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

I

icon - Variable in class genomicsnpanalyzer.Main

IconTableCellRenderer - Class in genomicsnpanalyzer.gui

IconTableCellRenderer(ImageIcon, String) - Constructor for class genomicsnpanalyzer.gui.IconTableCellRenderer

id - Variable in class genomicsnpanalyzer.entry.OmimEntry

id - Variable in class genomicsnpanalyzer.entry.Subject

id - Variable in class genomicsnpanalyzer.entry.VenterIndel

id - Variable in class genomicsnpanalyzer.entry.VenterSNP

id - Variable in class genomicsnpanalyzer.genomebrowser.entry.DGVCNV

id - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableDGVCNV

id - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableTaggedCNV

id - Variable in class genomicsnpanalyzer.genomebrowser.entry.TaggedCNV

idx - Variable in class genomicsnpanalyzer.entry.Cmd

idx - Variable in class genomicsnpanalyzer.entry.RawDataIndex

idx - Variable in class genomicsnpanalyzer.entry.RawDataIndexChr

idx - Variable in class genomicsnpanalyzer.entry.SortedOmimDisorder

idx - Variable in class genomicsnpanalyzer.entry.SortedOmimGene

illu1msnpidx - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserData

illumina1mFile - Variable in class genomicsnpanalyzer.entry.Project

Illumina1mSNPCoords - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserCoord

Illumina1mSNPHighlighIndex - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserCoord

Illumina1mSNPRegionCoord - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserCoord

illumina1msnps - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserBuffer

illumina1msnps - Variable in class genomicsnpanalyzer.longTask_genomeBrowse

IlluminaSnpHotspotCoord - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserCoord

IlluminaSnpHotspotOn - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserCoord

illuminaStrand - Variable in class genomicsnpanalyzer.entry.LociFunction

illuminaStrand - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

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

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

illusnp - Variable in class genomicsnpanalyzer.genomebrowser.entry.DisplaySectionSwitch

ImageWidth - Variable in class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserOptions

IMMUNEKEYWORDS - Static variable in class genomicsnpanalyzer.Worker

IncludeIndelTableHeaders - Variable in class genomicsnpanalyzer.Components

IncludeSNPTableHeaders - Variable in class genomicsnpanalyzer.Components

IncludeSVTableHeaders - Variable in class genomicsnpanalyzer.Components

indel - Variable in class genomicsnpanalyzer.genomebrowser.entry.DisplaySectionSwitch

IndelAnnotationParallelNum - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgConsHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgNumReadsHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgQualityHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgReads4IndelHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgReads4RefHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelAvgRMSHistImg - Variable in class genomicsnpanalyzer.CacheDataCenter

indelDataFile - Variable in class genomicsnpanalyzer.CacheDataCenter

indelDataFileIdx - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelFilterParallelNum - Variable in class genomicsnpanalyzer.CacheDataCenter

indelFunctionCache - Variable in class genomicsnpanalyzer.CacheDataCenter

indelFunctionFilter - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelFunctionFilter - Class in genomicsnpanalyzer

IndelFunctionFilter() - Constructor for class genomicsnpanalyzer.IndelFunctionFilter

Creates a new instance of SNPFilter

indelGeneCacheEnd - Variable in class genomicsnpanalyzer.CacheDataCenter

indelGeneCacheStart - Variable in class genomicsnpanalyzer.CacheDataCenter

indelHomFilter - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelHomFilter - Class in genomicsnpanalyzer

