: G-Index

genEpilogue() - generate epilogue R script to write data commands to put R created data into Temp/ folder for reading by MAExplorer when required by actions in the RLO specification.

generateTemplateButton - Variable in class PopupEditRscript

Generate R template code button

Generic_ID - Variable in class Gene

Generic Identifier - "if all else fails" the use may use some arbitrary unique ID

genericFlag - Variable in class Guesser

if true, don't put Clone opt.

geneSets - Static variable in class GeneList

list of all gene lists

genGridsFromNbrGenes - Static variable in class Config

Flag: generate grid coords from nbrGENES

GenNormalizationPlugin - class GenNormalizationPlugin.

This class implements a wrapper for a general purpose class GenericNormalizationPlugin MAExplorer plugin.

GenNormalizationPlugin(MaeJavaAPI, boolean) - Constructor for class GenNormalizationPlugin

GenNormalizationPlugin() - constructor ONLY for use with debugging using the mae.DBUG_GENERIC_NORM_PLUGIN flag to add (Analysis | Normalization | Test Generic Norm Plugin [DBUG]) to the normalization menu.

genomicDataStr - Variable in class ClusterGramCanvas

current gene genomic data

genomicDataStr - Static variable in class SpotFeatures

Strings generated by getSpotFeatures()

GenomicID - Variable in class Gene

(Optional) External Genomic IDs values if specified via the MaeConfig.txt or .mae startup files.

genomicViewerFlag - Variable in class MAExplorer

holds sGenomicMenu[cfg.nGenomicMenus] menu flags

genPrologue() - Method in class RgenDemo

genPrologue() - generate prologue R script to read data commands.

genRbits - Variable in class RscriptDescr

GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.

genRbits - Variable in class RgenDemo

Data R generation processing bits: RB_GENR_xxxx

genRbits - Variable in class PopupEditRscript

GenR Bits is a bit pattern of selected (R_GENR_xxxx) options used during .R script generation.

genRbits2String(int) - Method in class RgenDemo

genRbits2String() - create string representing the genRbits of the current RLayOut (RLO) of the instance

geoFullDataTableURL - Variable in class Config

Get full HTML list of a specific GEO microarray platform.

geoListOfPlatformsURL - Variable in class Config

Get HTML list of www.ncbi.nlm.nih.gov/geo Gene Express Omnibus GEO microarray platforms numbered GPL4, GPL5, ..."

geoPlatformID - Variable in class Config

GEO platform Identifier of the form "GPL"+.

get_abortFlag() - Method in class MJAstate

get_abortFlag() - get "abortFlag" flag status

get_addExprProfileFlag() - Method in class MJAreport

get_addExprProfileFlag() - get flag: add EP ratios in gene REPORTS

get_addHP_XYstatFlag() - Method in class MJAreport

get_addHP_XYstatFlag() - get flag: add HP_XY statistics in gene REPORTS

get_allowNegQuantDataFlag() - Method in class MJAstate

get_allowNegQuantDataFlag() - get "allowNegQuantData" flag status allow Negative Quantified intensity data

get_Clone_ID() - Method in class MJAgene

get_Clone_ID() - get Clone_ID for default gene, if exists

get_clusterNodeNbr() - Method in class MJAgene

get_clusterNodeNbr() - get clusterNodeNbr for default gene, if exists

get_clusterOnFilteredGenesFlag() - Method in class MJAcluster

get_clusterOnFilteredGenesFlag() - get flag to cluster on Filtered genes else All genes.

get_coeffOfVarTestMode() - Method in class MJAfilter

get_coeffOfVarTestMode() - get samples-to-use mode for testing coefficient of variation threshold.

get_conditionsData() - Method in class MJAstatistics

get_conditionsData() - data[0:nConditions-1][sampleNbrInClass] for computations of N-condition F-test

get_data() - Method in class MJAgene

get_data() - get data for default gene, if exists

get_data1() - Method in class MJAgene

get_data1() - get data1 for default gene, if exists

get_data2() - Method in class MJAgene

get_data2() - get data2 for default gene, if exists

get_dbEST3ID() - Method in class MJAgene

get_dbEST3ID() - get dbEST3 ID for default gene, if exists

get_dbEST5ID() - Method in class MJAgene

get_dbEST5ID() - get dbEST5 ID for default gene, if exists

get_defaultFloat() - Method in class MJAutil

get_defaultFloat() - default float value for conversions

get_deltaBinH() - Method in class MJAstatistics

get_deltaBinH() - width of the histogram bins computed as: nBinsH/(maxDataH-minDataH) previously computed

get_dF() - Method in class MJAstatistics

get_dF() - CALC: degrees of freedom previously computed

get_dKS() - Method in class MJAmath

get_dKS() - K-S statistic for Kolmogorov-Smirnov stat d & prob of the null hypothesis of 2 bins of data.

get_doGCFlag() - Method in class MJAstate

get_doGCFlag() - get "doGCflag" flag status invoke the Garbage Collector when have time as determined by the main idle loop

get_duplMIDlist() - Method in class MJAgene

get_duplMIDlist() - get list of MIDs for duplicate genes for default gene, if exists

get_f() - Method in class MJAstatistics

get_f() - CALC: calculated f statistic previously computed

get_fStat() - Method in class MJAstatistics

get_fStat() - CALC: f-statistic previously computed

get_gangSpotDuplicatesFlag() - Method in class MJAstate

get_gangSpotDuplicatesFlag() - get "gangSpotDuplicates" flag status display and report ganged (F1,F2) data else just F1 data

get_GenBankAcc3ID() - Method in class MJAgene

get_GenBankAcc3ID() - get GenBank Acc 3' ID for default gene, if exists

get_GenBankAcc5ID() - Method in class MJAgene

get_GenBankAcc5ID() - get GenBank Acc 5' ID for default gene, if exists

get_GenBankAccID() - Method in class MJAgene

get_GenBankAccID() - get GenBankAcc ID for default gene, if exists

get_Gene_Name() - Method in class MJAgene

get_Gene_Name() - get Gene_Name for default gene

get_Generic_ID() - Method in class MJAgene

get_Generic_ID() - get Generic_ID for default gene, if exists

get_genomicDB_URLs() - Method in class MJAgenomicDB

get_genomicDB_URLs() - get user-defined genomic DB URLs

get_GenomicID() - Method in class MJAgene

get_GenomicID() - geta list of additional genomic IDs for the default gene, if exists.

get_goodSpotTestMode() - Method in class MJAfilter

get_goodSpotTestMode() - get samples-to-use mode for testing for good spots (as determined by QualCheck field in .quant data files.

get_hist() - Method in class MJAstatistics

get_hist() - histogram of size [0:nBinsH-1] previously computed

get_HP_EclustersMembershioFlag() - Method in class MJAfilter

get_HP_EclustersMembershioFlag() - get flag for filter by HP-E clustering membership

get_HP_SampleName(int, boolean) - Method in class MJAsampleList

get_HP_SampleName() - get HP sample name for sample number

get_isZscoreNormFlag() - Method in class MJAstate

get_isZscoreNormFlag() - get "isZscoreNorm" flag status using one of the Zscore normalizations

get_LocusID() - Method in class MJAgene

get_LocusID() - get LocusID for default gene, if exists

get_Master_ID() - Method in class MJAgene

get_Master_ID() - get Master_ID for default gene

get_MasterGeneName() - Method in class MJAgene

get_MasterGeneName() - get MasterGeneName for default gene

get_maxDataH() - Method in class MJAstatistics

get_maxDataH() - max value in data[] for histogram previously computed

get_meanAbsDevH() - Method in class MJAstatistics

get_meanAbsDevH() - mean absolute deviation for histogram previously computed

get_meanH() - Method in class MJAstatistics

get_meanH() - mean of data[] for histogram previously computed

get_meanIdx() - Method in class MJAstatistics

get_meanIdx() - index of mean in hist[] previously computed

get_meansAllConditions() - Method in class MJAstatistics

get_meansAllConditions() - means of samples in each of the nConditions used in computation of N-condition F-test

get_medianH() - Method in class MJAstatistics

get_medianH() - mode of data[] for histogram previously computed

get_medianIdx() - Method in class MJAstatistics

get_medianIdx() - index of median in hist[] previously computed

get_minDataH() - Method in class MJAstatistics

get_minDataH() - min value in data[] for histogram previously computed

get_mnX() - Method in class MJAmath

get_mnX() - get mean X previously computed

get_mnY() - Method in class MJAmath

get_mnY() - get mean Y previously computed

get_modeH() - Method in class MJAstatistics

get_modeH() - mode of data[] for histogram previously computed

get_modeIdx() - Method in class MJAstatistics

get_modeIdx() - index of mode in hist[] previously computed

get_nBinsH() - Method in class MJAstatistics

get_nBinsH() - 0 if none.

