Serialized Form

Package genomicsnpanalyzer

Class genomicsnpanalyzer.CacheDataSave extends java.lang.Object implements Serializable

Serialized Fields

subjects

Subject[] subjects

transcriptSaves

TranscriptSave[] transcriptSaves

genes

Gene[] genes

keggPathways

java.lang.String[] keggPathways

gos

java.lang.String[] gos

EnsemblVarFunctions

java.lang.String[] EnsemblVarFunctions

EnsemblVarFunctionHash

java.util.Hashtable<K,V> EnsemblVarFunctionHash

Class genomicsnpanalyzer.DataSave extends java.lang.Object implements Serializable

Serialized Fields

lociFunctions

LociFunction[] lociFunctions

cnvLociFunctions

CNVLociFunction[] cnvLociFunctions

svLociFunctions

SVLociFunction[] svLociFunctions

subjects

Subject[] subjects

transcriptSaves

TranscriptSave[] transcriptSaves

genes

Gene[] genes

keggPathways

java.lang.String[] keggPathways

gos

java.lang.String[] gos

EnsemblVarFunctions

java.lang.String[] EnsemblVarFunctions

EnsemblVarFunctionHash

java.util.Hashtable<K,V> EnsemblVarFunctionHash

Class genomicsnpanalyzer.Dialog_sample extends javax.swing.JDialog implements Serializable

Serialized Fields

pSelector

javax.swing.JTextField pSelector

transSpanSelector

javax.swing.JTextField transSpanSelector

exonSpanSelector

javax.swing.JTextField exonSpanSelector

annotateNoSelector

javax.swing.JTextField annotateNoSelector

annotateSelector

javax.swing.JCheckBox annotateSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

p

double p

doesAnnotate

boolean doesAnnotate

transSpan

int transSpan

exonSpan

int exonSpan

annotatedNo

int annotatedNo

done

boolean done

Class genomicsnpanalyzer.OneKSave extends java.lang.Object implements Serializable

Serialized Fields

oneKHumGenomeLoci

OneKHumGenomeLoci[] oneKHumGenomeLoci

transcriptSaves

TranscriptSave[] transcriptSaves

genes

Gene[] genes

Package genomicsnpanalyzer.entry

Class genomicsnpanalyzer.entry.CNVFunction extends java.lang.Object implements Serializable

Serialized Fields

TranscriptSaveIdx

int TranscriptSaveIdx

function

byte function

cdsidx

int cdsidx

Class genomicsnpanalyzer.entry.CNVLociFunction extends java.lang.Object implements Serializable

Serialized Fields

indexid

int indexid

bytechr

byte bytechr

start

int start

end

int end

bases

byte[] bases

type

byte type

typeLoaded

java.lang.String typeLoaded

numReads

double numReads

consensus

double consensus

RMS

double RMS

reads4indel

double reads4indel

reads4ref

double reads4ref

quality

double quality

size

int size

inDGV

boolean inDGV

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

inVenter

boolean inVenter

venterIdx

int venterIdx

RMR

boolean RMR

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

layer

short layer

Class genomicsnpanalyzer.entry.CNVLociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

homStatus

byte homStatus

consensus

short consensus

RMS

short RMS

numreads

short numreads

reads4indel

short reads4indel

reads4ref

short reads4ref

quality

short quality

Class genomicsnpanalyzer.entry.Exon extends java.lang.Object implements Serializable

Serialized Fields

exonID

int exonID

start

int start

end

int end

Class genomicsnpanalyzer.entry.Function extends java.lang.Object implements Serializable

Serialized Fields

TranscriptSaveIdx

int TranscriptSaveIdx

function

byte function

ns

java.lang.String ns

nsTolPval

float nsTolPval

nsTolerable

boolean nsTolerable

Class genomicsnpanalyzer.entry.Gene extends java.lang.Object implements Serializable

