genomicsnpanalyzer
Class Components

java.lang.Object
  extended by genomicsnpanalyzer.Components

public class Components
extends java.lang.Object


Field Summary
 int AnnoatedChrom_transFinalH
           
 int AnnotatedChrom_bm
           
 int AnnotatedChrom_generalInterval
           
 int AnnotatedChrom_generalIntervalSmall
           
 int AnnotatedChrom_hCNV
           
 int AnnotatedChrom_hTrans
           
 int AnnotatedChrom_intervalCNV
           
 int AnnotatedChrom_intervalTrans
           
 int AnnotatedChrom_lm
           
 int AnnotatedChrom_plotChrlm
           
 int AnnotatedChrom_plotChry
           
 int AnnotatedChrom_plotw
           
 int AnnotatedChrom_rm
           
 int AnnotatedChrom_tm
           
 int AnnotatedChrom_totallm
           
 int AnnotatedChromRegionIndicatorH
           
 javax.swing.ImageIcon biotype24Icon
           
 javax.swing.ImageIcon biotypeIcon
           
 javax.swing.ImageIcon browse24Icon
           
 javax.swing.ImageIcon browseIcon
           
 BrowserControl browserControl
           
 int CaptionH
           
 ChrRgnImg chrimage
           
 javax.swing.ImageIcon chromosmeIcon
           
 java.lang.String[] CNVLociFunctionSubjectTableHeaders
           
 java.io.File currentFolder
           
 java.lang.String DataMode1
           
 java.lang.String DataMode2
           
 java.lang.String dbsnpFLAG
           
 javax.swing.ImageIcon deleteIcon
           
 javax.swing.ImageIcon dens24Icon
           
 javax.swing.ImageIcon densIcon
           
 java.lang.String densityPanelTitle
           
 Dialog_about dialog_about
           
 Dialog_buildBinRef dialog_binref
           
 Dialog_geneBiotypeFilter dialog_biotype
           
 Dialog_buildBinCoverage dialog_buildBinCov
           
 Dialog_checkSNP1M dialog_checksnp1m
           
 Dialog_checkSVrawcnv dialog_checksv
           
 Dialog_createChrWisePrj dialog_chrwise
           
 Dialog_comparePrjSNPs dialog_compsnps
           
 Dialog_ExtractSubjects dialog_extractSub
           
 Dialog_GBdisplayItem dialog_GBItems
           
 Dialog_OptionGenomeBrowser dialog_gboptions
           
 Dialog_GenomeBrowserShowDGVCNV dialog_GBShowDGVCNV
           
 Dialog_GenomeBrowserShowIndels dialog_GBShowIndels
           
 Dialog_GenomeBrowserShowIndIndel dialog_GBShowIndIndel
           
 Dialog_GenomeBrowserShowIndSNP dialog_GBShowIndSNP
           
 Dialog_GenomeBrowserShowIndSV dialog_GBShowIndSV
           
 Dialog_GenomeBrowserShowOneKSNP dialog_GBShowOneKSNP
           
 Dialog_GenomeBrowserShowSimpleSNPs dialog_GBShowSimpleSNPs
           
 Dialog_GenomeBrowserShowSNPs dialog_GBShowSNPs
           
 Dialog_GenomeBrowserShowSVs dialog_GBShowSVs
           
 Dialog_GenomeBrowserShowTaggedCNV dialog_GBShowTaggedCNV
           
 Dialog_GenomeBrowserShowTrans dialog_GBShowTrans
           
 Dialog_GenomeBrowserShowVarFeatures dialog_GBShowVarFeatures
           
 Dialog_GenomeBrowserShowVenterIndels dialog_GBShowVenIndels
           
 Dialog_GenomeBrowserShowVenterSNPs dialog_GBShowVenSNPs
           
 Dialog_geneFilter dialog_gene
           
 Dialog_analysis_prio_gene dialog_genepri
           
 Dialog_goFilter dialog_go
           
 Dialog_FilterHapmapFreq dialog_hapmapfreqfilter
           
 Dialog_selectIndelTableHeaders dialog_indelheader
           
 Dialog_IndelQualityFilter dialog_indelquality
           
 Dialog_createInputSubset dialog_inputsubset
           
 Dialog_keywordsearch dialog_keyword
           
 Dialog_list_het dialog_listhet
           
 Dialog_list_hom dialog_listhom
           
 Dialog_list_homhet dialog_listhomhet
           
 Dialog_omimDisorder dialog_omimdisorder
           
 Dialog_openProject dialog_openPrj
           
 Dialog_OptionThreadsAnnotation dialog_optAnnThreads
           
 Dialog_OptionFunctionDisplay dialog_optDispFun
           
 Dialog_outputRegionCov dialog_outputcov
           
 Dialog_pathwayFilter dialog_pathway
           
 Dialog_OptionMemory dialog_ram
           
 Dialog_analysis_rareDom dialog_raredom
           
 Dialog_FilterRegion dialog_regionfilter
           
 Dialog_searchGene dialog_searchgene
           
 Dialog_searchSNP dialog_searchsnp
           
 Dialog_showIndelSubjectDetails dialog_showindelsubject
           
 Dialog_showSNPSubjectDetails dialog_showlocisubject
           
 Dialog_showSVSubjectDetails dialog_showsvsubject
           
 Dialog_selectSNPTableHeaders dialog_snpheader
           
 Dialog_SNPQualityFilter dialog_snpquality
           
 Dialog_FilterSubject dialog_subfilter
           
 Dialog_summaryCoverageRegions dialog_sumCovRgn
           