get_nCond_dfBetween() - Method in class MJAstatistics

get_nCond_dfBetween() - get dfBetween degrees of freedom used in computation of N-condition F-test

get_nCond_dfWithin() - Method in class MJAstatistics

get_nCond_dfWithin() - get dfWithin degrees of freedom used in computation of N-condition F-test

get_nCond_pValue() - Method in class MJAstatistics

get_nCond_pValue() - get p-value computed of N-condition F-test

get_nCondFstat() - Method in class MJAstatistics

get_nCondFstat() - get f-statistic computed in N-condition F-test

get_nConditions() - Method in class MJAstatistics

get_nConditions() - get nConditions used in computation of N-condition F-test

get_nCondMeanSqBetweenVariance() - Method in class MJAstatistics

get_nCondMeanSqBetweenVariance() - get mnSqBetween variance used in computation of N-condition F-test

get_nCondMeanSqWithinVariance() - Method in class MJAstatistics

get_nCondMeanSqWithinVariance() - get mnSqWithin variance used in computation of N-condition F-test

get_nDuplGenes() - Method in class MJAgene

get_nDuplGenes() - # duplicate genes in duplMIDlist[] for default gene, if exists

get_nGeneClustersCnt() - Method in class MJAgene

get_nGeneClustersCnt() - get nGeneClustersCnt for default gene, if exists

get_nGenomicID() - Method in class MJAgene

get_nGenomicID() - get # additional genomic IDs in the GenomicID[] list for the default gene, if exists.

get_normHierClusterByRatioHPFlag() - Method in class MJAcluster

get_normHierClusterByRatioHPFlag() - get flag to that normalizing each HP-E gene expression vector dataV[1:nHP] by the ratio of HP-X dataV[HP-X].

get_NratiosToReport() - Method in class MJAfilter

get_NratiosToReport() - get # of ratios to report

get_nSamplesAllConditions() - Method in class MJAstatistics

get_nSamplesAllConditions() - # of samples in each of the nConditions used in computation of N-condition F-test

get_nXY() - Method in class MJAmath

get_nXY() - # of genes used in calcXYstat computation

get_okBetaCF() - Method in class MJAmath

get_okBetaCF() - test if nr_betaCF() was ok

get_okBetaI() - Method in class MJAmath

get_okBetaI() - test if nr_betai() was ok

get_okProbKS() - Method in class MJAmath

get_okProbKS() - test if Kolmogorov-Smirnov test was ok

get_pF() - Method in class MJAstatistics

get_pF() - CALC: f-test p-value w/NULL hypoth previously computed

get_plate_col() - Method in class MJAgene

get_plate_col) - get original plate_col for default gene, if exists

get_plate_row() - Method in class MJAgene

get_plate_row() - get original plate_row for default gene, if exists

get_plate() - Method in class MJAgene

get_plate() - get original plate for default gene, if exists

get_positiveQuantTestMode() - Method in class MJAfilter

get_positiveQuantTestMode() - get samples-to-use mode for testing for positive spot quantification values.

get_presentationViewFlag() - Method in class MJAstate

get_presentationViewFlag() - get "presentationView" flag status use larger fonts and graphics for presentations

get_probKS() - Method in class MJAmath

get_probKS() - probability of null hypoth same distrib for previously computed Kolmogorov-Smirnov stat d & prob of the null hypothesis of 2 bins of data.

get_properties() - Method in class MJAgene

get_properties() - get properties for default gene, if exists

get_pT() - Method in class MJAstatistics

get_pT() - CALC: t-test p-value w/NULL hypoth previously computed

get_pValue() - Method in class MJAgene

get_pValue() - get pValue for default gene, if exists

get_pValueThr() - Method in class MJAfilter

get_pValueThr() - get Sample p-Value for t-Test Filter threshold

get_ratioCy3Cy5RangeMode() - Method in class MJAfilter

get_ratioCy3Cy5RangeMode() - get inside/outside mode for testing sample Cy3/Cy5 ratio range.

get_ratioRangeMode() - Method in class MJAfilter

get_ratioRangeMode() - get inside/outside mode for testing sample ratio range.

get_rSq() - Method in class MJAmath

get_rSq() - get correlation coefficient previously computed

get_sampleIntensityRangeMode() - Method in class MJAfilter

get_sampleIntensityRangeMode() - get inside/outside mode for testing sample intensity range.

get_sdX() - Method in class MJAmath

get_sdX() - get standard deviation X previously computed

get_sdY() - Method in class MJAmath

get_sdY() - get standard deviation Y previously computed

get_spotIntensityCompareMode() - Method in class MJAfilter

get_spotIntensityCompareMode() - get how-to compare samples mode for testing spot intensity range.

get_spotIntensityRangeMode() - Method in class MJAfilter

get_spotIntensityRangeMode() - get inside/outside mode for testing spot intensity range.

get_spotIntensityTestMode() - Method in class MJAfilter

get_spotIntensityTestMode() - get samples-to-use mode for testing spot intensity range.

get_stdDevAllConditions() - Method in class MJAstatistics

get_stdDevAllConditions() - stdDev of samples in each of the nConditions used in computation of N-condition F-test

get_stdDevH() - Method in class MJAstatistics

get_stdDevH() - standard deviation of data[] for histogram previously computed

get_SwissProtID() - Method in class MJAgene

get_SwissProtID() - get SwissProt ID for default gene, if exists

get_t() - Method in class MJAstatistics

get_t() - CALC: t or t' statistic computed previously computed

get_thrClusterDist() - Method in class MJAfilter

get_thrClusterDist() - get Sample gene-gene cluster distance threshold

get_thrCR1() - Method in class MJAfilter

get_thrCR1() - get Sample Cy3/Cy5 lower limit CR1 threshold

get_thrCR2() - Method in class MJAfilter

get_thrCR2() - get Sample Cy3/Cy5 lower limit CR2 threshold

get_thrDiff() - Method in class MJAfilter

get_thrDiff() - get Sample diff (HP-X,HP-Y) Filter threshold

get_thrI1() - Method in class MJAfilter

get_thrI1() - get Sample Intensity lower limit I1 threshold

get_thrI2() - Method in class MJAfilter

get_thrI2() - get Sample Intensity lower limit I2 threshold

get_thrNbrClusters() - Method in class MJAfilter

get_thrNbrClusters() - get # of clusters in K-means clustering

get_thrPercentOK() - Method in class MJAfilter

get_thrPercentOK() - get % of samples meeting Spot Intensity criteria threshold

get_thrQualCheck() - Method in class MJAfilter

get_thrQualCheck) - get Sample QualCheck threshold

get_thrR1() - Method in class MJAfilter

get_thrR1() - get Sample Ratio lower limit R1 threshold

get_thrR2() - Method in class MJAfilter

get_thrR2() - get Sample Ratio lower limit R2 threshold

get_thrSI1() - Method in class MJAfilter

get_thrSI1() - get Spot Intensity lower limit SI1 threshold

get_thrSI2() - Method in class MJAfilter

get_thrSI2() - get Spot Intensity lower limit SI2 threshold

get_thrSpotCV() - Method in class MJAfilter

get_thrSpotCV() - get Sample spot Coefficient Of Variation Filter threshold

get_title() - Method in class MJAstatistics

get_title() - title for data used in histogram previously computed

get_UGclusterName() - Method in class MJAgene

get_UGclusterName() - get UGclusterName for default gene, if exists

get_Unigene_ID() - Method in class MJAgene

get_Unigene_ID() - get Unigene_ID for default gene, if exists

get_updatePseudoImgFlag() - Method in class MJAstate

get_updatePseudoArrayImageFlag() - get "updatePseudoArrayImage" flag status.

get_useAbsDiffFilterFlag() - Method in class MJAfilter

get_useAbsDiffFilterFlag() - get flag for filter by absolute diff |HP-X - HP-Y|

get_useAutoStateScrollersPopupFlag() - Method in class MJAfilter

get_useAutoStateScrollersPopupFlag() - flag for Auto state-scroller popup window

get_useClusterCountsDisplayFlag() - Method in class MJAcluster

get_useClusterCountsDisplayFlag() - get flag to show if gene cluster counts cluster method is active.