Serialized Fields

geneSymbol

java.lang.String geneSymbol

ncbiGeneID

int ncbiGeneID

keggPathIdx

java.util.ArrayList<E> keggPathIdx

goIdx

java.util.ArrayList<E> goIdx

Class genomicsnpanalyzer.entry.GenomicRegion extends java.lang.Object implements Serializable

Serialized Fields

bytechr

byte bytechr

start

int start

end

int end

Class genomicsnpanalyzer.entry.LociFunction extends java.lang.Object implements Serializable

Serialized Fields

bytechr

byte bytechr

loc

int loc

refAllele

byte refAllele

allele

byte allele

strand

byte strand

illuminaStrand

byte illuminaStrand

avgfscore1

float avgfscore1

avgfscore2

float avgfscore2

avgfscore3

float avgfscore3

avgfscore4

float avgfscore4

avgfscore5

float avgfscore5

avgfscore6

float avgfscore6

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

inVenter

boolean inVenter

venterIdx

int venterIdx

RMR

boolean RMR

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

Class genomicsnpanalyzer.entry.LociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

ambiguousAllele

byte ambiguousAllele

doublemutation

boolean doublemutation

bscore1

byte bscore1

bscore2

byte bscore2

bscore3

byte bscore3

bscore4

byte bscore4

bscore5

byte bscore5

bscore6

byte bscore6

Class genomicsnpanalyzer.entry.OneKHumGenomeLoci extends java.lang.Object implements Serializable

Serialized Fields

bytechr

byte bytechr

loc

int loc

refAllele

byte refAllele

allele

byte allele

strand

byte strand

illuminaStrand

byte illuminaStrand

refCount

short refCount

alleleCount

short alleleCount

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

functions

java.util.ArrayList<E> functions

Class genomicsnpanalyzer.entry.Repeat extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

strand

byte strand

match

short match

family

byte family

Class genomicsnpanalyzer.entry.SortableCNVLociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

homStatus

byte homStatus

consensus

short consensus

RMS

short RMS

numreads

short numreads

reads4indel

short reads4indel

reads4ref

short reads4ref

quality

short quality

Class genomicsnpanalyzer.entry.SortableLociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

ambiguousAllele

byte ambiguousAllele

doublemutation

boolean doublemutation

bscore1

byte bscore1

bscore2

byte bscore2

bscore3

byte bscore3

bscore4

byte bscore4

bscore5

byte bscore5

bscore6

byte bscore6

Class genomicsnpanalyzer.entry.SortableSVLociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

homStatus

byte homStatus

hmm_cnv_status

byte hmm_cnv_status

hmm_cnv_lods

float hmm_cnv_lods

numreads

double numreads

Class genomicsnpanalyzer.entry.Subject extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.String id

status

byte status

Class genomicsnpanalyzer.entry.SVFunction extends java.lang.Object implements Serializable

Serialized Fields

TranscriptSaveIdx

int TranscriptSaveIdx

function

byte function

Class genomicsnpanalyzer.entry.SVLociFunction extends java.lang.Object implements Serializable

Serialized Fields

indexid

int indexid

method

byte method

bytechr

byte bytechr

start

int start

end

int end

start_

int start_

end_

int end_

type

byte type

numReads

double numReads

size

int size

inDGV

boolean inDGV

DGVid

java.lang.String DGVid

DGVOverlap

double DGVOverlap

DGVOverlap2

double DGVOverlap2

RMR

boolean RMR

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

layer

short layer

Class genomicsnpanalyzer.entry.SVLociFunctionSubjectInf extends java.lang.Object implements Serializable

Serialized Fields

subjectIdx

short subjectIdx

homStatus

byte homStatus

hmm_cnv_status

byte hmm_cnv_status

hmm_cnv_lods

float hmm_cnv_lods

numreads

double numreads

Class genomicsnpanalyzer.entry.Transcript extends java.lang.Object implements Serializable

