A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A - Static variable in class genomicsnpanalyzer.Worker

AAs - Variable in class nsanalyzer.MappResult

accessionNum - Variable in class genomicsnpanalyzer.entry.HGNCEntry

act(ClosableTabbedPane, int) - Method in interface genomicsnpanalyzer.gui.CloseTabAction

act(ClosableTabbedPane, int) - Method in interface genomicsnpanalyzer.gui.SelectTabAction

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.Dialog_sample

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.DensityOverviewPane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_analysis_prio_gene

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_analysis_prio_var

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_analysis_rareDom

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_analysis_variantPosition

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_buildBinCoverage

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_buildBinRef

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_checkSNP1M

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_checkSVrawcnv

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_comparePrjSNPs

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_createChrWisePrj

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_createInputSubset

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_ExtractSubjects

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_FilterHapmapFreq

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_FilterRegion

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_FilterSubject

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GBdisplayItem

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_geneBiotypeFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_geneFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowDGVCNV

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndels

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndIndel

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSNP

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSV

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowOneKSNP

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSimpleSNPs

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSNPs

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSVs

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTaggedCNV

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTrans

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVarFeatures

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterIndels

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterSNPs

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_goFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_IndelQualityFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_keywordsearch

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_list_het

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_list_hom

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_list_homhet

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_omimDisorder

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_openProject

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_OptionFunctionDisplay

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_OptionGenomeBrowser

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_OptionMemory

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_OptionThreadsAnnotation

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_outputRegionCov

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_pathwayFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_searchGene

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_searchSNP

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_selectIndelTableHeaders

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_selectSNPTableHeaders

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_showIndelSubjectDetails

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_showSNPSubjectDetails

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_showSVSubjectDetails

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_SNPQualityFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_summary_indelsFun

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_summary_snpsFunMaf

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_summaryCoverageRegions

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.Dialog_SVQualityFilter

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.FilterSummaryPane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.GenomeBrowserPane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.IndelListTablePane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.IndelTable

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.MainContentPane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.MainLowerToolbar

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.MainUpperToolbar

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.SNPListTablePane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.SNPTable

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.SVListTablePane

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.SVTable

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.WindowNote

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.gui.WindowSequence

actionPerformed(ActionEvent) - Method in class genomicsnpanalyzer.Main

addDensityTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addFilterTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addGenomeBrowserTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addIndelTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addLogPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addProjectPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSNPListTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane_indel() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane_indel_nonrs() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane_indel_rs() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane_nonrs() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSummaryPane_rs() - Method in class genomicsnpanalyzer.gui.MainContentPane

addSVTabPane() - Method in class genomicsnpanalyzer.gui.MainContentPane

AExon - Class in genomicsnpanalyzer.genomebrowser.entry

AExon() - Constructor for class genomicsnpanalyzer.genomebrowser.entry.AExon

Creates a new instance of AExon

AGene - Class in genomicsnpanalyzer.genomebrowser.entry

AGene() - Constructor for class genomicsnpanalyzer.genomebrowser.entry.AGene

Creates a new instance of Gene

alias - Variable in class genomicsnpanalyzer.entry.HGNCEntry

allele - Variable in class genomicsnpanalyzer.entry.LociFunction

allele - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

allele - Variable in class genomicsnpanalyzer.entry.VenterIndel

allele - Variable in class genomicsnpanalyzer.entry.VenterSNP

allele - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

allele - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableOneKHumGenomeLoci

alleleCount - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

alleleCount - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableOneKHumGenomeLoci

alleles - Variable in class genomicsnpanalyzer.entry.VarFeature

alleles - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableVarFeature

ambiguousAllele - Variable in class genomicsnpanalyzer.entry.LociFunctionSubjectInf

ambiguousAllele - Variable in class genomicsnpanalyzer.entry.SortableLociFunctionSubjectInf

AmbiguousBase(String) - Static method in class genomicsnpanalyzer.Worker

AmbiguousByteBaseToStr(byte) - Static method in class genomicsnpanalyzer.Worker

AmbiguousStrBaseToByte(String) - Static method in class genomicsnpanalyzer.Worker

ancestralAllele - Variable in class genomicsnpanalyzer.genomebrowser.entry.ASNP

AnnoatedChrom_transFinalH - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_bm - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_generalInterval - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_generalIntervalSmall - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_hCNV - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_hTrans - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_intervalCNV - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_intervalTrans - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_lm - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_plotChrlm - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_plotChry - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_plotw - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_rm - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_tm - Variable in class genomicsnpanalyzer.Components

AnnotatedChrom_totallm - Variable in class genomicsnpanalyzer.Components

AnnotatedChromRegionIndicatorH - Variable in class genomicsnpanalyzer.Components

annotationFileDesc - Static variable in class genomicsnpanalyzer.entry.Project

annotationFileNumber - Static variable in class genomicsnpanalyzer.entry.Project

append(Color, String) - Method in class genomicsnpanalyzer.gui.ColorTextPane

append(Color, String, String) - Method in class genomicsnpanalyzer.gui.ColorTextPane

append(String) - Method in class genomicsnpanalyzer.gui.ColorTextPane

appendline(String) - Method in class genomicsnpanalyzer.gui.ColorTextPane

appendURL(String) - Method in class genomicsnpanalyzer.gui.ColorTextPane

AppTitle - Variable in class genomicsnpanalyzer.Main

ASNP - Class in genomicsnpanalyzer.genomebrowser.entry

ASNP() - Constructor for class genomicsnpanalyzer.genomebrowser.entry.ASNP

Creates a new instance of ASNP

ATranscript - Class in genomicsnpanalyzer.genomebrowser.entry

ATranscript() - Constructor for class genomicsnpanalyzer.genomebrowser.entry.ATranscript

Creates a new instance of ATranscript

avgfscore1 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore1 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgfscore2 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore2 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgfscore3 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore3 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgfscore4 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore4 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgfscore5 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore5 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgfscore6 - Variable in class genomicsnpanalyzer.entry.LociFunction

avgfscore6 - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

avgScore1HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter

avgScore2HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter

avgScore3HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter

avgScore4HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter

avgScore5HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter

avgScore6HistogramImg - Variable in class genomicsnpanalyzer.CacheDataCenter