get_useClusterDistanceCacheFlag() - Method in class MJAcluster

get_useClusterDistanceCacheFlag() - get flag to use cluster distance cache to speed up computations.

get_useCorrelationCoefficientFlag() - Method in class MJAcluster

get_useCorrelationCoefficientFlag() - get gene-gene distance metric flag.

get_useCVmeanElseMaxInFilterFlag() - Method in class MJAfilter

get_useCVmeanElseMaxInFilterFlag() - flag for use mean of CV else use max in Coefficient of Variation filter

get_useCy5OverCy3Flag() - Method in class MJAstate

get_useCy5OverCy3Flag() - get "useCy5OverCy3Flag" flag status Swap Cy3/Cy to Cy5/Cy3 for reporting purposes

get_useDbESTViewerFlag(boolean) - Method in class MJAgenomicDB

get_useDbESTViewerFlag() - access popup Web browser dbEST database

get_useDichromasyDisplayFlag() - Method in class MJAstate

get_useDichromasyDisplayFlag() - get "useDichromasyDisplay" flag status enable Dichromasy color-blindness display options

get_useEGLgeneListFilterFlag() - Method in class MJAfilter

get_useEGLgeneListFilterFlag() - flag for filter by genes in EGL

get_useEPrawIntensityValuesFlag() - Method in class MJAreport

get_useEPrawIntensityValuesFlag() - get flag: use Raw intensity for EP ratios in gene REPORTS

get_useExprProfileOverlayFlag() - Method in class MJAstate

get_useExprProfileOverlayFlag() - get "useExprProfileOverlay" flag status Plot EP list as overlay 2Dplot else scrollable EP list

get_useF_TestOCLFilterFlag() - Method in class MJAfilter

get_useF_TestOCLFilterFlag() - flag for filter passing ur.

get_useGenBankViewerFlag(boolean) - Method in class MJAgenomicDB

get_useGenBankViewerFlag() - access popup Web browser GenBank database

get_useGeneClassMbrFilterFlag() - Method in class MJAfilter

get_useGeneClassMbrFilterFlag() - flag for filter by GeneClass membership

get_useGeneSetFilterFlag() - Method in class MJAfilter

get_useGeneSetFilterFlag() - flag for filter by user gene set membership

get_useGoodGeneGIPOfilterFlag() - Method in class MJAfilter

get_useGoodGeneGIPOfilterFlag() - flag for filter by GIPO Good Genes List

get_useGoodSpotDataFlag() - Method in class MJAfilter

get_useGoodSpotDataFlag() - flag for filter by Good spot data

get_useHierClusterDisplayFlag() - Method in class MJAcluster

get_useHierClusterDisplayFlag() - get flag show hierarchical clusters in the pseudoarray image for All Filtered genes.

get_useHighRatiosFilterFlag() - Method in class MJAfilter

get_useHighRatiosFilterFlag() - flag for Use highest X/Y ratios filter

get_useHP_E_ListDataFlag() - Method in class MJAstate

get_useHP_E_ListDataFlag() - get "useMeanHPeListDataFlag" flag status use mean HP-E 'list' data else single current HP sample data

get_useHPxySetsDataFlag() - Method in class MJAstate

get_useHPxySetsDataFlag() - get "useHPxySetsData" flag status use mean HP-X,Y 'sets' data else HP-X,HP-Y single samples data

get_useIntensHistBinsFilterFlag() - Method in class MJAfilter

get_useIntensHistBinsFilterFlag() - flag for filter by Intensity histogram bin

get_useIntensityFilterFlag() - Method in class MJAfilter

get_useIntensityFilterFlag() - flag for filter by intensity threshold

get_useKmeansClusterCountsDispFlag() - Method in class MJAcluster

get_useKmeansClusterCountsDispFlag() - get flag show K-means cluster counts for all Filtered genes in the pseudoarray image.

get_useKStestXYsetsFilterFlag() - Method in class MJAfilter

get_useKStestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' KS-test

get_useLocksLinkViewerFlag(boolean) - Method in class MJAgenomicDB

get_useLocksLinkViewerFlag() - access popup Web browser LocusLink database

get_useLowRatiosFilterFlag() - Method in class MJAfilter

get_useLowRatiosFilterFlag() - flag for Use lowest X/Y ratios filter

get_useLSQmagnitudeNormalizationFlag() - Method in class MJAcluster

get_useLSQmagnitudeNormalizationFlag() - get flag to normalize cluster expression vector geneEPvect[] to 1.0 for clustering

get_useMadbViewerFlag(boolean) - Method in class MJAgenomicDB

get_useMadbViewerFlag() - access popup Web browser mAdb clone database

get_useMedianForKmeansClusteringFlag() - Method in class MJAcluster

get_useMedianForKmeansClusteringFlag() - get flag for K-median else K-means clustering

get_useMedMinerViewerFlag(boolean) - Method in class MJAgenomicDB

get_useMedMinerViewerFlag() - access popup Web browser MedMiner database

get_useMouseOverFlag() - Method in class MJAstate

get_useMouseOverFlag() - get "useMouseOver" flag status

get_useOmimViewerFlag(boolean) - Method in class MJAgenomicDB

get_useOmimViewerFlag() - access popup Web browser OMIM database

get_usePIRViewerFlag(boolean) - Method in class MJAgenomicDB

get_usePIRViewerFlag() - access popup Web browser PIR database

get_usePosQuantIntensDataFlag() - Method in class MJAfilter

get_usePosQuantIntensDataFlag() - get flag for filter by postive intensity data

get_useRatioCy3Cy5FilterFlag() - Method in class MJAfilter

get_useRatioCy3Cy5FilterFlag() - flag for filter by Cy3/Cy5 ratio range threshold

get_useRatioDataFlag() - Method in class MJAstate

get_useRatioDataFlag() - get "useRatioData" flag status data is Cy3/Cy5 ratio else Intensity

get_useRatioFilterFlag() - Method in class MJAfilter

get_useRatioFilterFlag() - flag for filter by ratio threshold

get_useRatioHistBinsFilterFlag() - Method in class MJAfilter

get_useRatioHistBinsFilterFlag() - flag for filter by Ratio histogram bin

get_useReplicateGenesFilterFlag() - Method in class MJAfilter

get_useReplicateGenesFilterFlag() - flag for filter by => 2 replicates/gene

get_useShortClusterDistanceCacheFlag() - Method in class MJAcluster

get_useShortClusterDistanceCacheFlag() - get flag t ouse short[] cluster distance cache to save memory

get_useSimilarGeneClusterDisplayFlag() - get flag to show if similar genes cluster method is active.

get_useSpotCVfilterFlag() - Method in class MJAfilter

get_useSpotCVfilterFlag() - get flag for filter by Spot Coefficient of Variation

get_useSpotIntensityFilterFlag() - Method in class MJAfilter

get_useSpotIntensityFilterFlag() - flag for filter by intensity threshold

get_useSwissProtViewerFlag(boolean) - Method in class MJAgenomicDB

get_useSwissProtViewerFlag() - access popup Web browser SwissProt database

get_useTest() - Method in class MJAstatistics

get_useTest() - CALC: 'B' or 'T' - t-test to use computed using F-statistic previously computed

get_useTtestXYfilterFlag() - Method in class MJAfilter

get_useTtestXYfilterFlag() - get flag for filter genes passing HP-X,-Y t-test

get_useTtestXYsetsFilterFlag() - Method in class MJAfilter

get_useTtestXYsetsFilterFlag() - flag for filter passing HP-X,HP-Y 'sets' t-test

get_useUniGeneViewerFlag(boolean) - Method in class MJAgenomicDB

get_useUniGeneViewerFlag() - access popup Web browser UniGene database

get_varianceAllConditions() - Method in class MJAstatistics

get_varianceAllConditions() - variance of samples in each of the nConditions used in computation of N-condition F-test

get_viewFilteredSpotsFlag() - Method in class MJAstate

get_viewFilteredSpotsFlag() - get "viewFilteredSpots" flag status in PseudoArray image show Filtered spots else don't show overlays

getActiveFilterPluginList() - Static method in class MAEPlugin.analysis.FilterPlugin

getActiveFilterPluginList() - Bean-style method for getting activeFilterPluginList.

