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
 

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