 Dialog_summary_indelsFun dialog_sumindel
           
 Dialog_summary_snpsFunMaf dialog_sumsnp
           
 Dialog_SVQualityFilter dialog_svquality
           
 Dialog_analysis_variantPosition dialog_varpos
           
 Dialog_analysis_prio_var dialog_varpri
           
 java.awt.image.BufferedImage downButtonImageA
           
 java.awt.image.BufferedImage downButtonImageB
           
 javax.swing.ImageIcon dropdownIcon
           
 java.lang.String EnsemblCEULabel
           
 java.lang.String EnsemblCHBLabel
           
 java.lang.String ensemblExonFlag
           
 java.lang.String ensemblGeneFlag
           
 java.lang.String ensemblGoFlag
           
 java.lang.String EnsemblJPTLabel
           
 java.lang.String ensemblsnpFLAG
           
 java.lang.String ensemblTranscriptFlag
           
 java.lang.String EnsemblYRILabel
           
 javax.swing.ImageIcon fileIcon
           
 javax.swing.ImageIcon filterIcon
           
 java.lang.String filterPanelTitle
           
 java.lang.String[] fullChrList
           
 java.lang.String[] GBScores1
           
 java.lang.String[] GBScores2
           
 javax.swing.ImageIcon gene24Icon
           
 javax.swing.ImageIcon geneIcon
           
 java.lang.String genomeBrowserPanelTitle
           
 javax.swing.ImageIcon genomicFeatureIcon
           
 javax.swing.ImageIcon go24Icon
           
 javax.swing.ImageIcon goIcon
           
 javax.swing.ImageIcon grayPointIncon
           
 javax.swing.ImageIcon greenPointIcon
           
 boolean[] IncludeIndelTableHeaders
           
 boolean[] IncludeSNPTableHeaders
           
 boolean[] IncludeSVTableHeaders
           
 java.lang.String indelListPanelTitle
           
 java.lang.String[] IndelTableHeaders
           
 boolean IsLiteEvalVersion
           
 javax.swing.ImageIcon itemIcon
           
 javax.swing.ImageIcon itemRIcon
           
 java.lang.String javaversion
           
 javax.swing.ImageIcon keyIcon
           
 java.util.ArrayList keywords
           
 javax.swing.ImageIcon list1Icon
           
 javax.swing.ImageIcon list24Icon
           
 javax.swing.ImageIcon list2Icon
           
 javax.swing.ImageIcon list3Icon
           
 javax.swing.ImageIcon listIcon
           
 javax.swing.ImageIcon load48Icon
           
 java.lang.String[] LociFunctionSubjectTableHeaders
           
 java.lang.String logPanelTitle
           
 MainContentPane mainContentPanel
           
 MainLowerToolbar mainLowerToolbar
           
 MainUpperToolbar mainUpperToolbar
           
 javax.swing.ImageIcon moveleftIcon
           
 javax.swing.ImageIcon moverightIcon
           
 javax.swing.ImageIcon new24Icon
           
 javax.swing.ImageIcon newIcon
           
 javax.swing.ImageIcon omim24Icon
           
 java.lang.String omimFLAG
           
 javax.swing.ImageIcon omimIcon
           
 java.lang.String[] OneKSNPTableHeaders
           
 javax.swing.ImageIcon open24Icon
           
 javax.swing.ImageIcon openE24Icon
           
 javax.swing.ImageIcon openEIcon
           
 javax.swing.ImageIcon pathway24Icon
           
 javax.swing.ImageIcon pathwayIcon
           
 javax.swing.ImageIcon peakIcon
           
 PieChart piechart
           
 java.awt.Color plotBaseBG
           
 java.lang.String plotBaseFontFace
           
 int plotBasefontsize
           
 int plotBaseFontStyle
           
 int plotBasePerLine
           
 java.lang.String[] plotBases
           
 int plotBaseScaleH
           
 int plotBaseScaleLegendCount
           
 int plotBaseScaleMajorCount
           
 int plotBaseScaleMajorH
           
 int plotBaseScaleMinorH
           
 java.awt.Color plotBG
           
 int plotBm
           
 PlotCNV plotCNV
           
static java.awt.Color plotCNVColor
           
static java.awt.Color plotCNVFillC
           
static java.awt.Color plotCNVInvFillC
           
 java.awt.Color plotCovBG
           
 java.awt.Color plotCoverageBG
           
 java.awt.Color plotCoverageFG
           
 int plotCoverageH
           
 int plotCoverageRecH
           
 int plotCoverageRgnH
           
 java.awt.Color PlotExistingSNPbgc
           
 java.awt.Color PlotExistingSNPfgc
           
 java.awt.Color plotGeneDrawColor
           
 java.awt.Color plotGeneFillColor
           
 java.awt.Color plotGridC
           
 PlotHistogram plotHistogram
           
 int plotLm
           
 java.awt.Color plotMaskBG
           
 short plotMaxCov4Color
           
 int plotMinPixelCov
           
 int plotMinPixelGeneRgn
           
 java.awt.Color plotOvBG
           
 int plotOvBm
           
 int plotOvChrH
           
 int plotOvChrW
           