getActiveNormalization() - Method in class MaeJavaAPI

getActiveNormalization() - get active normalization.

getActiveNormalization() - Static method in class MAEPlugin.analysis.NormalizationPlugin

getActiveNormalization() - Bean-style method for getting the activeNormalization.

getAdditionalParams() - Method in class Config

getAdditionalParams() - get additional params from .mae file or Applet etc.

getAllCondNames() - Method in class MJAcondition

getAllCondNames()- get a list of all condition names.

getAllF1F2dataForSample(float[], float[], int) - Method in class MJAsampleList

getAllF1F2dataForSample() - get all (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[]) for ALL gene data.

getAllGenRbits() - Method in class MJAReval

getAllGenRbits() - get GenR Bits using R_GENR_xxxx bits for current RLO.

getAllHP_XandYsamplesData(float[], float[], int, int) - Method in class MJAsampleList

getAllHP_XandYsamplesData() - get all (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[]) for ALL genes.

getAllHP_XandYsetDataForSample(float[], float[]) - Method in class MJAsampleList

getAllHP_XandYsetDataForSample() - get all HP-X, -Y 'sets' (X,Y) normalized data lists for sample in (Xdata[],Ydata[] for ALL genes.

getAllHPdataForSample(float[], int) - Method in class MJAsampleList

getAllHPdataForSample() - get all normalized (data,prop) list single sample's data for sample in (dataList[]) for ALL genes.

getAllMeanDataForCondition(float[], float[], String) - Method in class MJAsampleList

getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in in (meanData[], stdDevData[]) for data filtered by the specified gene list.

getAllMIDsForGene(String, int) - Method in class GipoTable

getAllMIDsForGene() - get Gene midList[] for gene name.

getAllProcessBits() - Method in class MJAReval

getAllRawF1F2DataAndBkgdForSample(float[], float[], float[], float[], int[], int[], int) - Method in class MJAsampleList

getAllawF1F2DataAndBkgdForSample() - get all spot list raw intensity and background data for genes and return it in the arrays pre-specified by the user.

getAllSampleNames() - Method in class MJAsampleList

getAllSampleNames()- get list of all active sample names used in DB

getAllSampleNamesInDB() - Method in class MJAcondition

getAllSampleNamesInDB() - get list of all sample names in the database

getArrayOfTabDelimitedTokens(String, int) - Method in class Table

getArrayOfTabDelimitedTokens() - get array of tab-delim tokens from table.

getBottomSeparator() - Method in class JavaCGIBridge

getBottomSeparator() - Returns the bottom separator for the object When getParsedData method is called, the object uses the bottom separator to determine where the rows of data inside the raw HTML output actually end.

getClassXname() - Method in class MJAsampleList

getClassXname() - get the current Class X name.

getClassYname() - Method in class MJAsampleList

getClassYname() - get the current Class Y name.

getClusterOfSimilarGenes() - get Hashtable list of gene cluster similar to seed gene.

getComputedMaxMeanEP() - Method in class MJAexprProfile

getComputedMaxMeanEP() - max mean of the current EP sample data

getCondIdxFromName(String) - Method in class PopupCondChooser

getCondIdxFromName() - Look up and return index of current cond.

getConditionByName(String) - Static method in class Condition

getConditionByName() - lookup Condition entry by name

getConditionIdxInOrderedCondList(Condition, String) - Method in class Condition

getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.

getConditionIdxInOrderedCondList(String, String) - Method in class MJAcondition

getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.

getConditionsInOrderedCondList(String) - Method in class MJAcondition

getConditionsInOrderedCondList() - get list of names conditions in OCL

getCondListLength() - Method in class Condition

getCondListLength() - get Condition list length

getCondListLength(String) - Method in class MJAcondition

getCondListLength() - get # of samples in the condition list

getCondListName() - Method in class Condition

getCondListName() - get Condition list name

getCondListsNames() - Method in class MJAcondition

getCondListsNames() - get list of active condition lists names

getCondListsSizes() - Method in class MJAcondition

getCondListsSizes() - get list of active condition lists sizes

getCondNameFromIdx(int) - Method in class PopupCondChooser

getCondNameFromIdx() - Look up and return name of current ocl.

getCondParamNames() - Method in class MJAcondition

getCondParamNames() - get list of condition parameter names for all conditions

getCondParamValues(String) - Method in class MJAcondition

getCondParamValues() - get list of parameter values for specific condition

getConfigAndPARAMvalue(String) - Method in class GetParams

getConfigAndPARAMvalue() - get Config then val for tag 1.

getConfigRowByRowIdx(int) - Method in class ConfigTable

getConfigRowByRowIdx() - get row of Config data table Row

getConfigRowFieldByName(int, String) - Method in class ConfigTable

getConfigRowFieldByName() - get row field data by array coords

getConfigRowFieldByRowFieldIdxes(int, int) - Method in class ConfigTable

getConfigRowFieldByRowFieldIdxses() - get row field by row and field indices

getConfigRowFieldByRowNameIdx(int, String) - Method in class ConfigTable

getConfigRowFieldByRowIdxName() - get row field by row index and name

getCorrCoefQuantDataList(int) - Method in class MJAsample

getCorrCoefQuantDataList() - get spot intensity correlation coefficient data for the given sample.

getCurCondition() - Method in class MJAcondition

getCurDateStr() - Static method in class Util

getCurDateStr() - return date string in the format of YYMMDDHHMMSS.

getCurGeneCol() - Method in class MJAgene

getCurGeneCol() - get the column in the grid for current gene

getCurGeneFeaturedata() - Static method in class SpotFeatures

getCurGeneFeaturedata() - get spot feature summary of current gene.

getCurGeneField() - Method in class MJAgene

getCurGeneField() - get the MID (Master Gene ID) number for current gene

getCurGeneGenomicdata() - Static method in class SpotFeatures

getCurGeneGenomicdata() - get spot feature summary of current gene.

getCurGeneGIDG() - Method in class MJAgene

getCurGeneGIDG() - get the GIDG (Ganged Grid layout ID) number for current gene

getCurGeneGrid() - Method in class MJAgene

getCurGeneGrid() - get the grid for current gene

getCurGeneMID() - Method in class MJAgene

getCurGeneMID() - get the MID (Master Gene ID) number for current gene

getCurGeneRow() - Method in class MJAgene

getCurGeneRow() - get the rowin the grid for current gene

getCurGeneXcoord() - Method in class MJAgene

getCurGeneXcoord() - get the X coordinate in the pseudoarray for current gene

getCurGeneXYGdata() - Static method in class SpotFeatures

getCurGeneXYGdata() - get spot quantitation summary of current gene.

getCurGeneYcoord() - Method in class MJAgene

getCurGeneYcoord() - get the Y coordinate in the pseudoarray for current gene

getCurOCL() - Method in class MJAcondition

getCurrent_HP_index() - Method in class MJAsampleList

getCurrent_HP_index() - get Current HP sample index.

getCurrent_HP_name(boolean) - Method in class MJAsampleList

getCurrent_HP_name() - get Current HP sample name

getCurrent_HP_X_index() - Method in class MJAsampleList

getCurrent_HP_X_index() - get Current HP-X sample index.

getCurrent_HP_X_name(boolean) - Method in class MJAsampleList

getCurrent_HP_X_name() - get Current HP-X sample name

getCurrent_HP_Y_index() - Method in class MJAsampleList

getCurrent_HP_Y_index() - get Current HP-Y sample index.

getCurrent_HP_Y_name(boolean) - Method in class MJAsampleList

getCurrent_HP_Y_name() - get Current HP-Y sample name

getCurrentGeneClassIndex() - Method in class MJAgeneList

getCurrentGeneClassIndex() - get index of current gene class in DB

getCurrentRLO() - Method in class Reval

getCurrentRLO() - get the current RLO analysis method object

getCurrentRLO() - Method in class RscriptDescr

getCurrentRLO() - return current RLO

getCurrentRLOid() - Method in class MJAReval

getCurrentRLOid() - get the current RLO analysis method id

getCurrentRLOmenuName() - Method in class MJAReval

getCurrentRLOmenuName() - get the current RLO analysis menu string name

getCurrentRLOmenuStubName() - Method in class MJAReval

getCurrentRLOmenuStubName() - get the current RLO analysis menu stub string name

getCurrentRLORscriptName() - Method in class MJAReval

getCurrentRLORscriptName() - get current RLO analysis .R script file name

getCVtestMode() - Method in class MJAproperty

getCVtestMode() - get Coefficient of Variation (CV) test mode: SS_MODE_xxxx

getData(String, String, String[], boolean) - Method in class Table

getData() - read the data and store it in the table.