Serialized Fields

bytechr

byte bytechr

stableID

java.lang.String stableID

transcriptID

int transcriptID

translationID

int translationID

geneID

int geneID

geneIdx

int geneIdx

strand

byte strand

seqRegionID

int seqRegionID

seqRegionStart

int seqRegionStart

seqRegionEnd

int seqRegionEnd

utr5

UTR utr5

utr3

UTR utr3

translation

Translation translation

exons

java.util.ArrayList<E> exons

cds

byte[] cds

cdscoor

int[] cdscoor

cdsHeader

byte[] cdsHeader

cdscoorHeader

int[] cdscoorHeader

isCanonical

boolean isCanonical

Class genomicsnpanalyzer.entry.TranscriptSave extends java.lang.Object implements Serializable

Serialized Fields

transcriptStableID

java.lang.String transcriptStableID

geneIdx

int geneIdx

Class genomicsnpanalyzer.entry.Translation extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

startExonID

int startExonID

endExonID

int endExonID

Class genomicsnpanalyzer.entry.UTR extends java.lang.Object implements Serializable

Serialized Fields

start

int start

end

int end

Class genomicsnpanalyzer.entry.VarFeature extends java.lang.Object implements Serializable

Serialized Fields

varID

int varID

bytechr

byte bytechr

start

int start

end

int end

type

byte[] type

isRsOrEns

boolean isRsOrEns

rsn

int rsn

alleles

byte[] alleles

strand

byte strand

ceuMinAllele

byte ceuMinAllele

ceuMaf

short ceuMaf

yriMinAllele

byte yriMinAllele

yriMaf

short yriMaf

chbMinAllele

byte chbMinAllele

chbMaf

short chbMaf

jptMinAllele

byte jptMinAllele

jptMaf

short jptMaf

Class genomicsnpanalyzer.entry.VenterIndel extends java.lang.Object implements Serializable

Serialized Fields

id

long id

bytechr

byte bytechr

start

int start

end

int end

type

byte type

het

byte het

strand

byte strand

allele

byte[] allele

rmr

boolean rmr

tr

boolean tr

Class genomicsnpanalyzer.entry.VenterSNP extends java.lang.Object implements Serializable

Serialized Fields

id

long id

bytechr

byte bytechr

loc

int loc

het

byte het

strand

byte strand

refallele

byte refallele

allele

byte allele

rmr

boolean rmr

tr

boolean tr

Package genomicsnpanalyzer.genomebrowser.entry

Class genomicsnpanalyzer.genomebrowser.entry.AExon extends java.lang.Object implements Serializable

Serialized Fields

start

double start

end

double end

strand

int strand

exonid

int exonid

Class genomicsnpanalyzer.genomebrowser.entry.AGene extends java.lang.Object implements Serializable

Serialized Fields

geneSymbol

java.lang.String geneSymbol

ncbiGeneID

int ncbiGeneID

keggPathIdx

java.util.ArrayList<E> keggPathIdx

goIdx

java.util.ArrayList<E> goIdx

biotype

java.lang.String biotype

description

java.lang.String description

geneid

int geneid

genestableid

java.lang.String genestableid

cononicalTransID

int cononicalTransID

Class genomicsnpanalyzer.genomebrowser.entry.ATranscript extends java.lang.Object implements Serializable

Serialized Fields

start

double start

end

double end

strand

int strand

exon

java.util.ArrayList<E> exon

genename

java.lang.String genename

geneDescription

java.lang.String geneDescription

biotype

java.lang.String biotype

transcriptID

java.lang.String transcriptID

ensemblGeneStableID

java.lang.String ensemblGeneStableID

ensemblTranscriptStableID

java.lang.String ensemblTranscriptStableID

GO

java.util.ArrayList<E> GO

layer

short layer

isCanonical

boolean isCanonical

Class genomicsnpanalyzer.genomebrowser.entry.DGVCNV extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.String id

landmark

java.lang.String landmark

bytechr

byte bytechr

start

int start

end

int end

type

java.lang.String type

reference

java.lang.String reference

refpubmedid

java.lang.String refpubmedid

platform

java.lang.String platform

gain

short gain

loss

short loss

totalgainloss

short totalgainloss

samples

java.lang.String samples

layer

short layer

Class genomicsnpanalyzer.genomebrowser.entry.GenomeBrowserBuffer extends java.lang.Object implements Serializable

