 pseudoimg
(package private)  DrawPseudoImage dwPI
          Global instance of draw pseudo image
(package private)  java.lang.String dynFileSeparator
          dynamic paths separator, "/" or "|", depends on OS and if using URL from Stand-Alone
(package private) static int EDIT_ADD
          Edited Gene List mouse click action mode: ADD gene on click
(package private) static int EDIT_NOP
          Edited Gene List mouse click action mode: NO-OP
(package private) static int EDIT_RMV
          Edited Gene List mouse click action mode: REMOVE gene on click
(package private)  int editMode
          EGL mode for 'edited gene list': EDIT_xxxx
(package private)  EditedGeneList egl
          Global instance of edit editedCL gene (clone) list
(package private)  EventMenu em
          Global instance of handle MenuItem and MenuItemCheckbox events
(package private)  boolean enableFIOcachingFlag
          Flag: stand-alone PARAM "enableFIOcaching"
(package private)  boolean F_TestOCLFilterFlag
          filter genes passing current OCL (Ordered Condition List) F-test
(package private)  Filter fc
          Global instance of data Filter gene operations
(package private) static java.lang.String fileBasePath
          either Applet or file I/O or standalone
(package private)  java.lang.String fileSeparator
          paths, "/" or "|", depends on OS
(package private)  FileIO fio
          Global instance of file and URL I/O
(package private)  boolean flickerXYflag
          Flicker HP-X and HP-Y in run() loop
(package private)  boolean gangSpotFlag
          Flag: report f1 or f1&f2 (ganged)
(package private)  GeneClass gct
          Global instance of Gene Class table
(package private)  boolean genBankViewerFlag
          GenBank popup browser Mode
(package private)  Gene gene
          Global instance of Gene
(package private)  boolean geneClassMbrFilterFlag
          filter genes by GeneClass mbrshp
(package private)  boolean[] genomicViewerFlag
          holds sGenomicMenu[cfg.nGenomicMenus] menu flags
(package private)  GipoTable gipo
          Global instance of GIPO table mapping genes to other data
(package private)  GenNormalizationPlugin gnp
          Only while debugging: if DBUG_GENERIC_NORM_PLUGIN is set for use with TestPlugin.
(package private)  int goodSpotTestMode
          Good Spot (QualChk) test mode: SS_MODE_xxxx
(package private)  GetParams gp
          Global instance of contains set of applet/configuration PARAM parsers
(package private)  GridCoords grcd
          Global instance of share grid coordinate mapper
(package private) static int HIER_CLUST_NEXT_MIN_LNKG
          Hierarchical clustering mode: next-minimum cluster linkage
(package private) static int HIER_CLUST_PGMA_LNKG
          Hierarchical clustering mode: Average-arithmetic linkage
(package private) static int HIER_CLUST_PGMC_LNKG
          Hierarchical clustering mode: Average-centroid linkage
(package private)  int hierClustMode
          Hier.Clustering linkage mode: HIER_CLUST_xxxxx
(package private)  boolean hierClustUnWtAvgFlag
          use UPGMA or WPGMA for computing the average node vector when hierarchical clustering.
(package private) static double[] histRatioBin
          preloaded set of legal ratios in [1/100 : 100]
(package private)  SampleSets hps
          Global instance of HP-X, HP-Y and HP-E sets and lists
(package private)  int iHPnbr
          # of entries in "image#" PARAM list.
(package private)  java.lang.String[] iImageFile
          image files to read allocated [MAX_HYB_SAMPLES+1]
(package private)  MaInfoTable infoDB
          Global instance of depricated "MaExplorerInfo.txt" DB list of .info data for entire DB.
(package private)  boolean intensFilterFlag
          filter genes by intensity threshold
(package private)  ArrayScroller is
          Global instance of ArrayScroller obj to hold pseudoarray image scrollable canvas
(package private)  java.lang.String[] iSampleName
          HP name from "image*" [1:iHPnbr] allocated [MAX_HYB_SAMPLES+1]
(package private)  boolean isAppletFlag
          Flag: cleared if enter through standalone main()
(package private)  boolean isLoggedInFlag
          set if valid login has been performed
(package private)  boolean isWinPCflag
          Flag: set to TRUE if any Windows PC
(package private)  boolean isWorkingMAE
          Flag indicating whether using the Working server (mae/) or not
(package private)  boolean isZscoreFlag
          Flag: is using one of the Zscore normalizations
(package private) static java.lang.String javaHome
          Standalone getProperties("java.home")
(package private)  boolean killAppletFlag
          Flag: set if do "Quit".
(package private)  boolean KS_TestXYsetsFilterFlag
          filter genes passing HP-X/-Y sets KS-test
(package private)  int LECBdebug
          Developer debug flag.
(package private)  boolean locusLinkViewerFlag
          LocusLink LocusID page popup browser Mode
(package private)  boolean lowRangeZoomFlag
          Scale pseudoarray image by 1/100 to zoom low-range values
(package private)  boolean mAdbViewerFlag
          mAdb Clone page popup browser Mode
(package private)  boolean madeChangesFlag
          made changes to DB so may want to SAVE DB
(package private) static java.lang.String MAE_STARTUP_FILE
          Default empty .mae startup database
(package private)  java.lang.String maeServerBase
          top level codebase for MAE server
(package private) static java.lang.String maeTitleVer
          Compiled MAExplorer title with version number
(package private)  int[] mapHPtoMenuName
          index of snHPName[] corresponding to iSampleName[] entry allocated [MAX_HYB_SAMPLES+1].
(package private) static int MARKER_CIRCLE
          pseudoarray canvas - draw circle of size radius
(package private) static int MARKER_CURRENT
          pseudoarray canvas - draw Current object
(package private) static int MARKER_GENES
          pseudoarray canvas - draw all spots in gene list
(package private) static int MARKER_KMEANS_CLUSTER
          pseudoarray canvas - draw K-means cluster #
(package private) static int MARKER_NONE
          pseudoarray canvas - No overlay
(package private) static int MARKER_PLUS
          pseudoarray canvas - draw 5x5 plus
(package private) static int MARKER_SQUARE
          pseudoarray canvas - draw square of size radius
(package private) static int MASTER_CLONE_ID
          Master masterIDmode Mode - clone ID
(package private) static int MASTER_DBEST3
          Master masterIDmode Mode - dbEST 3' ID
(package private) static int MASTER_DBEST5
          Master masterIDmode Mode - dbEST 5' ID
(package private) static int MASTER_GENBANK
          Master masterIDmode Mode - GenBank ID
(package private) static int MASTER_GENBANK3
          Master masterIDmode Mode - GenBank 3' ID
(package private) static int MASTER_GENBANK5
          Master masterIDmode Mode - GenBank 5' ID
(package private) static int MASTER_GENE_NAME
          Master masterNameMode Mode - gene name
(package private) static int MASTER_GENERIC_ID
          Master masterIDmode Mode - generic ID
(package private) static int MASTER_LOCUSLINK
          Master masterIDmode Mode - LocusLink ID
(package private) static int MASTER_OMIM
          Master masterIDmode Mode - OMIM ID
(package private) static int MASTER_SWISS_PROT
          Master masterIDmode Mode - SwissProt ID
(package private) static int MASTER_UG_ID
          Master masterIDmode Mode - UniGene ID
(package private) static int MASTER_UG_NAME
          Master masterNameMode Mode - UniGene name
(package private)  java.lang.String masterGeneName
          either "GeneName", "UGclusterName, etc"
(package private)  int masterIDmode
          either MASTER_CLONE_ID or MASTER_GENBANK or MASTER_GENBANK5 or MASTER_GENBANK3 or MASTER_UG_ID, MASTER_SWISS_PROT, MASTER_GENERIC_ID
(package private)  java.lang.String masterIDname
          either "CloneID", "UniGeneID, GenBank, etc"
(package private)  int masterNameMode
          either MASTER_GENE_NAME or MASTER_UG_NAME
static int MAX_COND_PARAM
          maximum number of Condition parameters
(package private) static int MAX_CONDITION_LISTS
          Max # of named sample condition lists.
(package private) static int MAX_HYB_SAMPLES
          Max # of hybridized array samples to load at one time
(package private)  int MAX_INTENSITY
          maximum # intensity values of .quant data
(package private) static int MAX_ORDERED_COND_LISTS
          maximum number of # of ordered condition lists slots available.
(package private) static int MAX_PROJECTS
          Maximum # of projects for project lists
(package private) static float MAX_RATIO
          maximum ratio for histogram of ratios histRatioBin[]
(package private) static int MAX_RATIO_HIST
          # of bins in histRatioBin[]
(package private)  int maxPreloadImgs
          PARAM max # images to preload set from "maxPreloadImages"
(package private)  MenuBarFrame mbf
          Global instance of Frame based MenuBar
(package private)  boolean medMinerViewerFlag
          MedMiner gene page popup browser Mode
(package private) static float MIN_RATIO
          Minimum ratio for histogram of ratios histRatioBin[]
static MaeJavaAPI mja
          Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins
(package private)  Maps mp
          Global instance of lookup table maps populated elsewhere
(package private)  boolean mReady
          Flag set when done initialization and ready to analyze
(package private) static MaHybridSample ms
          Current hybridized sample
(package private) static MaHybridSample msPrev
          Previous (last current) hybridized sample for garbage collection
(package private) static MaHybridSample msX
          Current HP-X hybridized sample
(package private) static MaHybridSample msY
          Current HP-Y hybridized sample
(package private) static int N_CONST_FILES
          # of files always read: MaExplorerConfig.txt GIPO-xxx.txt Samples.txt MaExplorerInfo.txt [DEPRICATED]
(package private) static int N_EST_QUANT_FILES
          default est # .quant files to load
(package private) static boolean NEVER
          Debugging flag - Always FALSE
(package private)  int nFilesRead
          # of files read so far
(package private)  int nFilesTotal
          # files always read + # .quant files.
(package private)  boolean noMsgReportFlag
          PARAM "noMsgReporting"
(package private)  boolean normByCalDNAflag
          normalize by Calibration DNA set
(package private)  boolean normByGeneSetFlag
          normalize by 'user gene set'
(package private)  boolean normByHousekeepGenesFlag
          normalize by housekeeping genes
(package private)  boolean normByLogMedianFlag
          normalize by HP log of median
(package private)  boolean normByMedianFlag
          normalize by HP median
(package private)  boolean normByZscoreFlag
          normalize by HP Zscore
(package private)  boolean normByZscoreMeanAbsDevLogFlag
          norm.
(package private)  boolean normByZscoreMeanStdDevLogFlag
          norm by Zscore log intens,stdDev.
(package private)  boolean normHCbyRatioHPflag
          set true if normalize Hier-Clustering dataV[h] by dataV[iDataV] else norm by HP[h] msListE[h].maQ.maxRI
(package private)  java.lang.String normName
          name of normalization method
(package private)  java.lang.String normNameDisp
          name of norm.
(package private)  int nValidPrj
          # of login verified projects
(package private)  OverlayMap olmap
          Global instance of scatterplot named overlay maps
(package private)  boolean omimViewerFlag
          OMIM popup browser Mode
private  boolean onceOnlyFlag
          flag to prevent multiple instances
(package private) static java.lang.String osName
          operating system Windows, SUNOS, etc
(package private)  java.lang.String otherUserName
          access other user name from Dialog
(package private)  int pHeight
          working size of pseudoarray image
(package private)  java.awt.Image pImage
          pseudo grayscale microarray image based on .quantspot intensity data.
(package private)  boolean pirViewerFlag
          PIR page popup browser Mode
(package private) static int PLOT_CLUSTER_GENES
          Popup plot mode: cluster similar genes plot
(package private) static int PLOT_CLUSTER_HIER
          Popup plot mode: hierarchical cluster genes plot
(package private) static int PLOT_CLUSTER_HYBSAMPLES
          Popup plot mode: cluster HP-samples plot
(package private) static int PLOT_CLUSTERGRAM
          Popup plot mode: clustergram genes plot
(package private) static int PLOT_EXPR_PROFILE
          Popup plot mode: expression profile plot
(package private) static int PLOT_F1_F2_INTENS
          Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot
(package private) static int PLOT_F1_F2_MVSA
          Popup plot mode: M vs A scatter plot of current sample
(package private) static int PLOT_HIST_F1F2_RATIO
          Popup plot mode: current HP F1/F2 ratio histogram plot
(package private) static int PLOT_HIST_HP_XY_RATIO
          Popup plot mode: HP-X/HP-Y ratio histogram plot
(package private) static int PLOT_HIST_HP_XY_SETS_RATIO
          Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot
(package private) static int PLOT_HP_XY_INTENS
          Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot
(package private) static int PLOT_INTENS_HIST
          Popup plot mode: current HP intensity histogram plot
(package private) static int PLOT_KMEANS_CLUSTERGRAM
          Popup plot mode: k-means cluster genes plot
(package private) static int PLOT_PSEUDO_F1F2_IMG
          Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red]
(package private) static int PLOT_PSEUDO_F1F2_RYG_IMG
          Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
(package private) static int PLOT_PSEUDO_HP_EP_CV_VALUE_IMG
          Pseudoarray image plot mode: display HP_EP 'list' CV coefficient of variation [0.0:1.0] as [black:white]
(package private) static int PLOT_PSEUDO_HP_XY_IMG
          Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red]
(package private) static int PLOT_PSEUDO_HP_XY_P_VALUE_IMG
          Pseudoarray image plot mode: display X,Y 'sets' p-Value [0.0:1.0] as [black:white]
(package private) static int PLOT_PSEUDO_HP_XY_RYG_IMG
          Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]
(package private) static int PLOT_PSEUDOIMG
          Pseudoarray image plot mode: Grayscale display current HP intensity
(package private)  int plotImageMode
          Pseudo array image plot mode: PLOT_xxxx_IMAGE
(package private) static java.lang.String pluginsDir
          Standalone /Plugins directory where optional MAEPlugins may be found
(package private)  int posQuantTestMode
          positive Quant data test mode: SS_MODE_xxxx
(package private)  boolean presentViewFlag
          Flag: use larger fonts, thicker lines, circles, plus, etc.
(package private)  boolean previousStartupState
          Flag that indicates if the startup .mae file exists in PREVIOUS database
(package private) static boolean PRINT_MEM_TIMES
          print memory times at key places
(package private) static java.lang.String prjListFile
          Standalone Sample DB project list DB file