getDataByGID(int, boolean, int) - Method in class MaHybridSample

getDataByGID() - get scaled intensity data specified by gid and data type.

getDbEstURL() - Method in class MJAstate

getDbEstURL() - get the current url value

getDefaultThreadJavaCGIBridgeTimeOut() - Static method in class JavaCGIBridge

getDefaultThreadJavaCGIBridgeTimeOut() - default communication time out Return default static value in milliseconds for the class.

getDoMeanPlotsFlag() - Method in class MJAexprProfile

getDoMeanPlotsFlag() - flag to generate mean plots (of the clusters) else individual plots

getEditMode() - Method in class MJAproperty

getEditMode() - get EGL mode for 'edited gene list': EDIT_xxxx

getEnumOrder() - Method in class HierClustNode

getEnumOrder() - lookup or RECURSIVELY compute enumOrder of this node.

getEPmaxMeanSampleData() - Method in class MJAexprProfile

getEPmaxMeanSampleData() - max mean normalized sample data scale factor computed over all samples and all genes being used in a list of expression profiles.

getEPsamplesCV(int) - Method in class MJAexprProfile

getEPsamplesCV() - opt.

getEPsamplesData(int) - Method in class MJAexprProfile

getEPsamplesData() - list of normalized HP-E samples data for MID.

getEPsamplesMean(int) - Method in class MJAexprProfile

getEPsamplesMean() - opt.

getEPsamplesStdDev(int) - Method in class MJAexprProfile

getEPsamplesStdDev() - opt.

getF1F2Data(float[], float[], int[], GeneList, boolean, boolean, boolean) - Method in class MaHybridSample

getF1F2Data() - get list spot (F1,F2)'s intensity data for data filtered genes and return it in the xList[1:n] is the field 1 data, yList[0:n-1] is field 2 data and the property in propList[0:n-1].

getF1F2dataForSample(float[], float[], int[], int, String) - Method in class MJAsampleList

getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) data for sample in (f1List[], f2List[], propList[]) for FILTERED data by the specified gene list.

getFGRCtoGIDmap() - Method in class MJAgeometry

getFGRCtoGIDmap() - get map of [field][grid][grid_row][grid_col] to gid (GridCoords index GID).

getField(String) - Method in class JavaCGIBridge

getField() - helper routine for parsing header key PFL - 8-7-00 See pg931, Patrick Chan etal, Java Class Libraries 2nd Ed, Vol 1.

getFieldSeparator() - Method in class JavaCGIBridge

getFieldSeparator() - Returns the field separator for the object.

getFilterState() - Static method in class MAEPlugin.analysis.FilterPlugin

getFilterState() - Static method for using getActiveFilter().

getFlag() - Method in class MAEPlugin.MAEPlugin

getFlag() - get the menu status (CheckBox) menuFlag

getFloatValFromLine(String, StringTokenizer) - Method in class UserState

getFloatValFromLine() - get next line and parse value for key 'name='.

getFlourescentLabel1Name() - Method in class MJAproperty

getFlourescentLabel1Name() - get current fluorescent label 1 name.

getFlourescentLabel2Name() - Method in class MJAproperty

getFlourescentLabel2Name() - get current fluorescent label 1 name.

getFrame() - Method in class MaeJavaAPI

getFrame() - provide the dominate Frame for other AWT components

getFrame() - Method in interface MAEPlugin.MAEStub

getFrame() - provides Frame for Dialogs and other AWT components that need frames.

getFullGEOplatformDataTableURL() - Method in class MJAproperty

getFullGEOplatformDataTableURL() - get URL for current full GEO platform data table

getFullRoutputFilePath() - Method in class MJAReval

getFullRoutputFilePath() - get full path of R output file after file setup

getFullRscriptInputPath() - Method in class MJAReval

getFullRscriptInputPath() - full path of R input script file after file setup

getFullRunRfilePath() - Method in class MJAReval

getFullRunRfilePath() - full path of batch R startup script file after file setup

getFullSampleTextBySampleNbr(int) - Method in class MJAsample

getFullSampleTextBySampleNbr() - lookup the full sample text description by sample number.

getGbid2LocusLinkURL() - Method in class MJAstate

getGbid2LocusLinkURL() - get the current url value

getGBSnames() - Method in class GeneBitSet

getGBSnames() - return String array of active Gene Bit Set names.

getGenBankCloneURL() - Method in class MJAstate

getGenBankCloneURL() - get the current url value

getGenBankCloneURLepilogue() - Method in class MJAstate

getGenBankCloneURLepilogue() - get the current url value

getGeneBankAccURL() - Method in class MJAstate

getGenBankAccURL() - get the current url value

getGeneBitsetData(String) - Method in class MJAgeneList

getGeneBitsetData() - get Hashtable list of GeneBitSet data by GeneBitSet name.

getGeneCardURL() - Method in class MJAstate

getGeneCardURL() - get the current url value

getGeneFeatureLine(int) - Static method in class MJAgene

getGeneFeatureLine() - get spot feature summary of gene.

getGeneFieldDataFromGeneList(String, String) - Method in class MJAgeneList

getGeneFieldDataFromGeneList() - get String list of Gene fields for gene list.

getGeneGenomicLine(int) - Static method in class MJAgene

getGeneGenomicLine() - get spot genomic data summary of gene.

getGeneList() - Method in class GeneList

getGeneList() - get gene mList[] data as Gene[].

getGeneListByName(String) - Method in class GeneList

getGeneListByName() - get GeneList if geneListName is a valid GeneList cName.

getGeneListData(String) - Method in class MJAgeneList

getGeneListData() - get Hashtable list of GeneList data by GeneList name.

getGeneListNames() - Method in class MJAgeneList

getGeneListNames() - get list of the names for all of the GeneLists

getGeneListOfCurrentGeneClass() - Method in class GeneClass

getGeneListOfCurrentGeneClass() - get the current GeneClass Gene List

getGeneListOfGeneClass(String) - Method in class GeneClass

getGeneListOfGeneClass() - return a Gene List for the gene class

getGeneMeasurementSummary(int, int) - Static method in class MJAgene

getGeneMeasurementSummary() - get spot quantitation summary of (gene,sample).

getGeneTabDelimFieldsStr(String, boolean, Table, Table) - Method in class Report

getGeneTabDelimFieldsStr() - create tab delimited gene fields string

getGEOplatformID() - Method in class MJAproperty

getGEOplatformID() - get current GEO platform ID for this database

getGIDtoFGRCmap() - Method in class MJAgeometry

getGIDtoFGRCmap() - get the map of GIDs to FGRC 5-tuples Each map entry is {gid, field, grid, row, column}

getGIDtoGangGIDmap() - Method in class MJAgeometry

getGIDtoGangGIDmap() - get the map from GIDs to Ganged GIDs

getGIDtoMIDmap() - Method in class MJAgeometry

getGIDtoMIDmap() - get the map from GIDs to MIDs

getGoodSpotTestMode() - Method in class MJAproperty

getGoodSpotTestMode() - get Good Spot (QualCheck) test mode: SS_MODE_xxxx

getGrandMeanCalDNA(boolean) - Method in class MJAsampleList

getGrandMeanCalDNA() - get compute grand mean of calibration DNA

getGrandMeanUseGeneSet(boolean) - Method in class MJAsampleList

getGrandMeanUseGeneSet() - get compute grand mean of 'Use Gene Set'

getGridIDnbr() - Method in class MJAgene

getGridIDnbr() - get the GID (Grid layout ID) number for current gene

getGridIndexMap() - Method in class MJAgeometry

getGridIndexMap() - get the map of mid to gene.

getHeaderField(int) - Method in class JavaCGIBridge

getHeaderField() - implements getHeaderField for HttpURLconnection.

getHeaderField(String) - Method in class JavaCGIBridge

getHeaderField() - implements HeaderField for HttpURLconnection.

getHeaders() - Method in class JavaCGIBridge

getHeaders() - help routine read header from HTTP connection.

getHelpStr() - Method in class PopupEditRscript

getHelpStr() - get popup edit help message.