Serialized Fields

keggPathways

java.lang.String[] keggPathways

gos

GOTerm[] gos

genes

AGene[] genes

dbsnps

java.util.ArrayList<E> dbsnps

dbsnphash

java.util.Hashtable<K,V> dbsnphash

transcripts

Transcript[][] transcripts

hapmapsnps

java.util.ArrayList<E> hapmapsnps

illumina1msnps

java.util.ArrayList<E> illumina1msnps

dgvcnvs

java.util.ArrayList<E> dgvcnvs

taggedcnvs

java.util.ArrayList<E> taggedcnvs

Class genomicsnpanalyzer.genomebrowser.entry.GOTerm extends java.lang.Object implements Serializable

Serialized Fields

term

java.lang.String term

linkage

java.lang.String linkage

ensemblAccID

java.lang.String ensemblAccID

Class genomicsnpanalyzer.genomebrowser.entry.SimpleSNP extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

bytechr

byte bytechr

pos

int pos

Class genomicsnpanalyzer.genomebrowser.entry.SortableCNVLociFunction extends java.lang.Object implements Serializable

Serialized Fields

indexid

int indexid

bytechr

byte bytechr

start

int start

end

int end

type

byte type

typeLoaded

java.lang.String typeLoaded

numReads

double numReads

consensus

double consensus

RMS

double RMS

reads4indel

double reads4indel

reads4ref

double reads4ref

quality

double quality

size

int size

bases

byte[] bases

inDGV

boolean inDGV

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

inVenter

boolean inVenter

venterIdx

int venterIdx

RMR

boolean RMR

layer

short layer

Class genomicsnpanalyzer.genomebrowser.entry.SortableDGVCNV extends java.lang.Object implements Serializable

Serialized Fields

id

java.lang.String id

landmark

java.lang.String landmark

bytechr

byte bytechr

start

int start

end

int end

type

java.lang.String type

reference

java.lang.String reference

refpubmedid

java.lang.String refpubmedid

platform

java.lang.String platform

gain

short gain

loss

short loss

totalgainloss

short totalgainloss

samples

java.lang.String samples

layer

short layer

Class genomicsnpanalyzer.genomebrowser.entry.SortableIndex extends java.lang.Object implements Serializable

Serialized Fields

originalIndex

int originalIndex

bytechr

byte bytechr

pos

int pos

Class genomicsnpanalyzer.genomebrowser.entry.SortableLociFunction extends java.lang.Object implements Serializable

Serialized Fields

index

int index

bytechr

byte bytechr

loc

int loc

allele

byte allele

refAllele

byte refAllele

strand

byte strand

illuminaStrand

byte illuminaStrand

avgfscore1

float avgfscore1

avgfscore2

float avgfscore2

avgfscore3

float avgfscore3

avgfscore4

float avgfscore4

avgfscore5

float avgfscore5

avgfscore6

float avgfscore6

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

inVenter

boolean inVenter

venterIdx

int venterIdx

RMR

boolean RMR

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

Class genomicsnpanalyzer.genomebrowser.entry.SortableOneKHumGenomeLoci extends java.lang.Object implements Serializable

Serialized Fields

bytechr

byte bytechr

loc

int loc

refAllele

byte refAllele

allele

byte allele

strand

byte strand

illuminaStrand

byte illuminaStrand

refCount

short refCount

alleleCount

short alleleCount

isRsOrEns

boolean isRsOrEns

rsn

int rsn

inHapmap

boolean inHapmap

inIllumina1M

boolean inIllumina1M

functions

java.util.ArrayList<E> functions

Class genomicsnpanalyzer.genomebrowser.entry.SortableSimpleSNP extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name

bytechr

byte bytechr

pos

int pos

Class genomicsnpanalyzer.genomebrowser.entry.SortableSVLociFunction extends java.lang.Object implements Serializable