(package private)  java.lang.String proxyServer
          base addr PARAM "proxyServer"
(package private) static int PSEUDOIMG_HEIGHT
          (600x900) size of pseudoarray image canvas
(package private) static int PSEUDOIMG_WIDTH
          (600x900) size of pseudoarray image canvas
(package private)  PopupRegistry pur
          Global instance of holds popup registry of all active popup windows and update handlers.
(package private)  int pWidth
          working size of pseudoarray image
(package private) static int QUALTYPE_ALPHA
          QualCheck type: Alphabetic codes
(package private) static int QUALTYPE_PROP_CODE
          QualCheck type: uses MAE Gene.xxxx prop QualCheck codes
(package private) static int QUALTYPE_THR
          QualCheck type: Uses [qualThr] QualCheck continuous data
(package private)  int qualTypeMode
          spot quality type mode: QUALTYPE_xxxx
(package private)  float r1
          PARAM "R1" MIN_RATIO range (HP-X/HP-Y)
(package private)  float r2
          PARAM "R2" MAX_RATIO range
(package private) static int RANGE_INSIDE
          rangeMode: Inside [v1:v2] for testing
(package private) static int RANGE_OUTSIDE
          rangeMode: Outsiide [v1:v2] for testing
(package private)  boolean ratioCy3Cy5FilterFlag
          filter genes by Cy3/Cy5 ratio threshold
(package private)  int ratioCy3Cy5RangeMode
          Cy3/Cy5 range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
(package private)  boolean ratioFilterFlag
          filter genes by ratio threshold
(package private)  boolean ratioMedianCorrectionFlag
          enable cy3/cy5 ratio median correction
(package private)  int ratioRangeMode
          Ratio range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE
(package private)  int reportMode
          Report type mode: RPT_xxxx.
(package private)  java.lang.String reportRatioStr
          either "F1/F2", "Cy3/Cy5", or "Cy5/Cy3"
(package private)  boolean reuseGUIframeFlag
          Flag: set if reuse main GUI frame
(package private)  boolean reuseXYcoordsFlag
          Flag: reuse HP[1] Quant xy coords for speedup
(package private) static int RPT_FMT_DYN
          Report format mode: dynamic spreadsheet report
(package private) static int RPT_FMT_TAB_DELIM
          Report format mode: tab-delimited report as TextArea
(package private) static int RPT_NONE
          Report mode: no report
(package private) static int RPT_TBL_ALL_GENES_CLUSTER
          Report mode: all genes clustering statistics
(package private) static int RPT_TBL_CALIB_DNA_STAT
          Report mode: array samples Calibration DNA statistics
(package private) static int RPT_TBL_CUR_GENE_CLUSTER
          Report mode: current gene clustering statistics
(package private) static int RPT_TBL_EDITED_GENE_LIST
          Report mode: Edited Gene List
(package private) static int RPT_TBL_EXPR_PROFILE
          Report mode: expression profiles of filtered genes [CHECK]
(package private) static int RPT_TBL_FILTERED_GENES
          Report mode: data Filtered genes
(package private) static int RPT_TBL_GENE_CLASS
          Report mode: genes in current GencClass
(package private) static int RPT_TBL_HIER_CLUSTER
          Report mode: hierarchical clusters gene statistics
(package private) static int RPT_TBL_HIGH_F1F2
          Report mode: highest N current HP F1/F2 ratio genes
(package private) static int RPT_TBL_HIGH_RATIO
          Report mode: highest N HP-X/HP-Y ratio genes
(package private) static int RPT_TBL_HP_DB_INFO
          Report mode: array report of extra Info samples data (DEPRICATED)
(package private) static int RPT_TBL_HP_HP_CORR
          Report mode: HP vs HP correlation coefficient for only filtered genes
(package private) static int RPT_TBL_HP_MN_VAR_STAT
          Report mode: array samples mean and variance statistics
(package private) static int RPT_TBL_HP_XY_SET_STAT
          Report mode: array samples set statistics
(package private) static int RPT_TBL_KMEANS_CLUSTER
          Report mode: K-means clustering statistics
(package private) static int RPT_TBL_LOW_F1F2
          Report mode: lowest N current HP F1/F2 ratio genes
(package private) static int RPT_TBL_LOW_RATIO
          Report mode: lowest N HP-X/HP-Y ratio genes
(package private) static int RPT_TBL_MAE_PRJ_DB
          Report mode: project database
(package private) static int RPT_TBL_MN_KMEANS_CLUSTER
          Report mode: mean clusters for K-means clusters statistics
(package private) static int RPT_TBL_NAMED_GENES
          Report mode: all named genes
(package private) static int RPT_TBL_NORMALIZATION_GENE_LIST
          Report mode:Normalization gene list statistics
(package private) static int RPT_TBL_OCL_STAT
          Report mode: Ordered Condition List gene statistics
(package private) static int RPT_TBL_SAMPLES_DB_INFO
          Report mode: array report of SamplesDB
(package private) static int RPT_TBL_SAMPLES_WEB_LINKS
          Report mode: array report with active Web links
(package private)  java.lang.String rptFontSize
          Report font size: "8pt", "10pt", or "12pt"
(package private)  int runLoopDelayMsec
          Flicker delay for run() loop delay also used for flicker
(package private)  java.lang.Thread runT
          main thread for run()
(package private) static java.lang.String saCodeBase
          Stand-alone PARAM "saCodeBase" overrides default
(package private)  SamplesTable sampDB
          The "Samples.txt" database list of the H.P.s in the entire database.
(package private)  int sampleIntensityRangeMode
          Sample intensity range mode for threshold: RANGE_INSIDE, RANGE_OUTSIDE
(package private)  boolean scaleDataToMaxIntensFlag
          normalize to maximum intensity
(package private)  int scrHeight
          Horizontal screen size
(package private)  int scrWidth
          Horizontal screen size
(package private)  SpotData sd
          Global instance of spot data object
(package private)  SpotFeatures sf
          Global instance of spot feature info
(package private)  StageNames sg
          Global instance of Staging names for menus etc
(package private)  boolean showEGLflag
          Display Flag: show edited gene list
(package private)  float sit1
          PARAM "SI1" 0 or MIN_INTENSITY (spot Intens.)
(package private)  float sit2
          PARAM "SI2" MAX_INTENSITY
(package private)  java.lang.String[] snHPDatabaseFileID
          (opt) list of DB file ID [1:snHPnbr]
(package private)  java.lang.String[] snHPFullStageText
          list for buildingn menus [1:snHPnbr]
(package private)  java.lang.String[] snHPMenuText
          list for building menus [1:snHPnbr]
(package private)  java.lang.String[] snHPName
          slist of tage HP name [1:snHPnbr]
(package private)  int snHPnbr
          # of entries in the Stage name list
(package private)  java.lang.String[] snHPSampleID
          list of free form sample names [1:snHPnbr]
(package private)  java.lang.String[] snImageFile
          list of image files to read [1:snHPnbr]
(package private)  boolean[] snNeedLogin
          (opt) sample requires login
(package private)  java.lang.String[] snPrjName
          list of Project names [1:snHPnbr]
(package private)  boolean[] snSwapCy5Cy3Data
          swap (Cy3,Cy5) field data for (Cy5,Cy3) for this HP
(package private)  boolean sortedGeneAndCloneIDListsFlag
          true if alphaList[] geneNames and numericList[] gene xxxx_IDs are sorted
(package private)  int spotIntensCompareMode
          Spot Intensity compare mode for threshold: COMPARE_xxxx
(package private)  boolean spotIntensFilterFlag
          filter genes by spot Intensity threshold
(package private)  int spotIntensRangeMode
          Spot intensity range mode for thresholds RANGE_OUTSIDE, RANGE_INSIDE
(package private)  int spotIntensTestMode
          spot intensity test mode: SS_MODE_xxxx
(package private)  int spotRad
          PARAM "SpotRadius"
(package private) static int SS_MODE_ELIST
          HP data Filter subset mode: F1F2 HP-E list - hps.msListE[]
(package private) static int SS_MODE_MS
          HP data Filter subset mode: F1F2 current HP - mae.ms
(package private) static int SS_MODE_XANDY_SETS
          HP data Filter subset mode: F1F2 HP-X AND HP-Y sets - hps.msListX(Y)[]
(package private) static int SS_MODE_XORY_SETS
          HP data Filter subset mode: F1F2 HP-X or HP-Y sets - hps.msListX(Y)[]
(package private) static int SS_MODE_XSET
          HP data Filter subset mode: F1F2 HP-X sets - hps.msListX[]
(package private) static int SS_MODE_XY
          HP data Filter subset mode: F1F2 HP-X and HP-Y - mae.msX and mae.msY
(package private) static int SS_MODE_YSET
          HP data Filter subset mode: F1F2 HP-Y sets - hps.msListY[]
(package private) static java.lang.String startupDir
          Standalone startup Directory where startupFile is found
(package private) static java.lang.String startupFile
          Standalone startup DB .mae file
(package private) static boolean startupFileExistsFlag
          Flag that indicates if the database startup .mae file exists
(package private)  Statistics stat
          Global instance of parametric & non-parametric stats
(package private)  StateScrollers stateScr
          holds popup state scrollers - note: created in MenuBarFrame!
(package private)  boolean swapRowsColsFlag
          PARAM flip array rows & columns
(package private)  boolean swissProtViewerFlag
          Swiss-Prot page popup browser Mode
(package private)  float t1
          PARAM "I1" 0 or MIN_INTENSITY (gene "intens")
(package private)  float t2
          PARAM "I2" MAX_INTENSITY
(package private)  int tblFmtMode
          Report table format mode: RPT_FMT_xxxx
(package private)  boolean testGenericNormPluginFlag
          If DBUG_GENERIC_NORM_PLUGIN, then debug GenericNormalizationPlugin within the code.
(package private)  boolean tTestXYfilterFlag
          filter genes passing HP-X/-Y t-test
(package private)  boolean tTestXYsetsFilterFlag
          filter genes passing HP-X/-Y sets t-test
(package private)  boolean uniGeneViewerFlag
          UniGene popup browser Mode
(package private)  boolean updatePseudoImgFlag
          update pseudo image - not saved in the State
(package private)  UserState us
          Global instance of User State methods
(package private)  boolean useClusterCountsDispFlag
          show gene clusters count
(package private)  boolean useClusterDistCacheFlag
          use cluster cache else recompute each time
(package private)  boolean useClusterDistFlag
          cluster distance thresholding
(package private)  boolean useCorrCoeffFlag
          use correlation coeffieient instead of Euclidian distance when clustering
(package private)  boolean useCVmeanElseMaxFlag
          use mean of CV else use max in CV filter
(package private)  boolean useCy5OverCy3Flag
          PARAM "useCy5/Cy3" else Cy3/Cy5
(package private)  boolean useDetValueSpotDataFlag
          filter genes with Spot (Detection value) data
(package private)  boolean useDichromasyFlag
          PARAM "useDichromasy" alt.
(package private)  boolean useDiffFilterFlag
          filter genes by abs diff(HP-X,HP-Y)
(package private)  boolean useEditedCLflag
          filter genes on Edited Gene List
(package private)  boolean useEPoverlayFlag
          Flag: Plot EP list as overlay 2Dplot else scrollable Grid of EPs
(package private)  boolean useEPrawIntensValFlag
          use Raw intensity for EP ratios in gene REPORTS
(package private)  boolean useGeneSetFilterFlag
          filter genes by useGeneSet mbrship
(package private)  boolean useGoodGeneCLflag
          filter by genes in Good Genes List
(package private)  boolean useGoodSpotDataFlag
          filter genes with Good Spot (QualChk) data
(package private)  boolean useGoodSpotsForGlobalStatsFlag
          use Good Spots data for computing global array statistics for normalization purposes on a per array basis, otherwise use all spot data.
(package private)  boolean useHierClusterDispFlag
          show hierarchical clusters
(package private)  boolean useHighRatiosFilterFlag
          "Use highest X/Y ratios filter"
(package private)  boolean useHPxySetDataFlag
          use HP-X,Y 'sets msListX/Y else HP-X,HP-Y msX/Y
(package private)  boolean useIntensHistCLflag
          filter genes on Intensity hist bin
(package private)  boolean useKmeansClusterCntsDispFlag
          show K-means clusters
(package private)  boolean useLowRatiosFilterFlag
          "Use lowest X/Y ratios filter"
(package private)  boolean useLSQmagNormFlag
          norm geneEPvect[] to 1.0 for clustering
(package private)  boolean useMeanHPeListDataFlag
          [TODO] use mean HP-E 'list' data else single current HP sample data
(package private)  boolean useMedianForKmeansClusteringFlag
          set true if use median instead of means of clusters in K-means clustering.
(package private)  boolean useMouseOverFlag
          PARAM "useMouseOver" for popup tracking balloons
(package private)  boolean useOnlyGenesWithNonZeroDensityFlag
          filter by genes with non-zero intensity - problem when do log() transform
(package private)  boolean usePosQuantDataFlag
          filter genes with positive quant data
(package private)  boolean usePseudoXYcoordsFlag
          PARAM use Pseudo XY coords else actual
(package private)  boolean useRatioDataFlag
          PARAM "useRatioData" Cy3/Cy5 else Intensity
(package private)  boolean useRatioHistCLflag
          filter genes on Ratio histogram bin
(package private)  boolean useReplicateGenesFlag
          filter by genes with at least 1 replicate
(package private)  boolean useRLOloggingFlag
          Flag: use time-stamped RLO logging files folders, else just Report/
(package private)  java.lang.String userName
          Dialog: current user login name
(package private)  java.lang.String userPasswd
          Dialog: current user password
(package private)  int userStateIdx
          current user state index
(package private)  java.lang.String userStateName
          current user state name
(package private)  boolean useShortClusterDistCacheFlag
          use short else float cluster cache, can save memory if really needed
(package private)  boolean useSimGeneClusterDispFlag
          show a cluster of similar genes for current gene
(package private)  boolean useSPLUSasComputingEngineFlag
          Flag: Use S-PLUS, else R, as computing engine
(package private)  boolean useSpotCVfilterFlag
          filter by Spot CV filter is enabled
(package private)  boolean useWebDBflag
          Flag: stand-alone PARAM "useWebDB" try WebDB before local directories
(package private)  Util util
          Global instance of Utility class
(package private)  java.lang.String[] validPrj
          [0:n-1] login verified projects
(package private) static java.lang.String VERSION
          Compiled Version constant for use in version comparison etc.
(package private) static java.lang.String verStr
          Compiled Date/Revision constants
(package private)  boolean viewFilteredSpotsFlag
          Flag: show Filtered spots
(package private) static int X_AXIS
          Code for assigning current HP to X-axis
(package private) static int Y_AXIS
          Code for assigning current HP to X-axis
 