getHierClusterOfGenes(String) - Method in class MJAcluster

getHierClusterOfGenes() - get Hashtable list of hierarchical gene cluster of genes.

getHierClustMode() - Method in class MJAproperty

getHierClustMode() - get hierarchical clustering linkage mode: HIER_CLUST_xxxxx

getHP_Elist_SampleIDs() - Method in class MJAsampleList

getHP_Elist_SampleIDs()- get list of HP-E 'list' sample IDs used in DB

getHP_Elist_SampleNames() - Method in class MJAsampleList

getHP_Elist_SampleNames()- get list of HP-E 'list' sample IDs used in DB

getHP_Elist_SampleNbrs() - Method in class MJAsampleList

getHP_Elist_SampleNbrs()- get list of HP-E 'list' sample numbers used in DB

getHP_XandYsamplesData(float[], float[], int[], int, int, String) - Method in class MJAsampleList

getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of X and Y samples data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data by the specified gene list.

getHP_XandYsetData(float[], float[], int[], GeneList, boolean, boolean) - Method in class CompositeDatabase

getHP_XandYsetData() - get list spot (HP-X,HP-Y) sets data passing the data filter mae.fc.workingCL.

getHP_XandYsetDataForSample(float[], float[], int[], String) - Method in class MJAsampleList

getHP_XandYsetDataForSample() - get normalized HP-X, -Y 'sets' (X,Y,prop) data lists for sample in (Xdata[],Ydata[], propList[] for FILTERED data by the specified gene list.

getHP_Xset_SampleIDs() - Method in class MJAsampleList

getHP_Xset_SampleIDs()- get list of HP-X 'set' sample IDs used in DB

getHP_Xset_SampleNames() - Method in class MJAsampleList

getHP_Xset_SampleNames()- get list of HP-X 'set' sample names used in DB

getHP_Xset_SampleNbrs() - Method in class MJAsampleList

getHP_Xset_SampleNbrs()- get list of HP-X 'set' sample numbers used in DB

getHP_XYsetsStatistics(int) - Method in class MJAsampleList

getHP_XYsetsStatistics() - get HP-X and HP-Y 'set statistics for gene.

getHP_Yset_SampleIDs() - Method in class MJAsampleList

getHP_Yset_SampleIDs()- get list of HP-Y 'set' sample IDs used in DB

getHP_Yset_SampleNames() - Method in class MJAsampleList

getHP_Yset_SampleNames()- get list of HP-Y 'set' sample names used in DB

getHP_Yset_SampleNbrs() - Method in class MJAsampleList

getHP_Yset_SampleNbrs()- get list of HP-Y 'set' sample numbers used in DB

getHPdataForSample(float[], int[], int, String) - Method in class MJAsampleList

getHPdataForSample() - get normalized filtered (data,prop) list single sample's data for sample in (dataList[], propList[]) for FILTERED data by the specified gene list.

getHPlist() - Method in class Condition

getHPlist() - get sample list for condition [1:nMScond]

getHPnbrInImage(MouseEvent) - Method in class ScrollableImageCanvas

getHPnbrInImage() - return HP # if within threshold distance

getHttpRequestInThread(URL, Hashtable) - Method in class JavaCGIBridge

getHttpRequestInThread() - Returns HTTP Request data to the thread that was launched to GET/POST data for a URL.

getIMAGE2GenBankURL() - Method in class MJAstate

getIMAGE2GenBankURL() - get the current url value

getIMAGE2unigeneURL() - Method in class MJAstate

getIMAGE2unigeneURL() - get the current url value

getImgCursor() - Method in class ArrayScroller

getImgCursor() - get the (x,y) scrollable cursor for this image

getImgCursorMax() - Method in class ArrayScroller

getImgCursorMax() - get the (x,y) scrollable image cursor maxima.

getImgPos() - Method in class ArrayScroller

getImgPos() - get the Image position

getImgPos() - Method in class ScrollableImageCanvas

getImgPos() - get the Image position (xImg,yImg).

getInputDataFileNames() - Method in class MJAReval

getInputDataFileNames() - get current RLO list of input data file names

getInputDataFileNames() - Method in class Reval

getInputDataFileNames() - get current RLO list of input data file names

getInputDataTypes() - Method in class MJAReval

getInputDataTypes() - get current RLO list of input data file types

getInputDataTypes() - Method in class Reval

getInputDataTypes() - get current RLO list of input data file types

getInputRscriptFileName() - Method in class MJAReval

getInputRscriptFileName() - get current name of .R input script file

getInputStream() - Method in class JavaCGIBridge

getInputStream() - implements getInputStream for HttpURLconnection.

getInstance() - Method in class MAEPlugin.MAEPlugin

getInstance() - returns Registry instance of this class or new if not loaded

getIntValFromLine(String, StringTokenizer) - Method in class UserState

getIntValFromLine() - get next line and parse value for key 'name='.

getJarResources() - Method in class MAEPlugin.JarClassLoader

getKey(String) - Static method in class JavaCGIBridge

getKey() - helper routine for parsing header field PFL - 8-7-00 See pg931, Patrick Chan etal, Java Class Libraries 2nd Ed, Vol 1.

getKeyValuePairs(Vector) - Method in class JavaCGIBridge

getKeyValuePairs() - cvt getParsedData to hashtable.

getKmeansClusters(String, int, int) - Method in class MJAcluster

getKmeansClusters() - get Hashtable list of K-means clustering data.

getLastorderedCondListName() - Method in class MJAexprProfile

getLastorderedCondListName() - get name of last ordered condition list computation computed using calcOrderedCondListExprProfile().

getListCondListsStr() - Method in class Condition

getListCondListsStr() - get a list of the names of the Condition lists

getListCondListsStr() - Method in class MJAcondition

getListCondListsStr() - get list of Conditions pretty-print string

getListFilterNames() - Method in class MJAfilter

getListFilterNames() - getlist of active data Filter names.

getListGeneBitSetsStr() - Method in class GeneBitSet

getListGeneBitSetsStr() - convert list of active GeneBitSets userBS[] to summary print string.

getListOfAllActiveHPsampleIndices() - Method in class MJAsampleList

getListOfAllActiveHPsampleIndices() - get list of all active sample HP indices.

getListOfGeneFieldsForMID(int) - Method in class MJAgeneList

getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID", "CloneID", "LocusID", "UniGeneID", "SwissProtID", "RefSeqID", "Master_ID", "MasterGeneName", "Generic_ID"

getListOfGEOplatformsURL() - Method in class MJAproperty

getListOfGEOplatformsURL() - get URL for list of current GEO platforms

getListOfHPEsampleIndices() - Method in class MJAsampleList

getListOfHPEsampleIndices() - get list of sample indices in HP-E list.

getListOfHPXsampleIndices() - Method in class MJAsampleList

getListOfHPXsampleIndices() - get list of sample indices in HP-X set.

getListOfHPYsampleIndices() - Method in class MJAsampleList

getListOfHPYsampleIndices() - get list of sample indices in HP-Y set.

getListOfMenuActionCmds() - Method in class MJAeval

getListOfMenuActionCmds() - get list of current menu action short-form commands

getListOfMenuActionLabels() - Method in class MJAeval

getListOfMenuActionLabels() - get list of current menu action commands labels

getListOfMenuCheckboxLabels() - Method in class MJAeval

getListOfMenuCheckboxLabels() - get list of current menu checkbox label commands.

getListOfMenuStubNames() - Static method in class MJAutil

getListOfMenuStubNames() - get list of menu stub names

getListofRLOids() - Method in class RscriptDescr

getListofRLOids() - get list of all IDs

getListofRLOmenuNames() - Method in class MJAReval

getListofRLOmenuNames() - get list of all menuNames

getListofRLOmenuNames() - Method in class Reval

getListofRLOmenuNames() - get list of all menuNames

getListofRLOmenuNames() - Method in class RscriptDescr

getListofRLOmenuNames() - get list of all menuNames

getListofRLOscriptNames() - Method in class MJAReval

getListofRLOscriptNames() - get list of all R script names

getListofRLOscriptNames() - Method in class Reval

getListofRLOscriptNames() - get list of all R script names

getListofRLOscriptNames() - Method in class RscriptDescr

getListofRLOscriptNames() - get list of all R script names

getListOfSampleMenuEntries() - Method in class MJAsampleList

getListOfSampleMenuEntries() - get list of sample menu names as appears in the MAExplorer Samples menu.