IndelHomFilter() - Constructor for class genomicsnpanalyzer.IndelHomFilter

Creates a new instance of SNPFilter

indelIndex - Variable in class genomicsnpanalyzer.CacheDataCenter

indelIndex - Variable in class genomicsnpanalyzer.longTaskPar_annotate

indelIndex - Variable in class genomicsnpanalyzer.longTaskPar_annotate_load

indelLength - Variable in class genomicsnpanalyzer.CacheDataCenter

indelLength - Variable in class genomicsnpanalyzer.longTaskPar_annotate

indelLength - Variable in class genomicsnpanalyzer.longTaskPar_annotate_load

indelListPanelTitle - Variable in class genomicsnpanalyzer.Components

IndelListTablePane - Class in genomicsnpanalyzer.gui

IndelListTablePane(Main) - Constructor for class genomicsnpanalyzer.gui.IndelListTablePane

indelLoaderInitiated - Variable in class genomicsnpanalyzer.CacheDataCenter

indelLocationCache - Variable in class genomicsnpanalyzer.CacheDataCenter

indelpane - Variable in class genomicsnpanalyzer.gui.MainContentPane

indelQualityFilter - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelQualityFilter - Class in genomicsnpanalyzer

IndelQualityFilter() - Constructor for class genomicsnpanalyzer.IndelQualityFilter

Creates a new instance of SNPFilter

indelRMRFilter - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelRMRFilter - Class in genomicsnpanalyzer

IndelRMRFilter() - Constructor for class genomicsnpanalyzer.IndelRMRFilter

Creates a new instance of SNPFilter

indelSelectedIndex - Variable in class genomicsnpanalyzer.CacheDataCenter

IndelTable - Class in genomicsnpanalyzer.gui

IndelTable(Main, IndelTableModel, String[]) - Constructor for class genomicsnpanalyzer.gui.IndelTable

IndelTableHeaders - Variable in class genomicsnpanalyzer.Components

IndelTableModel - Class in genomicsnpanalyzer.gui

IndelTableModel(String[], boolean[]) - Constructor for class genomicsnpanalyzer.gui.IndelTableModel

Creates a new instance of SNPTableModel

index - Variable in class genomicsnpanalyzer.entry.SortedGene

index - Variable in class genomicsnpanalyzer.entry.SortedGO

index - Variable in class genomicsnpanalyzer.entry.SortedPathway

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

indexCombo - Variable in class genomicsnpanalyzer.gui.SVListTablePane

indexid - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

indexid - Variable in class genomicsnpanalyzer.entry.SVLociFunction

indexid - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

indexid - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableSVLociFunction

indexLocCombo - Variable in class genomicsnpanalyzer.gui.SVListTablePane

inDGV - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

inDGV - Variable in class genomicsnpanalyzer.entry.SVLociFunction

inDGV - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

inDGV - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableSVLociFunction

inHapmap - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

inHapmap - Variable in class genomicsnpanalyzer.entry.LociFunction

inHapmap - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

inHapmap - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

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

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

inIllumina1M - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

inIllumina1M - Variable in class genomicsnpanalyzer.entry.LociFunction

inIllumina1M - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

inIllumina1M - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

inIllumina1M - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction

inIllumina1M - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableOneKHumGenomeLoci

init() - Method in class genomicsnpanalyzer.entry.HGNC

initComponents() - Method in class genomicsnpanalyzer.Main

initExon() - Method in class genomicsnpanalyzer.genomebrowser.entry.SortableTranscript

InitiateGeneSelectedIdx() - Method in class genomicsnpanalyzer.CacheDataCenter

InitiateGenomeBrowser() - Method in class genomicsnpanalyzer.gui.GenomeBrowserPane

InitiateIndelLoader() - Method in class genomicsnpanalyzer.CacheDataCenter

InitiateLocationCache(int, int[]) - Method in class genomicsnpanalyzer.CacheDataCenter

InitiateSNVLoader() - Method in class genomicsnpanalyzer.CacheDataCenter

InitiateSVLoader() - Method in class genomicsnpanalyzer.CacheDataCenter

inputFile - Variable in class genomicsnpanalyzer.entry.InputObject

InputHash - Variable in class genomicsnpanalyzer.entry.InputObjectMultiple

InputObject - Class in genomicsnpanalyzer.entry

InputObject() - Constructor for class genomicsnpanalyzer.entry.InputObject

Creates a new instance of InputObject

inputObject - Variable in class genomicsnpanalyzer.entry.Project

inputObjectCNV - Variable in class genomicsnpanalyzer.entry.Project

inputObjectHMMSV - Variable in class genomicsnpanalyzer.entry.Project

InputObjectMultiple - Class in genomicsnpanalyzer.entry

InputObjectMultiple() - Constructor for class genomicsnpanalyzer.entry.InputObjectMultiple