Fields inherited from class java.applet.Applet
accessibleContext, serialVersionUID, stub
 
Fields inherited from class java.awt.Panel
base, nameCounter
 
Fields inherited from class java.awt.Container
component, containerListener, containerSerializedDataVersion, dbg, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads
 
Fields inherited from class java.awt.Component
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
MAExplorer()
           
 
Method Summary
(package private)  void chkIfCache()
          chkIfCache() - check if set up to cache from Web DB.
(package private)  void cleanup()
          cleanup() - close up what needs to be closed and GC all structures Reset to initial state so can restart it...
private  void clearDynamicState()
          clearDynamicState() - reset dynamic state variables in MAE instance.
(package private)  MaHybridSample createSample(int hpNbr, java.lang.String hpName, java.lang.String sampleID, java.lang.String databaseFileID, java.lang.String oImageName, java.lang.String oMenuName, java.lang.String fullStageText, java.lang.String projectName, boolean needLoginFlag, boolean swapCy5Cy3DataFlag)
          createSample() - create and return a MaHybridSample hybridized sample object.
 void destroy()
          destroy() - destroy this class
(package private)  void destroy2()
          destroy2() - destroy this class, but clean up the mess of statics first.
private  void destroyStaticState()
          destroyStaticState() - reset static state variables in MAE instance
private  boolean doAnyLoginsRequired()
          doAnyLoginsRequired() - do any Web server logins required for PARAM images that access a Web server database of primary MAExplorer data.
 void init()
          init() - allocate,clear state, read PARAMs, build GUI and start things off.
(package private)  void logDRYROTerr(java.lang.String msg)
          logDRYROTerr() - add the dryrot error to the dryrotLogStr and log it by printing it to the system log.
static void main(java.lang.String[] args)
          main() - for MAExplorer started by standalone application.
 void paint(java.awt.Graphics g)
          paint() - generate viewable scrollable pseudoarray image with overlays.
(package private)  int percentDone()
          percentDone() - estimate percent of files done loading
(package private)  void quit()
          quit() - kill this application or Applet
(package private)  boolean readListOfSampleDataFiles()
          readListOfSampleDataFiles() - populate msList[1:nHP] data structures by reading the data files up to maxPreloadImgs.
(package private)  void resetDefaultstate()
          resetDefaultstate() - Reinitialize global user state.
(package private)  void resetImageAndState()
          resetImageAndState() - Re initialize whenever restart
 void run()
          run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change.
 void start()
          start() - (re)create GUI if needed, read PARAMs & start run thread.
 void stop()
          stop() - stop the thread.
 void update(java.awt.Graphics g)
          update() - redraw graphics
 