getListOfSampleNames() - Method in class MJAsampleList

getListOfSampleNames() - get list sample database file name (no .quant).

getListOfSampleProjectEntries() - Method in class MJAsampleList

getListOfSampleProjectEntries() - get list of sample project names.

getListOfSampleStageNames() - Method in class MJAsampleList

getListOfSampleStageNames() - get list of sample full stage text names.

getListScrollerNames() - Method in class MJAfilter

getListScrollerNames() - get list of ALL State Scrollers

getListsOfEPsamplesCV(int[]) - Method in class MJAexprProfile

getListsOfEPsamplesCV() - lists of normalized HP-E samples CoefOfVar EPs for list of MIDs.

getListsOfEPsamplesData(int[]) - Method in class MJAexprProfile

getListsOfEPsamplesData() - lists of normalized HP-E samples data EPs for list of MIDs.

getListsOfEPsamplesMean(int[]) - Method in class MJAexprProfile

getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs Compute expression profiles for all of the mid's in the midList[] that are legal (i.e.

getListsOfEPsamplesStdDev(int[]) - Method in class MJAexprProfile

getListsOfEPsamplesStdDev() - lists of normalized HP-E samples StdDev EPs for list of MIDs.

getListsOfOrderedCondListCVs() - Method in class MJAexprProfile

getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

getListsOfOrderedCondListMeans() - Method in class MJAexprProfile

getListsOfOrderedCondListMeans() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

getListsOfOrderedCondListNames() - Method in class MJAexprProfile

getListsOfOrderedCondListNames() is last conditions means[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

getListsOfOrderedCondListNbrs() - Method in class MJAexprProfile

getListsOfOrderedCondListNbrs() is last conditions sizes [] from ordered condition list computation computed using calcOrderedCondListExprProfile().

getListsOfOrderedCondListStdDevs() - Method in class MJAexprProfile

getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition list computation computed using calcOrderedCondListExprProfile().

getLocusLinkURL() - Method in class MJAstate

getLocusLinkURL() - get the current url value

getLongValFromLine(String, StringTokenizer) - Method in class UserState

getLongValFromLine() - get next line and parse value for key 'name='.

getMAdbURL() - Method in class MJAstate

getMAdbURL() - get the current url value

getMaeBrowserTitle() - Method in class MJAproperty

getMaeBrowserTitle() - get current browser MAExplorer title.

getMaeCurProjectPath() - Method in class MJAproperty

getMaeCurProjectPath() - get path of current project MAExplorer session.

getMaeDatabaseTitle() - Method in class MJAproperty

getMaeDatabaseTitle() - get current MAExplorer database title.

getMaeDbSubsetTitle() - Method in class MJAproperty

getMaeDbSubsetTitle() - get current MAExplorer DB subset title.

getMAERlibrBasePath() - Method in class MJAReval

getMAERlibrBasePath() - get current base path of MAExplorer MAELibr/ directory lives in "{installation directory}/".

getMAEstartupValue(String) - Method in class UserState

getMAEstartupValue() - get value from MAE startup file DB

getMAEStub() - Method in class MAEPlugin.MAEPlugin

getMAEStub() - get the menu stub for this instance of plugin

getMaps() - Method in class MJAgeometry

getMaps() - get Hashtable list of a MAExplorer maps

getMasterGeneIDMap() - Method in class MJAgeometry

getMasterGeneIDMap() - get the map of mid to gene.

getMasterGeneIDname() - Method in class MJAgeneList

getMasterGeneIDname() - get the type of name used for Master Gene ID

getMasterGeneName() - Method in class MJAgeneList

getMasterGeneName() - get the type of name used for Master Gene Name

getMasterIDMode() - Method in class MJAgeneList

getMasterIDMode() - get the mode of name used for Master Gene ID It will be either MASTER_GENE_NAME or MASTER_UG_NAME

getMasterNameMode() - Method in class MJAgeneList

getMasterGeneName() - get the mode of name used for Master Gene Name It will be either MASTER_GENE_NAME or MASTER_UG_NAME

getMaxCondListSize() - Method in class MJAcondition

getMaxCondListSize() - get maximum # of samples condition list can hold

getMaxFields() - Method in class MJAgeometry

getMaxFields() - get the number of Max replicate grid Fields

getMaxGenes() - Method in class MJAgeometry

getMaxGenes() - get number of genes in the database

getMaxGridCols() - Method in class MJAgeometry

getMaxGridCols() - get the number of columns/grid in the array

getMaxGridRows() - Method in class MJAgeometry

getMaxGridRows() - get the number of rows/grid in the array

getMaxGrids() - Method in class MJAgeometry

getMaxGrids() - get the number of Max Grids in the array not counting replicate fields.

getMaxNbrCondParams() - Method in class MJAcondition

getMaxNbrCondParams() - get maximum # of condition parameters DB may hold

getMaxNbrOCLParams() - Method in class MJAcondition

getMaxNbrOCLParams() - return max number of Ordered Condition List parameters.

getMaxNbrSamplesInDB() - Method in class MJAcondition

getMaxNbrSamplesInDB() - get maximum # of samples database list can hold

getMaxOrderedCondListSize() - Method in class MJAcondition

getMaxOrderedCondListSize() - get maximum # of condition lists that an ordered condition list can hold

getMeanDataForCondition(float[], float[], int[], String, String) - Method in class MJAsampleList

getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples' normalized data for genes in the specified gene list and samples in the condition list and save in (meanData[], stdDevData[], propList[]) for data filtered by the specified gene list.

getMedMinerURL() - Method in class MJAstate

getMedMinerURL() - get the current url value

getMedMinerURLepilogue() - Method in class MJAstate

getMedMinerURLepilogue() - get the current url value

getMenuHook() - Method in class MaeJavaAPI

getMenuHook() - get the menu hook for the plugin

getMenuHook() - Method in class MAEPlugin.MAEPlugin

getMenuHook() - get menu Item hook to put our instance of plugin

getMenuHook() - Method in interface MAEPlugin.MAEStub

getMenuHook() - method to retrieve the root menu

getMenuInsertionPointName() - Method in class MAEPlugin.MAEPlugin

getMenuInsertionPointName() - get the name of menu insertion point If it is not defined, then it returns null that indicates the Plugins menu.

getMenuItem() - Method in class MAEPlugin.MAEPlugin

getMenuItem() - get menu item for this instance of the plugin

getMenuTreeFromSamplesTable(MAExplorer) - Method in class StageNames

getMenuTreeFromSamplesTable() - build tree from Samples.txt Table

getMIDfromMaster_IDhashTable(String) - Method in class GipoTable

getMIDfromMaster_IDhashTable() - get Gene index (mid) given Master_ID.

getMIDindicesForFilterGeneList() - Method in class MJAgeneList

getMIDindicesForFilterGeneList() - get list MIDs for data Filter GeneList.

getMIDindicesFromGeneList(String) - Method in class MJAgeneList

getMIDindicesFromGeneList() - get list of GeneList MIDs by GeneList name.

getMIDtoGIDmap() - Method in class MJAgeometry

getMIDtoGIDmap() - get the map from MIDs to GIDs

getMinimumSize() - Method in class ClusterGramCanvas

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class Draw2Dplot

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class DrawClusterGram

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class StatusCanvas

getMinimumSize() - get the minimumpreferred size

getMinimumSize() - Method in class DrawHistogram

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class DrawRatioHistogram

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class ExprProfileCanvas

getMinimumSize() - get the minimum preferred size

getMinimumSize() - Method in class ExprProfilePanel

getMinimumSize() - get the minimumpreferred size

getMinimumSize() - Method in class ExprProfilePopup

getMinimumSize() - get the minimum preferred window size and add on room for the buttons at the bottom.

getMinimumSize() - Method in class ScrollableImageCanvas

getMinimumSize() - get the minimum current size of the canvas size

getNamedOrderedCondListIdx(String) - Method in class MJAcondition

getNamedOrderedCondListIdx() - get named ordered condition list index

getNbrActiveFilters() - Method in class MJAfilter

getNbrActiveFilters) - get number of active data Filters

getNbrAnalyses() - Method in class MJAReval

getNbrAnalyses() - get the number of analyses in the RLO DB

getNbrAnalyses() - Method in class Reval

getNbrAnalyses() - get the number of analyses in the RLO DB

getNbrCondLists() - Method in class MJAcondition

getNbrCondLists() - get # of active condition lists

getNbrCondParams() - Method in class MJAcondition

getNbrCondParams() - get the number of condition parameters

getNbrGeneBitSubsets() - Method in class MJAgeneList

getNbrGeneBitSubsets() - get total # of gene list bit subsets in DB

getNbrGenesPassingFilter() - Method in class MJAfilter

getNbrGenesPassingFilter() - get boolean flags for genes passing data Filter indexed by MID.