Creates a new instance of InputObject

inputObjectSV - Variable in class genomicsnpanalyzer.entry.Project

InputSource - Variable in class genomicsnpanalyzer.entry.Project

INTERGENIC - Static variable in class genomicsnpanalyzer.Worker

INTERGENIC_COLOR - Static variable in class genomicsnpanalyzer.Worker

interrupt() - Method in class genomicsnpanalyzer.SwingWorker

A new method that interrupts the worker thread.

IntoleranceSwicth - Variable in class genomicsnpanalyzer.SNPNSIntoleranceFilter

INTRONIC - Static variable in class genomicsnpanalyzer.Worker

INTRONIC_COLOR - Static variable in class genomicsnpanalyzer.Worker

INTRONIC_EXON_BOUNDARY - Static variable in class genomicsnpanalyzer.Worker

INTRONIC_EXON_BOUNDARY_COLOR - Static variable in class genomicsnpanalyzer.Worker

IntronicExonBoundary - Variable in class genomicsnpanalyzer.entry.Project

IntronicExonBoundaryIntoExon - Variable in class genomicsnpanalyzer.entry.Project

inv - Variable in class genomicsnpanalyzer.entry.SVTypeFilter

inVenter - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

inVenter - Variable in class genomicsnpanalyzer.entry.LociFunction

inVenter - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

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

isCanceled() - Method in class genomicsnpanalyzer.gui.MyProgressMonitor

isCanceled() - Method in class genomicsnpanalyzer.gui.MyProgressMonitor1

isCanonical - Variable in class genomicsnpanalyzer.entry.Transcript

isCanonical - Variable in class genomicsnpanalyzer.genomebrowser.entry.ATranscript

isCaseSensitive() - Method in class genomicsnpanalyzer.gui.Java2sAutoComboBox

isCaseSensitive() - Method in class genomicsnpanalyzer.gui.Java2sAutoTextField

isCellEditable(int, int) - Method in class genomicsnpanalyzer.gui.IndelTableModel

isCellEditable(int, int) - Method in class genomicsnpanalyzer.gui.SNPTableModel

isCellEditable(int, int) - Method in class genomicsnpanalyzer.gui.SVTableModel

isDone() - Method in class genomicsnpanalyzer.Dialog_sample

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_analysis_prio_gene

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_analysis_prio_var

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_analysis_rareDom

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_analysis_variantPosition

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_buildBinCoverage

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_buildBinRef

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_checkSNP1M

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_checkSVrawcnv

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_comparePrjSNPs

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_createChrWisePrj

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_createInputSubset

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_ExtractSubjects

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_FilterHapmapFreq

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_FilterRegion

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_FilterSubject

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GBdisplayItem

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_geneBiotypeFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_geneFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowDGVCNV

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndels

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndIndel

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSNP

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSV

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowOneKSNP

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSimpleSNPs

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSNPs

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSVs

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTaggedCNV

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTrans

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVarFeatures

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterIndels

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterSNPs

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_goFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_IndelQualityFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_keywordsearch

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_list_het

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_list_hom

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_list_homhet

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_omimDisorder

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_openProject

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_OptionFunctionDisplay

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_OptionGenomeBrowser

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_outputRegionCov

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_pathwayFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_searchGene