 int plotOvH
           
 int plotOvLm
           
 short plotOvMaxCov4Color
           
 java.awt.Color plotOVPenC
           
 double plotOvPixelPerCov
           
 int plotOvRm
           
 int plotOvScaleH
           
 int plotOvScaleMajorH
           
 int plotOvScaleMinorH
           
 int plotOvTm
           
 int plotOvW
           
 java.awt.Color plotPene
           
 int plotPixelPerCov
           
 int plotPixelPerGeneExt
           
 int plotPixelPerGeneInt
           
 java.awt.Color plotRegionFrameColor
           
 int plotRm
           
 int plotRowPerPlot
           
 java.awt.Color plotScaleColor
           
 int plotScalefontsize
           
 PlotScaleRuler plotScaleRuler
           
 PlotScore plotScore
           
 java.awt.Color PlotSequenceCNVbgc
           
 java.awt.Color PlotSequenceCNVfgc
           
 java.awt.Color PlotSequenceCNVfgc2
           
 java.awt.Color PlotSequenceSNPbgc
           
 java.awt.Color PlotSequenceSNPfgc
           
 int PlotSequenceSNPLineH
           
 int PlotSequenceSNPPlotH
           
 PlotSNP plotSNP
           
 int plotTm
           
 PlotTranscripts plotTranscript
           
static java.awt.Color plotTranscriptColor
           
 java.awt.Color popupColor
           
 java.awt.Font popupPlainFont
           
 java.awt.Color popupTitleBgColor
           
 java.awt.Color popupTitleFgColor
           
 javax.swing.ImageIcon prjIcon
           
 java.lang.String projectExt
           
 ProjectPane projectPanel
           
 java.lang.String projectPanelTitle
           
 java.lang.String pubmedFLAG
           
 javax.swing.ImageIcon region16Icon
           
 javax.swing.ImageIcon region24Icon
           
 javax.swing.ImageIcon resetIcon
           
 javax.swing.ImageIcon resetIcon24
           
 javax.swing.ImageIcon rightIcon
           
 int ScaleRulerBinNumber
           
 int ScaleRulerH
           
 int ScaleRulerLargeScaleH
           
 int ScaleRulerMedianScaleH
           
 int ScaleRulerSmallScaleH
           
 javax.swing.ImageIcon score24Icon
           
 javax.swing.ImageIcon score24Icon2
           
 javax.swing.ImageIcon score24Icon3
           
 java.text.NumberFormat scoreFormatter
           
 javax.swing.ImageIcon scoreIcon
           
 javax.swing.ImageIcon scoreIcon2
           
 javax.swing.ImageIcon scoreIcon3
           
 java.lang.String[] SNPScore
           
 java.lang.String[] SNPScoreMaq
           
 java.lang.String[] SNPTableHeaders
           
 javax.swing.ImageIcon subjectIcon
           
 java.lang.String summaryPanelTitle
           
 java.lang.String summaryPanelTitle_indel
           
 java.lang.String summaryPanelTitle_indel_nonrs
           
 java.lang.String summaryPanelTitle_indel_rs
           
 java.lang.String summaryPanelTitle_nonrs
           
 java.lang.String summaryPanelTitle_rs
           
 java.lang.String svListPanelTitle
           
 java.lang.String[] SVLociFunctionSubjectTableHeaders
           
 java.lang.String[] SVTableHeaders
           
 SysManager sysManager
           
 int TableLength
           
 java.lang.String TaggingCNVRef
           
 TestInput testInput
           
 java.lang.String uniprotFlag
           
 java.lang.String UnixBrowseCmd
           
 java.lang.String UpdateURL
           
 java.lang.String URL
           
 javax.swing.ImageIcon varIcon
           
 java.lang.String varListPanelTitle
           
 javax.swing.ImageIcon versionIcon
           
 java.lang.String VersionURL
           
 WindowNote windowNote
           
 javax.swing.ImageIcon x05Icon
           
 javax.swing.ImageIcon x2Icon
           
 javax.swing.ImageIcon zoominIcon
           
 javax.swing.ImageIcon zoomoutIcon
           
 
Constructor Summary
Components()
           
Components(Main parent)
          Creates a new instance of Components
 
Method Summary
 java.lang.String FormatPVal(double p)
           
 java.lang.String getEntrezGeneURL(java.lang.String genename)
           
 java.lang.String getEntrezSNPURL(java.lang.String snpname)
           
 java.lang.String getGenecardsGeneURL(java.lang.String genename)
           
 java.lang.String getGoURL(java.lang.String genename)
           
 java.lang.String getHapmapURL(java.lang.String Hapmapversion, java.lang.String target)
           
 java.lang.String getUCSCGeneURL(java.lang.String genename)
           
 java.lang.String getUCSCSNPURL(java.lang.String snpname)
           
 void setChrList(java.lang.String[] chrlist)
           
 void UpdateBrowserControl()
           
 void UpdateMaxChrLength(long[] chrLength)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