Serialized Fields

indexid

int indexid

bytechr

byte bytechr

start

int start

end

int end

start_

int start_

end_

int end_

type

byte type

numReads

double numReads

size

int size

inDGV

boolean inDGV

DGVid

java.lang.String DGVid

DGVOverlap

double DGVOverlap

DGVOverlap2

double DGVOverlap2

subjects

java.util.ArrayList<E> subjects

functions

java.util.ArrayList<E> functions

layer

short layer

RMR

boolean RMR

method

byte method

Class genomicsnpanalyzer.genomebrowser.entry.SortableTaggedCNV extends java.lang.Object implements Serializable

Serialized Fields

id

int id

bytechr

byte bytechr

hg17start

int hg17start

hg17end

int hg17end

hg18start

int hg18start

hg18end

int hg18end

population

java.lang.String population

maf

double maf

taggingRs

java.lang.String taggingRs

taggingRsPos

int taggingRsPos

r2

double r2

layer

short layer

Class genomicsnpanalyzer.genomebrowser.entry.SortableTranscript extends java.lang.Object implements Serializable

Serialized Fields

start

double start

end

double end

strand

int strand

exon

java.util.ArrayList<E> exon

genename

java.lang.String genename

geneDescription

java.lang.String geneDescription

biotype

java.lang.String biotype

transcriptID

java.lang.String transcriptID

ensemblGeneStableID

java.lang.String ensemblGeneStableID

ensemblTranscriptStableID

java.lang.String ensemblTranscriptStableID

GO

java.util.ArrayList<E> GO

display

boolean display

Class genomicsnpanalyzer.genomebrowser.entry.SortableVarFeature extends java.lang.Object implements Serializable

Serialized Fields

varID

int varID

bytechr

byte bytechr

start

int start

end

int end

type

java.lang.String type

isRsOrEns

boolean isRsOrEns

rsn

int rsn

alleles

java.lang.String alleles

Class genomicsnpanalyzer.genomebrowser.entry.TaggedCNV extends java.lang.Object implements Serializable

Serialized Fields

id

int id

bytechr

byte bytechr

hg17start

int hg17start

hg17end

int hg17end

hg18start

int hg18start

hg18end

int hg18end

population

java.lang.String population

maf

double maf

taggingRs

java.lang.String taggingRs

taggingRsPos

int taggingRsPos

r2

double r2

layer

short layer

Package genomicsnpanalyzer.gui

Class genomicsnpanalyzer.gui.ClosableTabbedPane extends javax.swing.JTabbedPane implements Serializable

Serialized Fields

closeTabAction

CloseTabAction closeTabAction

selectTabAction

SelectTabAction selectTabAction

myUI

ClosableTabbedPaneUI myUI

Class genomicsnpanalyzer.gui.ColorTextPane extends javax.swing.JTextPane implements Serializable

Serialized Fields

f

java.awt.Font f

plainf

java.awt.Font plainf

boldf

java.awt.Font boldf

bolditalicf

java.awt.Font bolditalicf

bigboldf

java.awt.Font bigboldf

bg

java.awt.Color bg

c

java.awt.Color c

usereditable

boolean usereditable

doc

javax.swing.text.StyledDocument doc

browseControl

BrowserControl browseControl

def

javax.swing.text.Style def

logF

java.io.File logF

logFileOn

boolean logFileOn

Class genomicsnpanalyzer.gui.DensityOverviewPane extends javax.swing.JPanel implements Serializable

Serialized Fields

parent

Main parent

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

selectedColor

java.awt.Color selectedColor

highlightColor

java.awt.Color highlightColor

solidHighlightColor

java.awt.Color solidHighlightColor

plotPane

genomicsnpanalyzer.gui.DensityOverviewPane.DensityPlotPane plotPane

saveImgButton

gButton saveImgButton

defaultW

int defaultW

defaultH

int defaultH

Class genomicsnpanalyzer.gui.Dialog_about extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

Class genomicsnpanalyzer.gui.Dialog_analysis_prio_gene extends javax.swing.JDialog implements Serializable