getNbrGeneSubsets() - Method in class MJAgeneList

getNbrGeneSubsets() - get total # of gene subsets in DB

getNbrGridIDs() - Method in class MJAgeometry

getNbrGridIDs() - get the number of genes

getNbrHPsamples() - Method in class MJAsampleList

getNbrHPsamples() - get # of ALL HP samples currently loaded in DB

getNbrMasterIDs() - Method in class MJAgeometry

getNbrMasterIDs() - get the number of Master Gene IDs

getNbrOrderedCondLists() - Method in class MJAcondition

getNbrOrderedCondLists() - get # of active ordered condition lists

getNbrSpecialGeneSubsets() - Method in class MJAgeneList

getNbrSpecialGeneSubsets() - get # of special gene subsets in DB

getNbrSpots() - Method in class MJAgeometry

getNbrSpots() - get the number of Nbr Spots in entire array

getNextInt(StringTokenizer) - Method in class UserState

getNextInt() - parse next int from StringTokenizer the integers are separated by ',' or '\n'.

getNextStrNameValFromLine(StringTokenizer) - Method in class UserState

getNextStrNameValFromLine() - get next line and parse 'name=value\n'.

getNormalizationState() - Method in class MaeJavaAPI

getNormalizationState() - update Normalization state based on normalization method selected in plugins.

getNormalizationState() - Method in interface MAEPlugin.MAEStub

getNormalizationState() - alias to: EventMenu.getNormalizationState used by: NormalizationPlugin

getNormalizationState() - Static method in class MAEPlugin.analysis.NormalizationPlugin

getNormalizationState() - Static method for using testing getActiveNormalization().

getNormHP_XandYdata(float[], float[], int[], GeneList, MaHybridSample, MaHybridSample, boolean, boolean) - Method in class CompositeDatabase

getNormHP_XandYdata() - get normalized list spot (HP-X,HP-Y) data passing data filter ml or mae.fc.workingCL.

getNormMethod() - Method in class MJAnormalization

getNormMethod() - get name of current normalization method

getNormMethodDisplayName() - Method in class MJAnormalization

getNormMethodDisplayName() - get display name of current normalization method

getNormToOneFlag() - Method in class MJAexprProfile

getNormToOneFlag() - flag of normalize expression profile to 1.0 flag

getNthValueByName(String, int) - Method in class ConfigTable

getNthValueByName() - get n'th Configuration table Value by Name

getNumberedParamList(String) - Method in class GetParams

getNumberedParamList() - get a numbered parameter list The parameters are of the form: "image1", "image2", ...

getNumberPlugins() - Static method in class MAEPlugin.MAEPlugin

getNumberPlugins() - get the number of plugins (loaded).

getNumbersOfGenesInGeneSubsets() - Method in class MJAgeneList

getNumbersOfGenesInGeneSubsets() - get list of # genes in each of the gene subsets

getObjPos() - Method in class ArrayScroller

getObjPos() - get the object position

getObjPos() - Method in class ScrollableImageCanvas

getObjPos() - get the object position (xObj,yObj).

getOCLidxFromName(String) - Method in class PopupOrderedCondChooser

getOCLidxFromName() - Look up and return index of current ocl.

getOCLnameFromIdx(int) - Method in class PopupOrderedCondChooser

getOCLnameFromIdx() - Look up and return name of current ocl.

getOrderedCondListsNames() - Method in class MJAcondition

getOrderedCondListsNames() - get list of active ordered condition lists names

getOrderedCondListsSizes() - Method in class MJAcondition

getOrderedCondListsSizes() - get list of active ordered condition lists sizes

getOrderedCondNamesInCondList(String) - Method in class MJAcondition

getOrderedCondNamesInCondList() - get a list of all condition names in ordered cond list

getOrderedCondParamNames() - Method in class MJAcondition

getOrderedCondParamNames() - return list of Ordered condition paramter names.

getOrderedCondParamValues(String) - Method in class MJAcondition

getOrderedCondParamValues() - return list of Ordered condition paramter values.

getOutputDataFileNames() - Method in class MJAReval

getOutputDataFileNames() - get current RLO list of output data file names.

getOutputDataFileNames() - Method in class Reval

getOutputDataFileNames() - get current RLO list of output data file names.

getOutputDataTypes - Variable in class RgenDemo

Output types [0:nOutputFiles-1] if any

getOutputDataTypes() - Method in class MJAReval

getOutputDataTypes() - get current RLO list of output data file types

getOutputDataTypes() - Method in class Reval

getOutputDataTypes() - get current RLO list of output data file types

getOutputStream() - Method in class JavaCGIBridge

getOutputStream() - implements getOutputStream for HttpURLconnection.

GetParams - class GetParams.

This class get the argument list from the Applet or .mae startup file.

GetParams(MAExplorer) - Constructor for class GetParams

GetParams() - constructor

getParamVal(String) - Method in class GetParams

getParamVal() - get parameter from Configuration database file

getParsedData(URL) - Method in class JavaCGIBridge

getParsedData() - returns parsed data in form of Vector of Vectors containing the returned fields inside of a Vector of returned rows.

getParsedData(URL, Hashtable) - Method in class JavaCGIBridge

getParsedData() - returns parsed data in form of Vector of Vectors Returns parsed data in the form of a Vector of Vectors containing the returned fields inside of a Vector of returned rows.

getPassword() - Method in class MJAproperty

getPassword() - get current user password name if exists

getPirURL() - Method in class MJAstate

getPirURL() - get the current url value

getPlate(int) - Method in class SpotFeatures

getPlate(gid) - return the Plate coords Grid[r,c] as B3,4 etc.

getPlotModeImage() - Method in class MJAproperty

getPlotModeImage() - get pseudoarray image plot mode: PLOT_xxxx_IMAGE

getPluginDescription() - Method in class MAEPlugin.MAEPlugin

getPluginDescription() - returns a human readable description of the Plugin if any is defined by the plugin writer.

getPluginDescription() - Method in interface MAEPlugin.PluginStub

getPluginDescription() - returns a human readable description of the Plugin.

getPluginDescription() - Method in class MAEPlugin.popup.PluginLoader

getPluginDescription() - This returns a human readable description of the Plugin

getPluginDescription() - Method in class MAEPlugin.popup.PluginUnLoader

getPluginDescription() - This returns a human readable description of the Plugin

getPluginFileName() - Method in class MAEPlugin.MAEPlugin

getPluginFileName() - returns the plugin file name without the ".jar"

getPluginFileName() - Method in interface MAEPlugin.PluginStub

getPluginFileName() - returns the plugin file name without the ".jar"

getPluginHashState(String, String) - Method in class MJAstate

getPluginHashState() - get state object value from MAEPlugin hash state storage.

getPluginHashState(String, String, boolean) - Method in class MJAstate

getPluginHashState() - get boolean state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashState(String, String, byte) - Method in class MJAstate

getPluginHashState() - get byte state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashState(String, String, double) - Method in class MJAstate

getPluginHashState() - get double state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashState(String, String, float) - Method in class MJAstate

getPluginHashState() - get float state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashState(String, String, int) - Method in class MJAstate

getPluginHashState() - get int state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashState(String, String, long) - Method in class MJAstate

getPluginHashState() - get long state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store.

getPluginHashStateFileName() - Method in class MJAstate

getPluginHashStateFileName() - get the MAEPlugin hash state disk file name.

getPluginName() - Method in class MAEPlugin.MAEPlugin

getPluginName() - This is the human readable name for use in menu labels

getPluginName() - Method in interface MAEPlugin.PluginStub

getPluginName() - returns the human readable name for use in labels.

getPlugins() - Static method in class MAEPlugin.MAEPlugin

getPlugins() - gets Registry list of MAEPlugins

getPosQuantTestMode() - Method in class MJAproperty

getPosQuantTestMode() - get positive Quant data test mode: SS_MODE_xxxx

getPreferredSize_DEPRICATED() - Method in class StateScrollers