genomicsnpanalyzer
Class Components

java.lang.Object
  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)