Methods inherited from class java.applet.Applet
getAccessibleContext, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus
 
Methods inherited from class java.awt.Panel
, addNotify, constructComponentName
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, adjustListeningChildren, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventImpl, dispatchEventToSelf, doLayout, eventEnabled, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMouseEventTarget, getPreferredSize, getWindow, initIDs, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, nextFocus, numListening, paintComponents, paintHeavyweightComponents, paramString, postProcessKeyEvent, postsOldMouseEvents, preferredSize, preProcessKeyEvent, print, printComponents, printHeavyweightComponents, processContainerEvent, processEvent, proxyEnableEvents, proxyRequestFocus, readObject, remove, remove, removeAll, removeContainerListener, removeNotify, setFocusOwner, setFont, setLayout, transferFocus, validate, validateTree, writeObject
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkit, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, resetGC, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, show, size, toString, transferFocus
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, wait, wait, wait
 

Field Detail

VERSION

static final java.lang.String VERSION
Compiled Version constant for use in version comparison etc.

maeTitleVer

static final java.lang.String maeTitleVer
Compiled MAExplorer title with version number

verStr

static final java.lang.String verStr
Compiled Date/Revision constants

DBUG_TEST_PLUGIN_FLAG

static boolean DBUG_TEST_PLUGIN_FLAG
Enable testing MAEPlugin from the intial menu without dynamic MAEPlugin loading of the class. THIS IS NEVER ENABLED IN OFFICIAL RELEASES... The class that the Plugin invokes should be linked with MAExplorer and invoked by a new() in TestPlugin menu that then invokes the class. This means that you need to edit the TestPluginCode.java code to invoke the code you want to debug with MAExplorer.

DBUG_TEST_R_OR_SPLUS_CHECKBOX

static final boolean DBUG_TEST_R_OR_SPLUS_CHECKBOX
Test the code to let the user switch between R or S-Plus as the statistics evaluation engine.

DBUG_MAERlibr_ZIP_UPDATE

static final boolean DBUG_MAERlibr_ZIP_UPDATE
If debugging MAERlibr.zip file update. This switches the way we update the MAERlibr from the maexplorer.sourceforge.net server.

MAE_STARTUP_FILE

static final java.lang.String MAE_STARTUP_FILE
Default empty .mae startup database

DEF_BASESERVER

static final java.lang.String DEF_BASESERVER
Default microarray database server. This is Web server where "/MAExplorer/" lives, but should be changed via the Config file to other servers. It will not hurt though if it is not changed.

onceOnlyFlag

private boolean onceOnlyFlag
flag to prevent multiple instances

CONSOLE_FLAG

static boolean CONSOLE_FLAG
Debugging flag - Always TRUE

NEVER

static boolean NEVER
Debugging flag - Always FALSE

DEBUG

static final boolean DEBUG
General purpose debugging flag. This flag also sets LECBdebug used to enable ALL menus while debugging

DBUG_LOGIN

static final boolean DBUG_LOGIN
Debugging variablen - debugging CGI login locally

DBUG_HCN

static final boolean DBUG_HCN
debugging HierClustNode lists

DBUG_STANDALONE

static final boolean DBUG_STANDALONE
debugging Stand-Alone code

DBUG_GENOMIC_URLS_FLAG

static boolean DBUG_GENOMIC_URLS_FLAG
debugging Genomic Menu/URLs

DBUG_QUALCHK_QUANT_FLAG

static final boolean DBUG_QUALCHK_QUANT_FLAG
debugging QualCheck

DBUG_MEDMINER_FLAG

static final boolean DBUG_MEDMINER_FLAG
debugging MedMiner Menu/URLs

PRINT_MEM_TIMES

static final boolean PRINT_MEM_TIMES
print memory times at key places

DBUG_SET_EGL_FROM_DENDROGRAM

static final boolean DBUG_SET_EGL_FROM_DENDROGRAM
if debugging setting EGL set from subtree of HCN dendrogram

CANVAS_WRAPAROUND_BUG

static final boolean CANVAS_WRAPAROUND_BUG
if debugging CANVAS_WRAPAROUND_BUG

DBUG_NORM_PLUGIN

static final boolean DBUG_NORM_PLUGIN
if debugging NormalizationPlugins using the PluginLoader

DBUG_GENERIC_NORM_PLUGIN

static final boolean DBUG_GENERIC_NORM_PLUGIN
[DEBUGGING] If debugging a plugin extending NormalizationPlugin, you may debug it in the MAExplorer core image by temporarily including in in the code. THIS IS NEVER ENABLED IN OFFICIAL RELEASES... We use a wrapper class GenNormalizationPlugin instance gnp that in turn generates a GenericNormalizationPlugin and calls it as required. Only the gnp is visible to the MAExplorer code. We add this dummy menu item in the code to make it easier to debug "pipeline" types of MAEPlugin.Analysis.xxxx plugins. This: 1. creates gnp and testGenericNormPluginFlag instances in MAExplorer 2. creates miNRMtestGenericNormPlugin menu item instance in MenuBarFrame 3. handles miNRMtestGenericNormPlugin event in EventMenu to toggle testGenericNormPluginFlag 4. tests testGenericNormPluginFlag instance in CompositeDatabase and call gnp.XXXX() methods 5. tests testGenericNormPluginFlag instance in MaHybridSample and call gnp.XXXX() methods

gnp

GenNormalizationPlugin gnp
Only while debugging: if DBUG_GENERIC_NORM_PLUGIN is set for use with TestPlugin.

DBUG_CV_DISPLAY_EPLIST

static final boolean DBUG_CV_DISPLAY_EPLIST
if debugging display the CV of HP-EP samples as colors [0:1.0] lie for p-value display.

LECBdebug

int LECBdebug
Developer debug flag. This is 0 if debugging, -1 otherwise and is used for building menus while developing code. We set it to 0 either explicitly or by the DEBUG flag.

applet

java.applet.Applet applet
"this" applet instance for MAExplorer main class

PSEUDOIMG_WIDTH

static final int PSEUDOIMG_WIDTH
(600x900) size of pseudoarray image canvas

PSEUDOIMG_HEIGHT

static final int PSEUDOIMG_HEIGHT
(600x900) size of pseudoarray image canvas

X_AXIS

static final int X_AXIS
Code for assigning current HP to X-axis

Y_AXIS

static final int Y_AXIS
Code for assigning current HP to X-axis

MAX_PROJECTS

static final int MAX_PROJECTS
Maximum # of projects for project lists

MAX_HYB_SAMPLES

static final int MAX_HYB_SAMPLES
Max # of hybridized array samples to load at one time

MAX_CONDITION_LISTS

static final int MAX_CONDITION_LISTS
Max # of named sample condition lists. Worst case is one sample/condition list which defaults to an expression profile.

MAX_COND_PARAM

public static final int MAX_COND_PARAM
maximum number of Condition parameters

MAX_ORDERED_COND_LISTS

static final int MAX_ORDERED_COND_LISTS
maximum number of # of ordered condition lists slots available.

N_EST_QUANT_FILES

static final int N_EST_QUANT_FILES
default est # .quant files to load

N_CONST_FILES

static final int N_CONST_FILES
# of files always read: MaExplorerConfig.txt GIPO-xxx.txt Samples.txt MaExplorerInfo.txt [DEPRICATED]

startupFileExistsFlag

static boolean startupFileExistsFlag
Flag that indicates if the database startup .mae file exists

previousStartupState

boolean previousStartupState
Flag that indicates if the startup .mae file exists in PREVIOUS database

configFile

java.lang.String configFile
Default Configuration file: "MaExplorerConfig.txt"

is

ArrayScroller is
Global instance of ArrayScroller obj to hold pseudoarray image scrollable canvas

clg

ClusterGenes clg
Global instance of Cluster Genes object

cdb

CompositeDatabase cdb
Global instance of composite database object

cdList

Condition cdList
Global instance of condition list tables

cfg

Config cfg
Global instance of Configuration and state variables including top level file, URL configs, etc.

cfgDB

ConfigTable cfgDB
Global instance of configuration data from MaExplorerConfig.txt file

grcd

GridCoords grcd
Global instance of share grid coordinate mapper

dwPI

DrawPseudoImage dwPI
Global instance of draw pseudo image

egl

EditedGeneList egl
Global instance of edit editedCL gene (clone) list

em

EventMenu em
Global instance of handle MenuItem and MenuItemCheckbox events

fio

FileIO fio
Global instance of file and URL I/O

fc

Filter fc
Global instance of data Filter gene operations

gene

Gene gene
Global instance of Gene

gct

GeneClass gct
Global instance of Gene Class table

ccd

GeneGeneDist ccd
Global instance of Gene-Gene distances

clLst

GeneList clLst
Global instance of GeneList contains gene (clone) list tables

gipo

GipoTable gipo
Global instance of GIPO table mapping genes to other data

gp

GetParams gp
Global instance of contains set of applet/configuration PARAM parsers

mja

public static MaeJavaAPI mja
Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins

infoDB

MaInfoTable infoDB
Global instance of depricated "MaExplorerInfo.txt" DB list of .info data for entire DB.

mp

Maps mp
Global instance of lookup table maps populated elsewhere

mbf

MenuBarFrame mbf
Global instance of Frame based MenuBar

olmap

OverlayMap olmap
Global instance of scatterplot named overlay maps

pur

PopupRegistry pur
Global instance of holds popup registry of all active popup windows and update handlers.

hps

SampleSets hps
Global instance of HP-X, HP-Y and HP-E sets and lists

sampDB

SamplesTable sampDB
The "Samples.txt" database list of the H.P.s in the entire database.

sd

SpotData sd
Global instance of spot data object

sf

SpotFeatures sf
Global instance of spot feature info

sg

StageNames sg
Global instance of Staging names for menus etc

stateScr

StateScrollers stateScr
holds popup state scrollers - note: created in MenuBarFrame!