prjIcon

public javax.swing.ImageIcon prjIcon

listIcon

public javax.swing.ImageIcon listIcon

list24Icon

public javax.swing.ImageIcon list24Icon

open24Icon

public javax.swing.ImageIcon open24Icon

openEIcon

public javax.swing.ImageIcon openEIcon

openE24Icon

public javax.swing.ImageIcon openE24Icon

load48Icon

public javax.swing.ImageIcon load48Icon

dens24Icon

public javax.swing.ImageIcon dens24Icon

densIcon

public javax.swing.ImageIcon densIcon

pathway24Icon

public javax.swing.ImageIcon pathway24Icon

pathwayIcon

public javax.swing.ImageIcon pathwayIcon

gene24Icon

public javax.swing.ImageIcon gene24Icon

geneIcon

public javax.swing.ImageIcon geneIcon

new24Icon

public javax.swing.ImageIcon new24Icon

newIcon

public javax.swing.ImageIcon newIcon

go24Icon

public javax.swing.ImageIcon go24Icon

goIcon

public javax.swing.ImageIcon goIcon

biotype24Icon

public javax.swing.ImageIcon biotype24Icon

biotypeIcon

public javax.swing.ImageIcon biotypeIcon

region16Icon

public javax.swing.ImageIcon region16Icon

region24Icon

public javax.swing.ImageIcon region24Icon

keyIcon

public javax.swing.ImageIcon keyIcon

deleteIcon

public javax.swing.ImageIcon deleteIcon

resetIcon

public javax.swing.ImageIcon resetIcon

resetIcon24

public javax.swing.ImageIcon resetIcon24

filterIcon

public javax.swing.ImageIcon filterIcon

subjectIcon

public javax.swing.ImageIcon subjectIcon

versionIcon

public javax.swing.ImageIcon versionIcon

itemIcon

public javax.swing.ImageIcon itemIcon

itemRIcon

public javax.swing.ImageIcon itemRIcon

chromosmeIcon

public javax.swing.ImageIcon chromosmeIcon

fileIcon

public javax.swing.ImageIcon fileIcon

browseIcon

public javax.swing.ImageIcon browseIcon

browse24Icon

public javax.swing.ImageIcon browse24Icon

grayPointIncon

public javax.swing.ImageIcon grayPointIncon

greenPointIcon

public javax.swing.ImageIcon greenPointIcon

rightIcon

public javax.swing.ImageIcon rightIcon

moveleftIcon

public javax.swing.ImageIcon moveleftIcon

moverightIcon

public javax.swing.ImageIcon moverightIcon

zoominIcon

public javax.swing.ImageIcon zoominIcon

zoomoutIcon

public javax.swing.ImageIcon zoomoutIcon

dropdownIcon

public javax.swing.ImageIcon dropdownIcon

list1Icon

public javax.swing.ImageIcon list1Icon

list2Icon

public javax.swing.ImageIcon list2Icon

list3Icon

public javax.swing.ImageIcon list3Icon

varIcon

public javax.swing.ImageIcon varIcon

genomicFeatureIcon

public javax.swing.ImageIcon genomicFeatureIcon

scoreIcon

public javax.swing.ImageIcon scoreIcon

score24Icon

public javax.swing.ImageIcon score24Icon

scoreIcon2

public javax.swing.ImageIcon scoreIcon2

score24Icon2

public javax.swing.ImageIcon score24Icon2

scoreIcon3

public javax.swing.ImageIcon scoreIcon3

score24Icon3

public javax.swing.ImageIcon score24Icon3

x2Icon

public javax.swing.ImageIcon x2Icon

x05Icon

public javax.swing.ImageIcon x05Icon

omimIcon

public javax.swing.ImageIcon omimIcon

omim24Icon

public javax.swing.ImageIcon omim24Icon

peakIcon

public javax.swing.ImageIcon peakIcon

downButtonImageA

public java.awt.image.BufferedImage downButtonImageA

downButtonImageB

public java.awt.image.BufferedImage downButtonImageB

UnixBrowseCmd

public java.lang.String UnixBrowseCmd

VersionURL

public java.lang.String VersionURL

UpdateURL

public java.lang.String UpdateURL

URL

public java.lang.String URL

projectExt

