Serialized Form

Package MAEPlugin

Class MAEPlugin.DuplicatePluginLoadException implements Serializable

Class MAEPlugin.MaxNumberPluginsException implements Serializable

Class MAEPlugin.PluginException implements Serializable

Class MAExplorer implements Serializable

Serialized Fields

onceOnlyFlag

boolean onceOnlyFlag

flag to prevent multiple instances

gnp

GenNormalizationPlugin gnp

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

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

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

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

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

proxyServer

java.lang.String proxyServer

base addr PARAM "proxyServer"

maeServerBase

java.lang.String maeServerBase

top level codebase for MAE server

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

cacheDir

java.lang.String cacheDir

Standalone /Cache directory for saving data downloaded for array Web server.

reuseGUIframeFlag

boolean reuseGUIframeFlag

Flag: set if reuse main GUI frame

isWinPCflag

boolean isWinPCflag

Flag: set to TRUE if any Windows PC

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

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

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"

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