stat

Statistics stat
Global instance of parametric & non-parametric stats

us

UserState us
Global instance of User State methods

util

Util util
Global instance of Utility class

clstrSamp

ClusterSamples clstrSamp
Global instance of ClusterSamples class

dryRotExcept

DryRotException dryRotExcept
Global instance of DryRotException class

ms

static MaHybridSample ms
Current hybridized sample

msPrev

static MaHybridSample msPrev
Previous (last current) hybridized sample for garbage collection

msX

static MaHybridSample msX
Current HP-X hybridized sample

msY

static MaHybridSample msY
Current HP-Y hybridized sample

curHP

static int curHP
Current hybridized sample index for hps.msList[]

curHP_X

static int curHP_X
Current HP-X sample index for hps.msList[]

curHP_Y

static int curHP_Y
Current HP-Y sample index for hps.msList[]

classNameX

java.lang.String classNameX
"HP-X 'set'" name for msListX[] HPs

classNameY

java.lang.String classNameY
"HP-Y 'set'" name for msListY[] HPs

scrWidth

int scrWidth
Horizontal screen size

scrHeight

int scrHeight
Horizontal screen size

dbID

static java.lang.String dbID
Unique Database ID ("DIDxxxxxx") - used as prefix for State/ files

date

static java.lang.String date
startup date

osName

static java.lang.String osName
operating system Windows, SUNOS, etc

codeBase

static java.lang.String codeBase
full codebase path for /mae/ on MAE svr

saCodeBase

static java.lang.String saCodeBase
Stand-alone PARAM "saCodeBase" overrides default

proxyServer

java.lang.String proxyServer
base addr PARAM "proxyServer"

maeServerBase

java.lang.String maeServerBase
top level codebase for MAE server

fileBasePath

static java.lang.String fileBasePath
either Applet or file I/O or standalone

docCodeBase

java.lang.String docCodeBase
codebase where the documentation Reference Manual is kept

fileSeparator

java.lang.String fileSeparator
paths, "/" or "|", depends on OS

dynFileSeparator

java.lang.String dynFileSeparator
dynamic paths separator, "/" or "|", depends on OS and if using URL from Stand-Alone

defSAprjName

java.lang.String defSAprjName
Standalone current project DB name

defDir

static java.lang.String defDir
Default standalone directory (=null JWS hack)

defStartupFile

static java.lang.String defStartupFile
Default standalone .mae startup file

defSAwebAddr

static java.lang.String defSAwebAddr
Default standalone assoc. DB web address

startupDir

static java.lang.String startupDir
Standalone startup Directory where startupFile is found

startupFile

static java.lang.String startupFile
Standalone startup DB .mae file

prjListFile

static java.lang.String prjListFile
Standalone Sample DB project list DB file

cacheDir

java.lang.String cacheDir
Standalone /Cache directory for saving data downloaded for array Web server.

pluginsDir

static java.lang.String pluginsDir
Standalone /Plugins directory where optional MAEPlugins may be found

javaHome

static java.lang.String javaHome
Standalone getProperties("java.home")

reuseGUIframeFlag

boolean reuseGUIframeFlag
Flag: set if reuse main GUI frame

isWinPCflag

boolean isWinPCflag
Flag: set to TRUE if any Windows PC

browserTitle

static java.lang.String browserTitle
browser title

otherUserName

java.lang.String otherUserName
access other user name from Dialog

userName

java.lang.String userName
Dialog: current user login name

userPasswd

java.lang.String userPasswd
Dialog: current user password

curPrjName

static java.lang.String curPrjName
current project being requested

validPrj

java.lang.String[] validPrj
[0:n-1] login verified projects

nValidPrj

int nValidPrj
# of login verified projects

isLoggedInFlag

boolean isLoggedInFlag
set if valid login has been performed

userStateName

java.lang.String userStateName
current user state name

userStateIdx

int userStateIdx
current user state index

pImage

java.awt.Image pImage
pseudo grayscale microarray image based on .quantspot intensity data. This image is shared by ALL HPs and is recompute if current HP changes.

pWidth

int pWidth
working size of pseudoarray image

pHeight

int pHeight
working size of pseudoarray image

MAX_INTENSITY

int MAX_INTENSITY
maximum # intensity values of .quant data

MIN_RATIO

static final float MIN_RATIO
Minimum ratio for histogram of ratios histRatioBin[]

MAX_RATIO

static final float MAX_RATIO
maximum ratio for histogram of ratios histRatioBin[]

histRatioBin

static final double[] histRatioBin
preloaded set of legal ratios in [1/100 : 100]

MAX_RATIO_HIST

static final int MAX_RATIO_HIST
# of bins in histRatioBin[]

MARKER_NONE

static final int MARKER_NONE
pseudoarray canvas - No overlay

MARKER_PLUS

static final int MARKER_PLUS
pseudoarray canvas - draw 5x5 plus

MARKER_CIRCLE

static final int MARKER_CIRCLE
pseudoarray canvas - draw circle of size radius

MARKER_SQUARE

static final int MARKER_SQUARE
pseudoarray canvas - draw square of size radius

MARKER_GENES

static final int MARKER_GENES
pseudoarray canvas - draw all spots in gene list

MARKER_CURRENT

static final int MARKER_CURRENT
pseudoarray canvas - draw Current object

MARKER_KMEANS_CLUSTER

static final int MARKER_KMEANS_CLUSTER
pseudoarray canvas - draw K-means cluster #

MASTER_GENE_NAME

static final int MASTER_GENE_NAME
Master masterNameMode Mode - gene name

MASTER_UG_NAME

static final int MASTER_UG_NAME
Master masterNameMode Mode - UniGene name

MASTER_CLONE_ID

static final int MASTER_CLONE_ID
Master masterIDmode Mode - clone ID

MASTER_GENBANK

static final int MASTER_GENBANK
Master masterIDmode Mode - GenBank ID

MASTER_GENBANK5

static final int MASTER_GENBANK5
Master masterIDmode Mode - GenBank 5' ID

MASTER_GENBANK3

static final int MASTER_GENBANK3
Master masterIDmode Mode - GenBank 3' ID

MASTER_UG_ID

static final int MASTER_UG_ID
Master masterIDmode Mode - UniGene ID

MASTER_DBEST5

static final int MASTER_DBEST5
Master masterIDmode Mode - dbEST 5' ID

MASTER_DBEST3

static final int MASTER_DBEST3
Master masterIDmode Mode - dbEST 3' ID

MASTER_SWISS_PROT

static final int MASTER_SWISS_PROT
Master masterIDmode Mode - SwissProt ID

MASTER_LOCUSLINK

static final int MASTER_LOCUSLINK
Master masterIDmode Mode - LocusLink ID

MASTER_OMIM

static final int MASTER_OMIM
Master masterIDmode Mode - OMIM ID

MASTER_GENERIC_ID

static final int MASTER_GENERIC_ID
Master masterIDmode Mode - generic ID

QUALTYPE_ALPHA

static final int QUALTYPE_ALPHA
QualCheck type: Alphabetic codes

QUALTYPE_PROP_CODE

static final int QUALTYPE_PROP_CODE
QualCheck type: uses MAE Gene.xxxx prop QualCheck codes

QUALTYPE_THR

static final int QUALTYPE_THR
QualCheck type: Uses [qualThr] QualCheck continuous data

DRAW_PLUS

static final int DRAW_PLUS
Plotting types - draw plus symbol in scatter plot

DRAW_CIRCLE

static final int DRAW_CIRCLE
Plotting types - draw circle symbol in scatter plot

DRAW_BOX

static final int DRAW_BOX
Plotting types - draw box symbol in scatter plot

DRAW_BIN

static final int DRAW_BIN
Plotting types - draw histogram bin

RANGE_INSIDE

static final int RANGE_INSIDE
rangeMode: Inside [v1:v2] for testing

RANGE_OUTSIDE

static final int RANGE_OUTSIDE
rangeMode: Outsiide [v1:v2] for testing

COMPARE_ALL

static final int COMPARE_ALL
range-compare mode: spot intensity of samples - ALL samples must comply

COMPARE_ANY

static final int COMPARE_ANY
range-compare mode: spot intensity of samples - ANY samples must comply

COMPARE_PRODUCT

static final int COMPARE_PRODUCT
range-compare mode: spot intensity of samples - PRODUCT of samples must comply

COMPARE_SUM

static final int COMPARE_SUM
range-compare mode: spot intensity of samples - SUM samples must comply

COMPARE_AT_MOST

static final int COMPARE_AT_MOST
range-compare mode: spot intensity of samples - AT MOST n samples must comply

COMPARE_AT_LEAST

static final int COMPARE_AT_LEAST
range-compare mode: spot intensity of samples - AT LEAST n samples must comply

SS_MODE_MS

static final int SS_MODE_MS
HP data Filter subset mode: F1F2 current HP - mae.ms

SS_MODE_XY

static final int SS_MODE_XY
HP data Filter subset mode: F1F2 HP-X and HP-Y - mae.msX and mae.msY

SS_MODE_XSET

static final int SS_MODE_XSET
HP data Filter subset mode: F1F2 HP-X sets - hps.msListX[]

SS_MODE_YSET

static final int SS_MODE_YSET
HP data Filter subset mode: F1F2 HP-Y sets - hps.msListY[]

SS_MODE_XORY_SETS

static final int SS_MODE_XORY_SETS
HP data Filter subset mode: F1F2 HP-X or HP-Y sets - hps.msListX(Y)[]

SS_MODE_XANDY_SETS

static final int SS_MODE_XANDY_SETS
HP data Filter subset mode: F1F2 HP-X AND HP-Y sets - hps.msListX(Y)[]

SS_MODE_ELIST

static final int SS_MODE_ELIST
HP data Filter subset mode: F1F2 HP-E list - hps.msListE[]

EDIT_NOP

static final int EDIT_NOP
Edited Gene List mouse click action mode: NO-OP

EDIT_ADD

static final int EDIT_ADD
Edited Gene List mouse click action mode: ADD gene on click

EDIT_RMV

static final int EDIT_RMV
Edited Gene List mouse click action mode: REMOVE gene on click

PLOT_PSEUDOIMG

static final int PLOT_PSEUDOIMG
Pseudoarray image plot mode: Grayscale display current HP intensity

PLOT_PSEUDO_HP_XY_RYG_IMG

static final int PLOT_PSEUDO_HP_XY_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]

PLOT_PSEUDO_F1F2_RYG_IMG

static final int PLOT_PSEUDO_F1F2_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red]

PLOT_PSEUDO_F1F2_IMG

static final int PLOT_PSEUDO_F1F2_IMG
Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red]

PLOT_PSEUDO_HP_XY_IMG

static final int PLOT_PSEUDO_HP_XY_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red]

PLOT_PSEUDO_HP_XY_P_VALUE_IMG

static final int PLOT_PSEUDO_HP_XY_P_VALUE_IMG
Pseudoarray image plot mode: display X,Y 'sets' p-Value [0.0:1.0] as [black:white]

PLOT_PSEUDO_HP_EP_CV_VALUE_IMG

static final int PLOT_PSEUDO_HP_EP_CV_VALUE_IMG
Pseudoarray image plot mode: display HP_EP 'list' CV coefficient of variation [0.0:1.0] as [black:white]