public java.lang.String projectExt

DataMode1

public java.lang.String DataMode1

DataMode2

public java.lang.String DataMode2

IsLiteEvalVersion

public boolean IsLiteEvalVersion

testInput

public TestInput testInput

sysManager

public SysManager sysManager

browserControl

public BrowserControl browserControl

javaversion

public java.lang.String javaversion

scoreFormatter

public java.text.NumberFormat scoreFormatter

TaggingCNVRef

public java.lang.String TaggingCNVRef

dbsnpFLAG

public java.lang.String dbsnpFLAG

pubmedFLAG

public java.lang.String pubmedFLAG

ensemblsnpFLAG

public java.lang.String ensemblsnpFLAG

ensemblGeneFlag

public java.lang.String ensemblGeneFlag

ensemblTranscriptFlag

public java.lang.String ensemblTranscriptFlag

ensemblExonFlag

public java.lang.String ensemblExonFlag

ensemblGoFlag

public java.lang.String ensemblGoFlag

omimFLAG

public java.lang.String omimFLAG

uniprotFlag

public java.lang.String uniprotFlag

EnsemblCEULabel

public java.lang.String EnsemblCEULabel

EnsemblCHBLabel

public java.lang.String EnsemblCHBLabel

EnsemblJPTLabel

public java.lang.String EnsemblJPTLabel

EnsemblYRILabel

public java.lang.String EnsemblYRILabel

dialog_about

public Dialog_about dialog_about

dialog_openPrj

public Dialog_openProject dialog_openPrj

dialog_pathway

public Dialog_pathwayFilter dialog_pathway

dialog_go

public Dialog_goFilter dialog_go

dialog_gene

public Dialog_geneFilter dialog_gene

dialog_biotype

public Dialog_geneBiotypeFilter dialog_biotype

dialog_keyword

public Dialog_keywordsearch dialog_keyword

dialog_GBShowTrans

public Dialog_GenomeBrowserShowTrans dialog_GBShowTrans

dialog_GBShowSNPs

public Dialog_GenomeBrowserShowSNPs dialog_GBShowSNPs

dialog_GBShowIndSNP

public Dialog_GenomeBrowserShowIndSNP dialog_GBShowIndSNP

dialog_GBShowVarFeatures

public Dialog_GenomeBrowserShowVarFeatures dialog_GBShowVarFeatures

dialog_GBShowOneKSNP

public Dialog_GenomeBrowserShowOneKSNP dialog_GBShowOneKSNP

dialog_GBShowSimpleSNPs

public Dialog_GenomeBrowserShowSimpleSNPs dialog_GBShowSimpleSNPs

dialog_GBShowDGVCNV

public Dialog_GenomeBrowserShowDGVCNV dialog_GBShowDGVCNV

dialog_GBShowTaggedCNV

public Dialog_GenomeBrowserShowTaggedCNV dialog_GBShowTaggedCNV

dialog_GBShowIndels

public Dialog_GenomeBrowserShowIndels dialog_GBShowIndels

dialog_GBShowIndIndel

public Dialog_GenomeBrowserShowIndIndel dialog_GBShowIndIndel

dialog_GBShowSVs

public Dialog_GenomeBrowserShowSVs dialog_GBShowSVs

dialog_GBShowIndSV

public Dialog_GenomeBrowserShowIndSV dialog_GBShowIndSV

dialog_GBShowVenSNPs

public Dialog_GenomeBrowserShowVenterSNPs dialog_GBShowVenSNPs

dialog_GBShowVenIndels

public Dialog_GenomeBrowserShowVenterIndels dialog_GBShowVenIndels

dialog_GBItems

public Dialog_GBdisplayItem dialog_GBItems

dialog_ram

public Dialog_OptionMemory dialog_ram

dialog_gboptions

public Dialog_OptionGenomeBrowser dialog_gboptions

dialog_optDispFun

public Dialog_OptionFunctionDisplay dialog_optDispFun

dialog_optAnnThreads

public Dialog_OptionThreadsAnnotation dialog_optAnnThreads

dialog_searchgene

public Dialog_searchGene dialog_searchgene

dialog_searchsnp

public Dialog_searchSNP dialog_searchsnp

dialog_binref

public Dialog_buildBinRef dialog_binref

dialog_inputsubset

public Dialog_createInputSubset dialog_inputsubset

dialog_snpquality

public Dialog_SNPQualityFilter dialog_snpquality