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_searchSNP

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_selectIndelTableHeaders

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_selectSNPTableHeaders

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_showIndelSubjectDetails

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_showSNPSubjectDetails

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_showSVSubjectDetails

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_SNPQualityFilter

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_summary_indelsFun

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_summary_snpsFunMaf

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_summaryCoverageRegions

isDone() - Method in class genomicsnpanalyzer.gui.Dialog_SVQualityFilter

isDouble(String) - Method in class genomicsnpanalyzer.TestInput

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

isDouble01(String) - Method in class genomicsnpanalyzer.TestInput

isEvenInt(int) - Method in class genomicsnpanalyzer.TestInput

IsExonSplice3(byte[]) - Static method in class genomicsnpanalyzer.Worker

IsExonSplice5(byte[]) - Static method in class genomicsnpanalyzer.Worker

isInitialized() - Method in class genomicsnpanalyzer.longTask_genomeBrowse

isInt(String) - Method in class genomicsnpanalyzer.TestInput

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

IsLiteEvalVersion - Variable in class genomicsnpanalyzer.Components

IsLiteEvalVersion() - Method in class genomicsnpanalyzer.SysManager

isMacPlatform() - Method in class genomicsnpanalyzer.gui.BrowserControl

isOn() - Method in class genomicsnpanalyzer.entry.SVMethodFilter

isOn() - Method in class genomicsnpanalyzer.entry.SVTypeFilter

isOn() - Method in class genomicsnpanalyzer.IndelFunctionFilter

isOn() - Method in class genomicsnpanalyzer.IndelHomFilter

isOn() - Method in class genomicsnpanalyzer.IndelQualityFilter

isOn() - Method in class genomicsnpanalyzer.IndelRMRFilter

isOn() - Method in class genomicsnpanalyzer.RegionFilter

isOn() - Method in class genomicsnpanalyzer.SNPFunctionFilter

isOn() - Method in class genomicsnpanalyzer.SNPHapmapFreqFilter

isOn() - Method in class genomicsnpanalyzer.SNPHomFilter

isOn() - Method in class genomicsnpanalyzer.SNPNSIntoleranceFilter

isOn() - Method in class genomicsnpanalyzer.SNPQualityFilter

isOn() - Method in class genomicsnpanalyzer.SNPRefFilter

isOn() - Method in class genomicsnpanalyzer.SNPRMRFilter

isOn() - Method in class genomicsnpanalyzer.SVFunctionFilter

isOn() - Method in class genomicsnpanalyzer.SVQualityFilter

isPosDouble(String) - Method in class genomicsnpanalyzer.TestInput

isPosInt(String) - Method in class genomicsnpanalyzer.TestInput

isPValue(String) - Method in class genomicsnpanalyzer.TestInput

isRefOnly() - Method in class genomicsnpanalyzer.SNPRefFilter

isRmrOnly() - Method in class genomicsnpanalyzer.IndelRMRFilter

isRmrOnly() - Method in class genomicsnpanalyzer.SNPRMRFilter

isRsOrEns - Variable in class genomicsnpanalyzer.entry.CNVLociFunction

isRsOrEns - Variable in class genomicsnpanalyzer.entry.LociFunction

isRsOrEns - Variable in class genomicsnpanalyzer.entry.OneKHumGenomeLoci

isRsOrEns - Variable in class genomicsnpanalyzer.entry.VarFeature

isRsOrEns - Variable in class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction

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

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

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

isStrict() - Method in class genomicsnpanalyzer.gui.Java2sAutoComboBox

isStrict() - Method in class genomicsnpanalyzer.gui.Java2sAutoTextField

isValidGenomicRegion(String) - Method in class genomicsnpanalyzer.TestInput

isWindowsPlatform() - Method in class genomicsnpanalyzer.gui.BrowserControl

Try to determine whether this application is running under Windows or some other platform by examing the "os.name" property.

itemIcon - Variable in class genomicsnpanalyzer.Components

itemRIcon - Variable in class genomicsnpanalyzer.Components

itemStateChanged(ItemEvent) - Method in class genomicsnpanalyzer.gui.GenomeBrowserPane

itemStateChanged(ItemEvent) - Method in class genomicsnpanalyzer.gui.SVListTablePane