PLOT_F1_F2_INTENS

static final int PLOT_F1_F2_INTENS
Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot

PLOT_HP_XY_INTENS

static final int PLOT_HP_XY_INTENS
Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot

PLOT_F1_F2_MVSA

static final int PLOT_F1_F2_MVSA
Popup plot mode: M vs A scatter plot of current sample

PLOT_INTENS_HIST

static final int PLOT_INTENS_HIST
Popup plot mode: current HP intensity histogram plot

PLOT_HIST_F1F2_RATIO

static final int PLOT_HIST_F1F2_RATIO
Popup plot mode: current HP F1/F2 ratio histogram plot

PLOT_HIST_HP_XY_RATIO

static final int PLOT_HIST_HP_XY_RATIO
Popup plot mode: HP-X/HP-Y ratio histogram plot

PLOT_HIST_HP_XY_SETS_RATIO

static final int PLOT_HIST_HP_XY_SETS_RATIO
Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot

PLOT_EXPR_PROFILE

static final int PLOT_EXPR_PROFILE
Popup plot mode: expression profile plot

PLOT_CLUSTER_GENES

static final int PLOT_CLUSTER_GENES
Popup plot mode: cluster similar genes plot

PLOT_CLUSTER_HIER

static final int PLOT_CLUSTER_HIER
Popup plot mode: hierarchical cluster genes plot

PLOT_CLUSTER_HYBSAMPLES

static final int PLOT_CLUSTER_HYBSAMPLES
Popup plot mode: cluster HP-samples plot

PLOT_CLUSTERGRAM

static final int PLOT_CLUSTERGRAM
Popup plot mode: clustergram genes plot

PLOT_KMEANS_CLUSTERGRAM

static final int PLOT_KMEANS_CLUSTERGRAM
Popup plot mode: k-means cluster genes plot

HIER_CLUST_PGMA_LNKG

static final int HIER_CLUST_PGMA_LNKG
Hierarchical clustering mode: Average-arithmetic linkage

HIER_CLUST_PGMC_LNKG

static final int HIER_CLUST_PGMC_LNKG
Hierarchical clustering mode: Average-centroid linkage

HIER_CLUST_NEXT_MIN_LNKG

static final int HIER_CLUST_NEXT_MIN_LNKG
Hierarchical clustering mode: next-minimum cluster linkage

RPT_NONE

static final int RPT_NONE
Report mode: no report

RPT_TBL_HIGH_RATIO

static final int RPT_TBL_HIGH_RATIO
Report mode: highest N HP-X/HP-Y ratio genes

RPT_TBL_LOW_RATIO

static final int RPT_TBL_LOW_RATIO
Report mode: lowest N HP-X/HP-Y ratio genes

RPT_TBL_HIGH_F1F2

static final int RPT_TBL_HIGH_F1F2
Report mode: highest N current HP F1/F2 ratio genes

RPT_TBL_LOW_F1F2

static final int RPT_TBL_LOW_F1F2
Report mode: lowest N current HP F1/F2 ratio genes

RPT_TBL_FILTERED_GENES

static final int RPT_TBL_FILTERED_GENES
Report mode: data Filtered genes

RPT_TBL_GENE_CLASS

static final int RPT_TBL_GENE_CLASS
Report mode: genes in current GencClass

RPT_TBL_NAMED_GENES

static final int RPT_TBL_NAMED_GENES
Report mode: all named genes

RPT_TBL_SAMPLES_DB_INFO

static final int RPT_TBL_SAMPLES_DB_INFO
Report mode: array report of SamplesDB

RPT_TBL_HP_DB_INFO

static final int RPT_TBL_HP_DB_INFO
Report mode: array report of extra Info samples data (DEPRICATED)

RPT_TBL_SAMPLES_WEB_LINKS

static final int RPT_TBL_SAMPLES_WEB_LINKS
Report mode: array report with active Web links

RPT_TBL_EXPR_PROFILE

static final int RPT_TBL_EXPR_PROFILE
Report mode: expression profiles of filtered genes [CHECK]

RPT_TBL_HP_XY_SET_STAT

static final int RPT_TBL_HP_XY_SET_STAT
Report mode: array samples set statistics

RPT_TBL_CUR_GENE_CLUSTER

static final int RPT_TBL_CUR_GENE_CLUSTER
Report mode: current gene clustering statistics

RPT_TBL_ALL_GENES_CLUSTER

static final int RPT_TBL_ALL_GENES_CLUSTER
Report mode: all genes clustering statistics

RPT_TBL_KMEANS_CLUSTER

static final int RPT_TBL_KMEANS_CLUSTER
Report mode: K-means clustering statistics

RPT_TBL_MN_KMEANS_CLUSTER

static final int RPT_TBL_MN_KMEANS_CLUSTER
Report mode: mean clusters for K-means clusters statistics

RPT_TBL_EDITED_GENE_LIST

static final int RPT_TBL_EDITED_GENE_LIST
Report mode: Edited Gene List

RPT_TBL_NORMALIZATION_GENE_LIST

static final int RPT_TBL_NORMALIZATION_GENE_LIST
Report mode:Normalization gene list statistics

RPT_TBL_HP_HP_CORR

static final int RPT_TBL_HP_HP_CORR
Report mode: HP vs HP correlation coefficient for only filtered genes

RPT_TBL_CALIB_DNA_STAT

static final int RPT_TBL_CALIB_DNA_STAT
Report mode: array samples Calibration DNA statistics

RPT_TBL_HP_MN_VAR_STAT

static final int RPT_TBL_HP_MN_VAR_STAT
Report mode: array samples mean and variance statistics

RPT_TBL_HIER_CLUSTER

static final int RPT_TBL_HIER_CLUSTER
Report mode: hierarchical clusters gene statistics

RPT_TBL_MAE_PRJ_DB

static final int RPT_TBL_MAE_PRJ_DB
Report mode: project database

RPT_TBL_OCL_STAT

static final int RPT_TBL_OCL_STAT
Report mode: Ordered Condition List gene statistics

RPT_FMT_TAB_DELIM

static final int RPT_FMT_TAB_DELIM
Report format mode: tab-delimited report as TextArea

RPT_FMT_DYN

static final int RPT_FMT_DYN
Report format mode: dynamic spreadsheet report

maxPreloadImgs

int maxPreloadImgs
PARAM max # images to preload set from "maxPreloadImages"

iSampleName

java.lang.String[] iSampleName
HP name from "image*" [1:iHPnbr] allocated [MAX_HYB_SAMPLES+1]

iImageFile

java.lang.String[] iImageFile
image files to read allocated [MAX_HYB_SAMPLES+1]

iHPnbr

int iHPnbr
# of entries in "image#" PARAM list. The mae.hps.msList[1:mae.hps.nHP] is derived from this and modified from snHPName[] list.

snHPnbr

int snHPnbr
# of entries in the Stage name list

mapHPtoMenuName

int[] mapHPtoMenuName
index of snHPName[] corresponding to iSampleName[] entry allocated [MAX_HYB_SAMPLES+1].

snHPName

java.lang.String[] snHPName
slist of tage HP name [1:snHPnbr]

snHPSampleID

java.lang.String[] snHPSampleID
list of free form sample names [1:snHPnbr]

snHPDatabaseFileID

java.lang.String[] snHPDatabaseFileID
(opt) list of DB file ID [1:snHPnbr]

snImageFile

java.lang.String[] snImageFile
list of image files to read [1:snHPnbr]

snHPMenuText

java.lang.String[] snHPMenuText
list for building menus [1:snHPnbr]

snHPFullStageText

java.lang.String[] snHPFullStageText
list for buildingn menus [1:snHPnbr]

snPrjName

java.lang.String[] snPrjName
list of Project names [1:snHPnbr]

snNeedLogin

boolean[] snNeedLogin
(opt) sample requires login

snSwapCy5Cy3Data

boolean[] snSwapCy5Cy3Data
swap (Cy3,Cy5) field data for (Cy5,Cy3) for this HP

sortedGeneAndCloneIDListsFlag

boolean sortedGeneAndCloneIDListsFlag
true if alphaList[] geneNames and numericList[] gene xxxx_IDs are sorted

nFilesRead

int nFilesRead
# of files read so far

nFilesTotal

int nFilesTotal
# files always read + # .quant files. i.e. = N_CONST_FILES + N_EST_QUANT_FILES.

runLoopDelayMsec

int runLoopDelayMsec
Flicker delay for run() loop delay also used for flicker

runT

java.lang.Thread runT
main thread for run()

spotRad

int spotRad
PARAM "SpotRadius"

canvasHSize

static int canvasHSize
PARAM "CanvasHorSize"

canvasVSize

static int canvasVSize
PARAM "CanvasVertSize"

sit1

float sit1
PARAM "SI1" 0 or MIN_INTENSITY (spot Intens.)

sit2

float sit2
PARAM "SI2" MAX_INTENSITY

t1

float t1
PARAM "I1" 0 or MIN_INTENSITY (gene "intens")

t2

float t2
PARAM "I2" MAX_INTENSITY

r1

float r1
PARAM "R1" MIN_RATIO range (HP-X/HP-Y)

r2

float r2
PARAM "R2" MAX_RATIO range

cr1

float cr1
PARAM "CR1" MIN_RATIO range (i.e. Cy3/Cy5)

cr2

float cr2
PARAM "CR2" MAX_RATIO range

rptFontSize

java.lang.String rptFontSize
Report font size: "8pt", "10pt", or "12pt"

dryrotLogStr

java.lang.String dryrotLogStr
List of dryrot messages if any occur. Should be null.