dialog_indelquality

public Dialog_IndelQualityFilter dialog_indelquality

dialog_svquality

public Dialog_SVQualityFilter dialog_svquality

dialog_checksnp1m

public Dialog_checkSNP1M dialog_checksnp1m

dialog_compsnps

public Dialog_comparePrjSNPs dialog_compsnps

dialog_checksv

public Dialog_checkSVrawcnv dialog_checksv

dialog_showlocisubject

public Dialog_showSNPSubjectDetails dialog_showlocisubject

dialog_showindelsubject

public Dialog_showIndelSubjectDetails dialog_showindelsubject

dialog_showsvsubject

public Dialog_showSVSubjectDetails dialog_showsvsubject

dialog_buildBinCov

public Dialog_buildBinCoverage dialog_buildBinCov

dialog_chrwise

public Dialog_createChrWisePrj dialog_chrwise

dialog_genepri

public Dialog_analysis_prio_gene dialog_genepri

dialog_varpri

public Dialog_analysis_prio_var dialog_varpri

dialog_varpos

public Dialog_analysis_variantPosition dialog_varpos

dialog_raredom

public Dialog_analysis_rareDom dialog_raredom

dialog_listhom

public Dialog_list_hom dialog_listhom

dialog_listhet

public Dialog_list_het dialog_listhet

dialog_listhomhet

public Dialog_list_homhet dialog_listhomhet

dialog_sumsnp

public Dialog_summary_snpsFunMaf dialog_sumsnp

dialog_sumindel

public Dialog_summary_indelsFun dialog_sumindel

dialog_outputcov

public Dialog_outputRegionCov dialog_outputcov

dialog_snpheader

public Dialog_selectSNPTableHeaders dialog_snpheader

dialog_indelheader

public Dialog_selectIndelTableHeaders dialog_indelheader

dialog_omimdisorder

public Dialog_omimDisorder dialog_omimdisorder

dialog_subfilter

public Dialog_FilterSubject dialog_subfilter

dialog_regionfilter

public Dialog_FilterRegion dialog_regionfilter

dialog_hapmapfreqfilter

public Dialog_FilterHapmapFreq dialog_hapmapfreqfilter

dialog_sumCovRgn

public Dialog_summaryCoverageRegions dialog_sumCovRgn

dialog_extractSub

public Dialog_ExtractSubjects dialog_extractSub

windowNote

public WindowNote windowNote

currentFolder

public java.io.File currentFolder

fullChrList

public java.lang.String[] fullChrList

TableLength

public int TableLength

plotBasePerLine

public int plotBasePerLine

plotRowPerPlot

public int plotRowPerPlot

plotBaseFontFace

public java.lang.String plotBaseFontFace

plotBaseFontStyle

public int plotBaseFontStyle

plotBasefontsize

public int plotBasefontsize

plotScalefontsize

public int plotScalefontsize

plotPixelPerCov

public int plotPixelPerCov

plotMinPixelCov

public int plotMinPixelCov

plotBaseScaleMajorH

public int plotBaseScaleMajorH

plotBaseScaleMinorH

public int plotBaseScaleMinorH

plotBaseScaleH

public int plotBaseScaleH

plotBaseScaleMajorCount

public int plotBaseScaleMajorCount

plotBaseScaleLegendCount

public int plotBaseScaleLegendCount

plotCoverageRgnH

public int plotCoverageRgnH

plotCoverageRecH

public int plotCoverageRecH

plotCoverageH

public int plotCoverageH

plotCoverageBG

public java.awt.Color plotCoverageBG

plotCoverageFG

public java.awt.Color plotCoverageFG

plotPixelPerGeneExt

public int plotPixelPerGeneExt

plotPixelPerGeneInt

public int plotPixelPerGeneInt

plotMinPixelGeneRgn

public int plotMinPixelGeneRgn

plotGeneDrawColor

public java.awt.Color plotGeneDrawColor

plotGeneFillColor

public java.awt.Color plotGeneFillColor

plotTm

public int plotTm

plotLm

public int plotLm

plotRm

public int plotRm

plotBm

public int plotBm

plotBases

public java.lang.String[] plotBases

plotBG

public java.awt.Color plotBG

plotPene

public java.awt.Color plotPene

plotScaleColor

public java.awt.Color plotScaleColor

plotGridC

public java.awt.Color plotGridC

plotBaseBG

public java.awt.Color plotBaseBG

plotMaskBG

public java.awt.Color plotMaskBG

plotCovBG

public java.awt.Color plotCovBG

plotMaxCov4Color

public short plotMaxCov4Color

plotOvW

public int plotOvW

plotOvH

public int plotOvH

plotOvChrW

public int plotOvChrW

plotOvChrH

public int plotOvChrH

plotOvTm

public int plotOvTm

plotOvLm

public int plotOvLm

plotOvRm

public int plotOvRm

plotOvBm

public int plotOvBm

plotOvScaleH

public int plotOvScaleH

plotOvScaleMajorH

public int plotOvScaleMajorH

plotOvScaleMinorH

public int plotOvScaleMinorH

plotOvPixelPerCov

public double plotOvPixelPerCov

plotOvBG

public java.awt.Color plotOvBG

plotOVPenC

public java.awt.Color plotOVPenC

plotOvMaxCov4Color

public short plotOvMaxCov4Color

mainContentPanel

public MainContentPane mainContentPanel

projectPanel

public ProjectPane projectPanel

mainLowerToolbar

public MainLowerToolbar mainLowerToolbar

mainUpperToolbar

public MainUpperToolbar mainUpperToolbar

piechart

public PieChart piechart

chrimage

public ChrRgnImg chrimage

plotTranscript

public PlotTranscripts plotTranscript

plotScaleRuler

public PlotScaleRuler plotScaleRuler

plotSNP

public PlotSNP plotSNP

plotCNV

public PlotCNV plotCNV

plotHistogram

public PlotHistogram plotHistogram

plotScore

public PlotScore plotScore

varListPanelTitle

public java.lang.String varListPanelTitle

indelListPanelTitle

public java.lang.String indelListPanelTitle

svListPanelTitle

public java.lang.String svListPanelTitle

genomeBrowserPanelTitle

public java.lang.String genomeBrowserPanelTitle

densityPanelTitle

public java.lang.String densityPanelTitle

filterPanelTitle

public java.lang.String filterPanelTitle

logPanelTitle

public java.lang.String logPanelTitle

projectPanelTitle

public java.lang.String projectPanelTitle

summaryPanelTitle

public java.lang.String summaryPanelTitle

summaryPanelTitle_nonrs

public java.lang.String summaryPanelTitle_nonrs

summaryPanelTitle_rs

public java.lang.String summaryPanelTitle_rs

summaryPanelTitle_indel

public java.lang.String summaryPanelTitle_indel

summaryPanelTitle_indel_nonrs

public java.lang.String summaryPanelTitle_indel_nonrs

summaryPanelTitle_indel_rs

public java.lang.String summaryPanelTitle_indel_rs

GBScores1

public java.lang.String[] GBScores1

GBScores2

public java.lang.String[] GBScores2

SNPScoreMaq

public java.lang.String[] SNPScoreMaq

SNPScore

public java.lang.String[] SNPScore

keywords

public java.util.ArrayList keywords

AnnotatedChrom_generalInterval

public int AnnotatedChrom_generalInterval

AnnotatedChrom_generalIntervalSmall

public int AnnotatedChrom_generalIntervalSmall

AnnotatedChrom_intervalTrans

public int AnnotatedChrom_intervalTrans

AnnotatedChrom_hTrans

public int AnnotatedChrom_hTrans

AnnotatedChrom_intervalCNV

public int AnnotatedChrom_intervalCNV

AnnotatedChrom_hCNV

public int AnnotatedChrom_hCNV

AnnoatedChrom_transFinalH

public int AnnoatedChrom_transFinalH

AnnotatedChrom_tm

public int AnnotatedChrom_tm

AnnotatedChrom_rm

public int AnnotatedChrom_rm

AnnotatedChrom_bm

public int AnnotatedChrom_bm

AnnotatedChrom_lm

public int AnnotatedChrom_lm

AnnotatedChrom_plotChry

public int AnnotatedChrom_plotChry