showEGLflag

boolean showEGLflag
Display Flag: show edited gene list

mReady

boolean mReady
Flag set when done initialization and ready to analyze

isWorkingMAE

boolean isWorkingMAE
Flag indicating whether using the Working server (mae/) or not

plotImageMode

int plotImageMode
Pseudo array image plot mode: PLOT_xxxx_IMAGE

editMode

int editMode
EGL mode for 'edited gene list': EDIT_xxxx

hierClustMode

int hierClustMode
Hier.Clustering linkage mode: HIER_CLUST_xxxxx

qualTypeMode

int qualTypeMode
spot quality type mode: QUALTYPE_xxxx

posQuantTestMode

int posQuantTestMode
positive Quant data test mode: SS_MODE_xxxx

goodSpotTestMode

int goodSpotTestMode
Good Spot (QualChk) test mode: SS_MODE_xxxx

detValueSpotTestMode

int detValueSpotTestMode
Spot (Detection Value) test mode: SS_MODE_xxxx

reportMode

int reportMode
Report type mode: RPT_xxxx. Not saved in state

tblFmtMode

int tblFmtMode
Report table format mode: RPT_FMT_xxxx

spotIntensTestMode

int spotIntensTestMode
spot intensity test mode: SS_MODE_xxxx

spotIntensRangeMode

int spotIntensRangeMode
Spot intensity range mode for thresholds RANGE_OUTSIDE, RANGE_INSIDE

spotIntensCompareMode

int spotIntensCompareMode
Spot Intensity compare mode for threshold: COMPARE_xxxx

sampleIntensityRangeMode

int sampleIntensityRangeMode
Sample intensity range mode for threshold: RANGE_INSIDE, RANGE_OUTSIDE

ratioRangeMode

int ratioRangeMode
Ratio range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE

ratioCy3Cy5RangeMode

int ratioCy3Cy5RangeMode
Cy3/Cy5 range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE

cvTestMode

int cvTestMode
CV test mode: SS_MODE_xxxx

isAppletFlag

boolean isAppletFlag
Flag: cleared if enter through standalone main()

useWebDBflag

boolean useWebDBflag
Flag: stand-alone PARAM "useWebDB" try WebDB before local directories

enableFIOcachingFlag

boolean enableFIOcachingFlag
Flag: stand-alone PARAM "enableFIOcaching"

cacheFIOflag

boolean cacheFIOflag
Flag: if enabled, it first checks the /Cache directory for all http:// codebase files and if not in the cache, it saves the file in the cache after reading it from the Web.

madeChangesFlag

boolean madeChangesFlag
made changes to DB so may want to SAVE DB

useCy5OverCy3Flag

boolean useCy5OverCy3Flag
PARAM "useCy5/Cy3" else Cy3/Cy5

useMouseOverFlag

boolean useMouseOverFlag
PARAM "useMouseOver" for popup tracking balloons

flickerXYflag

boolean flickerXYflag
Flicker HP-X and HP-Y in run() loop

lowRangeZoomFlag

boolean lowRangeZoomFlag
Scale pseudoarray image by 1/100 to zoom low-range values

isZscoreFlag

boolean isZscoreFlag
Flag: is using one of the Zscore normalizations

useEPoverlayFlag

boolean useEPoverlayFlag
Flag: Plot EP list as overlay 2Dplot else scrollable Grid of EPs

swapRowsColsFlag

boolean swapRowsColsFlag
PARAM flip array rows & columns

useRatioDataFlag

boolean useRatioDataFlag
PARAM "useRatioData" Cy3/Cy5 else Intensity

useHPxySetDataFlag

boolean useHPxySetDataFlag
use HP-X,Y 'sets msListX/Y else HP-X,HP-Y msX/Y

useMeanHPeListDataFlag

boolean useMeanHPeListDataFlag
[TODO] use mean HP-E 'list' data else single current HP sample data

allowNegQuantDataFlag

boolean allowNegQuantDataFlag
PARAM "allowNegQuantDataFlag"

updatePseudoImgFlag

boolean updatePseudoImgFlag
update pseudo image - not saved in the State

usePseudoXYcoordsFlag

boolean usePseudoXYcoordsFlag
PARAM use Pseudo XY coords else actual

dualXYpseudoPlotFlag

boolean dualXYpseudoPlotFlag
Flag: plot mean HP-X in F1, HP-Y in F2 pseudoimg

reuseXYcoordsFlag

boolean reuseXYcoordsFlag
Flag: reuse HP[1] Quant xy coords for speedup

noMsgReportFlag

boolean noMsgReportFlag
PARAM "noMsgReporting"

dieFlag

boolean dieFlag
Flag: call quit() if flag set to exit run(). Not saved in state

abortFlag

boolean abortFlag
Flag: set true by the STOP button. Not saved in state

doGCflag

boolean doGCflag
Flag: run the Garbage Collector. Not saved in state

killAppletFlag

boolean killAppletFlag
Flag: set if do "Quit". Not saved in state

viewFilteredSpotsFlag

boolean viewFilteredSpotsFlag
Flag: show Filtered spots

useDichromasyFlag

boolean useDichromasyFlag
PARAM "useDichromasy" alt. colors

gangSpotFlag

boolean gangSpotFlag
Flag: report f1 or f1&f2 (ganged)

presentViewFlag

boolean presentViewFlag
Flag: use larger fonts, thicker lines, circles, plus, etc. for presentation viewing

useSPLUSasComputingEngineFlag

boolean useSPLUSasComputingEngineFlag
Flag: Use S-PLUS, else R, as computing engine

useRLOloggingFlag

boolean useRLOloggingFlag
Flag: use time-stamped RLO logging files folders, else just Report/

masterGeneName

java.lang.String masterGeneName
either "GeneName", "UGclusterName, etc"

masterIDname

java.lang.String masterIDname
either "CloneID", "UniGeneID, GenBank, etc"

masterNameMode

int masterNameMode
either MASTER_GENE_NAME or MASTER_UG_NAME

masterIDmode

int masterIDmode
either MASTER_CLONE_ID or MASTER_GENBANK or MASTER_GENBANK5 or MASTER_GENBANK3 or MASTER_UG_ID, MASTER_SWISS_PROT, MASTER_GENERIC_ID

reportRatioStr

java.lang.String reportRatioStr
either "F1/F2", "Cy3/Cy5", or "Cy5/Cy3"

normNameDisp

java.lang.String normNameDisp
name of norm. method in Status display

normName

java.lang.String normName
name of normalization method

useGoodSpotsForGlobalStatsFlag

boolean useGoodSpotsForGlobalStatsFlag
use Good Spots data for computing global array statistics for normalization purposes on a per array basis, otherwise use all spot data.

bkgdCorrectFlag

boolean bkgdCorrectFlag
calc: I'= Intensity - background

ratioMedianCorrectionFlag

boolean ratioMedianCorrectionFlag
enable cy3/cy5 ratio median correction

normByHousekeepGenesFlag

boolean normByHousekeepGenesFlag
normalize by housekeeping genes

normByGeneSetFlag

boolean normByGeneSetFlag
normalize by 'user gene set'

normByCalDNAflag

boolean normByCalDNAflag
normalize by Calibration DNA set

normByZscoreFlag

boolean normByZscoreFlag
normalize by HP Zscore

normByMedianFlag

boolean normByMedianFlag
normalize by HP median

normByLogMedianFlag

boolean normByLogMedianFlag
normalize by HP log of median

normByZscoreMeanStdDevLogFlag

boolean normByZscoreMeanStdDevLogFlag
norm by Zscore log intens,stdDev.

normByZscoreMeanAbsDevLogFlag

boolean normByZscoreMeanAbsDevLogFlag
norm. by Zscore log intens,meanAbsDev

scaleDataToMaxIntensFlag

boolean scaleDataToMaxIntensFlag
normalize to maximum intensity

testGenericNormPluginFlag

boolean testGenericNormPluginFlag
If DBUG_GENERIC_NORM_PLUGIN, then debug GenericNormalizationPlugin within the code. If the DBUG_GENERIC_NORM_PLUGIN is enabled, then the GenNormalizationPlugin) gnp will exist and point to the instance. The menu item appears in the menu: (Analysis | Normalization | "Test Generic Norm Plugin [DBUG]")

useCorrCoeffFlag

boolean useCorrCoeffFlag
use correlation coeffieient instead of Euclidian distance when clustering

hierClustUnWtAvgFlag

boolean hierClustUnWtAvgFlag
use UPGMA or WPGMA for computing the average node vector when hierarchical clustering.

normHCbyRatioHPflag

boolean normHCbyRatioHPflag
set true if normalize Hier-Clustering dataV[h] by dataV[iDataV] else norm by HP[h] msListE[h].maQ.maxRI

useMedianForKmeansClusteringFlag

boolean useMedianForKmeansClusteringFlag
set true if use median instead of means of clusters in K-means clustering.

genBankViewerFlag

boolean genBankViewerFlag
GenBank popup browser Mode

dbESTviewerFlag

boolean dbESTviewerFlag
dbEST popup browser Mode

uniGeneViewerFlag

boolean uniGeneViewerFlag
UniGene popup browser Mode

omimViewerFlag

boolean omimViewerFlag
OMIM popup browser Mode

mAdbViewerFlag

boolean mAdbViewerFlag
mAdb Clone page popup browser Mode

locusLinkViewerFlag

boolean locusLinkViewerFlag
LocusLink LocusID page popup browser Mode

medMinerViewerFlag

boolean medMinerViewerFlag
MedMiner gene page popup browser Mode

swissProtViewerFlag

boolean swissProtViewerFlag
Swiss-Prot page popup browser Mode

pirViewerFlag

boolean pirViewerFlag
PIR page popup browser Mode

genomicViewerFlag

boolean[] genomicViewerFlag
holds sGenomicMenu[cfg.nGenomicMenus] menu flags

useEPrawIntensValFlag

boolean useEPrawIntensValFlag
use Raw intensity for EP ratios in gene REPORTS

addExprProfileFlag

boolean addExprProfileFlag
set for EP ratios in gene REPORTS

addHP_XYstatFlag

boolean addHP_XYstatFlag
set for HP_XY statistics in gene REPORTS

addOCLstatFlag

boolean addOCLstatFlag
set for OCL statics statistics in gene REPORTS

autoStateScrPopupFlag

boolean autoStateScrPopupFlag
Auto state-scroller popup windown assoc w/Filters

useLowRatiosFilterFlag

boolean useLowRatiosFilterFlag
"Use lowest X/Y ratios filter"

useHighRatiosFilterFlag

boolean useHighRatiosFilterFlag
"Use highest X/Y ratios filter"

spotIntensFilterFlag

boolean spotIntensFilterFlag
filter genes by spot Intensity threshold

intensFilterFlag

boolean intensFilterFlag
filter genes by intensity threshold

ratioFilterFlag

boolean ratioFilterFlag
filter genes by ratio threshold

ratioCy3Cy5FilterFlag

boolean ratioCy3Cy5FilterFlag
filter genes by Cy3/Cy5 ratio threshold

geneClassMbrFilterFlag

boolean geneClassMbrFilterFlag
filter genes by GeneClass mbrshp

useGeneSetFilterFlag

boolean useGeneSetFilterFlag
filter genes by useGeneSet mbrship

useRatioHistCLflag

boolean useRatioHistCLflag
filter genes on Ratio histogram bin

useIntensHistCLflag

boolean useIntensHistCLflag
filter genes on Intensity hist bin

useEditedCLflag

boolean useEditedCLflag
filter genes on Edited Gene List

useGoodGeneCLflag

boolean useGoodGeneCLflag
filter by genes in Good Genes List

useReplicateGenesFlag

boolean useReplicateGenesFlag
filter by genes with at least 1 replicate

useCVmeanElseMaxFlag

boolean useCVmeanElseMaxFlag
use mean of CV else use max in CV filter

tTestXYfilterFlag

boolean tTestXYfilterFlag
filter genes passing HP-X/-Y t-test

tTestXYsetsFilterFlag

boolean tTestXYsetsFilterFlag
filter genes passing HP-X/-Y sets t-test

KS_TestXYsetsFilterFlag

boolean KS_TestXYsetsFilterFlag
filter genes passing HP-X/-Y sets KS-test

F_TestOCLFilterFlag

boolean F_TestOCLFilterFlag
filter genes passing current OCL (Ordered Condition List) F-test