AnnotatedChrom_plotChrlm

public int AnnotatedChrom_plotChrlm

AnnotatedChrom_totallm

public int AnnotatedChrom_totallm

AnnotatedChrom_plotw

public int AnnotatedChrom_plotw

plotTranscriptColor

public static java.awt.Color plotTranscriptColor

plotCNVColor

public static java.awt.Color plotCNVColor

plotCNVFillC

public static java.awt.Color plotCNVFillC

plotCNVInvFillC

public static java.awt.Color plotCNVInvFillC

plotRegionFrameColor

public java.awt.Color plotRegionFrameColor

AnnotatedChromRegionIndicatorH

public int AnnotatedChromRegionIndicatorH

CaptionH

public int CaptionH

ScaleRulerBinNumber

public int ScaleRulerBinNumber

ScaleRulerLargeScaleH

public int ScaleRulerLargeScaleH

ScaleRulerMedianScaleH

public int ScaleRulerMedianScaleH

ScaleRulerSmallScaleH

public int ScaleRulerSmallScaleH

ScaleRulerH

public int ScaleRulerH

PlotSequenceSNPPlotH

public int PlotSequenceSNPPlotH

PlotSequenceSNPLineH

public int PlotSequenceSNPLineH

PlotSequenceSNPbgc

public java.awt.Color PlotSequenceSNPbgc

PlotSequenceSNPfgc

public java.awt.Color PlotSequenceSNPfgc

PlotSequenceCNVbgc

public java.awt.Color PlotSequenceCNVbgc

PlotSequenceCNVfgc

public java.awt.Color PlotSequenceCNVfgc

PlotSequenceCNVfgc2

public java.awt.Color PlotSequenceCNVfgc2

PlotExistingSNPbgc

public java.awt.Color PlotExistingSNPbgc

PlotExistingSNPfgc

public java.awt.Color PlotExistingSNPfgc

popupColor

public java.awt.Color popupColor

popupTitleBgColor

public java.awt.Color popupTitleBgColor

popupTitleFgColor

public java.awt.Color popupTitleFgColor

popupPlainFont

public java.awt.Font popupPlainFont

SNPTableHeaders

public java.lang.String[] SNPTableHeaders

IncludeSNPTableHeaders

public boolean[] IncludeSNPTableHeaders

IndelTableHeaders

public java.lang.String[] IndelTableHeaders

IncludeIndelTableHeaders

public boolean[] IncludeIndelTableHeaders

OneKSNPTableHeaders

public java.lang.String[] OneKSNPTableHeaders

SVTableHeaders

public java.lang.String[] SVTableHeaders

IncludeSVTableHeaders

public boolean[] IncludeSVTableHeaders

LociFunctionSubjectTableHeaders

public java.lang.String[] LociFunctionSubjectTableHeaders

CNVLociFunctionSubjectTableHeaders

public java.lang.String[] CNVLociFunctionSubjectTableHeaders

SVLociFunctionSubjectTableHeaders

public java.lang.String[] SVLociFunctionSubjectTableHeaders
Constructor Detail

Components

public Components(Main parent)
Creates a new instance of Components


Components

public Components()
Method Detail

getHapmapURL

public java.lang.String getHapmapURL(java.lang.String Hapmapversion,
                                     java.lang.String target)

getEntrezGeneURL

public java.lang.String getEntrezGeneURL(java.lang.String genename)

getEntrezSNPURL

public java.lang.String getEntrezSNPURL(java.lang.String snpname)

getGenecardsGeneURL

public java.lang.String getGenecardsGeneURL(java.lang.String genename)

getUCSCGeneURL

public java.lang.String getUCSCGeneURL(java.lang.String genename)

getUCSCSNPURL

public java.lang.String getUCSCSNPURL(java.lang.String snpname)

getGoURL

public java.lang.String getGoURL(java.lang.String genename)

setChrList

public void setChrList(java.lang.String[] chrlist)

UpdateBrowserControl

public void UpdateBrowserControl()

UpdateMaxChrLength

public void UpdateMaxChrLength(long[] chrLength)

FormatPVal

public java.lang.String FormatPVal(double p)