useSpotCVfilterFlag

boolean useSpotCVfilterFlag
filter by Spot CV filter is enabled

clusterHP_EfilterFlag

boolean clusterHP_EfilterFlag
filter genes by cluster HP-E

useDiffFilterFlag

boolean useDiffFilterFlag
filter genes by abs diff(HP-X,HP-Y)

usePosQuantDataFlag

boolean usePosQuantDataFlag
filter genes with positive quant data

useGoodSpotDataFlag

boolean useGoodSpotDataFlag
filter genes with Good Spot (QualChk) data

useDetValueSpotDataFlag

boolean useDetValueSpotDataFlag
filter genes with Spot (Detection value) data

useOnlyGenesWithNonZeroDensityFlag

boolean useOnlyGenesWithNonZeroDensityFlag
filter by genes with non-zero intensity - problem when do log() transform

clusterOnFilteredCLflag

boolean clusterOnFilteredCLflag
cluster on Filtered/All genes

useClusterDistFlag

boolean useClusterDistFlag
cluster distance thresholding

useSimGeneClusterDispFlag

boolean useSimGeneClusterDispFlag
show a cluster of similar genes for current gene

useClusterCountsDispFlag

boolean useClusterCountsDispFlag
show gene clusters count

useHierClusterDispFlag

boolean useHierClusterDispFlag
show hierarchical clusters

useKmeansClusterCntsDispFlag

boolean useKmeansClusterCntsDispFlag
show K-means clusters

useLSQmagNormFlag

boolean useLSQmagNormFlag
norm geneEPvect[] to 1.0 for clustering

useClusterDistCacheFlag

boolean useClusterDistCacheFlag
use cluster cache else recompute each time

useShortClusterDistCacheFlag

boolean useShortClusterDistCacheFlag
use short else float cluster cache, can save memory if really needed
Constructor Detail

MAExplorer

public MAExplorer()
Method Detail

main

public static void main(java.lang.String[] args)
main() - for MAExplorer started by standalone application.
Parameters:
args - is the command line arg list

clearDynamicState

private void clearDynamicState()
clearDynamicState() - reset dynamic state variables in MAE instance.

destroyStaticState

private void destroyStaticState()
destroyStaticState() - reset static state variables in MAE instance
See Also:
ClusterGenes.cleanup(), CompositeDatabase.cleanup(), Condition.cleanup(), EventMenu.cleanup(), GeneGeneDist.cleanup(), GeneList.cleanup(), HierClustNode.cleanup(), Util.cleanup()

resetDefaultstate

void resetDefaultstate()
resetDefaultstate() - Reinitialize global user state. Anything in this method should be able to be set during runtime from the "Reset" menu. If called from the MENU, call Config again to reset from PARAM values.
See Also:
Config.getStateParamValues()

init

public void init()
init() - allocate,clear state, read PARAMs, build GUI and start things off. Clear state, read PARAMs, build GUI and start things off. This code can be called repeatedly to restart MAExplorer on a difference saCodeBase.
Overrides:
init in class java.applet.Applet
See Also:
Component.repaint(), CompositeDatabase, CompositeDatabase.recalcNorms(java.lang.String, boolean), CompositeDatabase.setOBJtoGID(int, MaHybridSample), Config.getStateParamValues(), Config.setupFullpathFilenames(), Config.setupPathBase(MAExplorer), Condition, DrawPseudoImage, EditedGeneList, EventMenu, EventMenu.setPlotState(java.awt.CheckboxMenuItem), Filter, Filter.computeWorkingGeneList(), FileIO, Gene, GeneClass, GeneClass.assignGeneNames2StaticGeneList(), GeneClass.setCurrentGeneClassName(java.lang.String), GeneClass.setupSpecialGeneLists(), GeneClass.updateStdGenePartitions(), GeneGeneDist, GeneList, GetParams, GipoTable, GipoTable.copyGBCTdataToStaticGeneDB(), GipoTable.copyGeneNamesTableFile(), GridCoords, MaeJavaAPI, MaeJavaAPI.initStateAndMJAchildren(MAExplorer), Maps, MaInfoTable, MenuBarFrame, MenuBarFrame.callAllStartupPlugins(), MenuBarFrame.enableMenus(java.lang.String), MenuBarFrame.redoMenuBar(), Frame.setTitle(java.lang.String), PopupRegistry, SamplesTable, SampleSets, SamplesTable.readListOfSampleNames(), Component.repaint(), StageNames, StageNames.getMenuTreeFromSamplesTable(MAExplorer), SpotData, SpotFeatures, Statistics, SimpleTable.freeTable(), UserState, Util, Util.chkDirFinalSeparator(java.lang.String, java.lang.String), Util.getRatioStr(), Util.popupDryrotMsgsAndQuit(), Util.popupViewer(java.net.URL, java.lang.String, java.lang.String), Util.showMsg(java.lang.String), Util.showMsg2(java.lang.String), Util.showMsg3(java.lang.String), doAnyLoginsRequired(), clearDynamicState(), destroy2(), destroyStaticState(), Applet.getParameter(java.lang.String), readListOfSampleDataFiles(), Component.repaint(), resetDefaultstate()

start

public void start()
start() - (re)create GUI if needed, read PARAMs & start run thread.
Overrides:
start in class java.applet.Applet

stop

public void stop()
stop() - stop the thread.
Overrides:
stop in class java.applet.Applet

run

public void run()
run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change. [2] Check to see if need to garbage collect
Specified by:
run in interface java.lang.Runnable
See Also:
FileIO.logMsgln(java.lang.String), PopupRegistry.checkStringPopupTimeouts(int), Component.repaint(), Util.sleepMsec(int), destroy(), stop()

paint

public void paint(java.awt.Graphics g)
paint() - generate viewable scrollable pseudoarray image with overlays.
Overrides:
paint in class java.awt.Container
Parameters:
g - is graphics context
See Also:
ArrayScroller.syncScrollerAccess()

update

public void update(java.awt.Graphics g)
update() - redraw graphics
Overrides:
update in class java.awt.Container
Parameters:
g - is graphics context

doAnyLoginsRequired

private boolean doAnyLoginsRequired()
doAnyLoginsRequired() - do any Web server logins required for PARAM images that access a Web server database of primary MAExplorer data.
Returns:
true if ok.
See Also:
Util.popupDryrotMsgsAndQuit(), Util.showMsg(java.lang.String), UserState.validateUserProject(java.lang.String, java.lang.String, java.lang.String), logDRYROTerr(java.lang.String)

readListOfSampleDataFiles

boolean readListOfSampleDataFiles()
readListOfSampleDataFiles() - populate msList[1:nHP] data structures by reading the data files up to maxPreloadImgs. If the user wants more, then they will load them manually.
Returns:
true if successful in reading ALL of the samples.
See Also:
Condition.addCondList(java.lang.String, MaHybridSample[], int, int), GetParams.setDefParam(java.lang.String, boolean), MenuBarFrame.setHP_XYlabels(), MaHybridSample, SampleSets.addHPtoDB(MaHybridSample, int), SampleSets.setHPlistsFromPARAM(), Util.popupDryrotMsgsAndQuit(), UserState.restoreCondLists(), createSample(int, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean)

createSample

MaHybridSample createSample(int hpNbr,
                            java.lang.String hpName,
                            java.lang.String sampleID,
                            java.lang.String databaseFileID,
                            java.lang.String oImageName,
                            java.lang.String oMenuName,
                            java.lang.String fullStageText,
                            java.lang.String projectName,
                            boolean needLoginFlag,
                            boolean swapCy5Cy3DataFlag)
createSample() - create and return a MaHybridSample hybridized sample object. For all hpNbr > 1, read the .quant filedata. Then when we need the image in the future, eg. when we switch the mae.ms (current displayed HP) from the Samples menu, the it sets mae.ms= mae.msList[npNbr] to install new current ms.
Parameters:
hpNbr - is the sample number
hpName - is the sample file name
sampleID - is the free-form name of the sample
databaseFileID - is the optional database file ID (used with mAdb)
oImageName - is the optional image file name
oMenuName - is the name of this sample as it appears in the menu
fullStageText - is the full text specification of this sample
projectName - project this database belongs to
needLoginFlag - requires login to access data from Web server if needed.
swapCy5Cy3DataFlag - set if swap Cy3 and Cy5 channels.
Returns:
a new MaHybridSample object otherwise null if failed.
See Also:
MaHybridSample

chkIfCache

void chkIfCache()
chkIfCache() - check if set up to cache from Web DB. Make sure /Cache directory exists and if not, it creates it.

resetImageAndState

void resetImageAndState()
resetImageAndState() - Re initialize whenever restart
See Also:
resetDefaultstate(), GeneClass.setupSpecialGeneLists(), Component.repaint()

quit

void quit()
quit() - kill this application or Applet
See Also:
Component.setVisible(boolean), Window.dispose()

percentDone

int percentDone()
percentDone() - estimate percent of files done loading
Returns:
a percentage in the range of [0 to 100]
See Also:
Util.showMsg3(java.lang.String)

cleanup

void cleanup()
cleanup() - close up what needs to be closed and GC all structures Reset to initial state so can restart it...
See Also:
destroyStaticState(), FileIO.logMsgln(java.lang.String)

destroy

public void destroy()
destroy() - destroy this class
Overrides:
destroy in class java.applet.Applet
See Also:
destroy2()

destroy2

void destroy2()
destroy2() - destroy this class, but clean up the mess of statics first.
See Also:
FileIO.closeLogFile(), FileIO.logMsgln(java.lang.String), cleanup()

logDRYROTerr

void logDRYROTerr(java.lang.String msg)
logDRYROTerr() - add the dryrot error to the dryrotLogStr and log it by printing it to the system log.
Parameters:
msg - is the dryrot message to print
See Also:
FileIO.logMsg(java.lang.String)