Serialized Fields

proteinTruncationOnlyRadio

javax.swing.JRadioButton proteinTruncationOnlyRadio

includeNSRadio

javax.swing.JRadioButton includeNSRadio

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

onlyIntolerantNSCheck

javax.swing.JCheckBox onlyIntolerantNSCheck

homCoverageCheck

javax.swing.JCheckBox homCoverageCheck

homCoverageText

javax.swing.JTextField homCoverageText

homCoverageTextSex

javax.swing.JTextField homCoverageTextSex

homCoverageTextCtrl

javax.swing.JTextField homCoverageTextCtrl

homCoverageTextSexCtrl

javax.swing.JTextField homCoverageTextSexCtrl

maxCtrlFreqText

javax.swing.JTextField maxCtrlFreqText

minCaseFreqText

javax.swing.JTextField minCaseFreqText

maxCtrlFreqTextDom

javax.swing.JTextField maxCtrlFreqTextDom

minCaseFreqTextDom

javax.swing.JTextField minCaseFreqTextDom

maxCtrlFreq

int maxCtrlFreq

minCaseFreq

int minCaseFreq

maxCtrlFreqDom

int maxCtrlFreqDom

minCaseFreqDom

int minCaseFreqDom

recessiveButton

javax.swing.JRadioButton recessiveButton

dominantButton

javax.swing.JRadioButton dominantButton

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

IncludeNS

boolean IncludeNS

ExcludeControl

boolean ExcludeControl

ExcludeVenter

boolean ExcludeVenter

onlyIntolerantNS

boolean onlyIntolerantNS

includeHomCoverage

boolean includeHomCoverage

homCov

int homCov

homCovSex

int homCovSex

homCovCtrl

int homCovCtrl

homCovSexCtrl

int homCovSexCtrl

recessive

boolean recessive

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_analysis_prio_var extends javax.swing.JDialog implements Serializable

Serialized Fields

proteinTruncationOnlyRadio

javax.swing.JRadioButton proteinTruncationOnlyRadio

includeNSRadio

javax.swing.JRadioButton includeNSRadio

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

onlyIntolerantNSCheck

javax.swing.JCheckBox onlyIntolerantNSCheck

homCoverageCheck

javax.swing.JCheckBox homCoverageCheck

homCoverageText

javax.swing.JTextField homCoverageText

homCoverageTextSex

javax.swing.JTextField homCoverageTextSex

homCoverageTextCtrl

javax.swing.JTextField homCoverageTextCtrl

homCoverageTextSexCtrl

javax.swing.JTextField homCoverageTextSexCtrl

recessiveButton

javax.swing.JRadioButton recessiveButton

dominantButton

javax.swing.JRadioButton dominantButton

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

IncludeNS

boolean IncludeNS

ExcludeControl

boolean ExcludeControl

ExcludeVenter

boolean ExcludeVenter

onlyIntolerantNS

boolean onlyIntolerantNS

includeHomCoverage

boolean includeHomCoverage

homCov

int homCov

homCovSex

int homCovSex

homCovCtrl

int homCovCtrl

homCovSexCtrl

int homCovSexCtrl

recessive

boolean recessive

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_analysis_rareDom extends javax.swing.JDialog implements Serializable

Serialized Fields

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

excludeVenter

boolean excludeVenter

maxCtrlFreqTextDom

javax.swing.JTextField maxCtrlFreqTextDom

minCaseFreqTextDom

javax.swing.JTextField minCaseFreqTextDom

maxCtrlFreqDom

int maxCtrlFreqDom

minCaseFreqDom

int minCaseFreqDom

dominantButton

javax.swing.JRadioButton dominantButton

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_analysis_variantPosition extends javax.swing.JDialog implements Serializable

Serialized Fields

proteinTruncationOnlyRadio

javax.swing.JRadioButton proteinTruncationOnlyRadio

includeNSRadio

javax.swing.JRadioButton includeNSRadio

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

IncludeNS

boolean IncludeNS

ExcludeControl

boolean ExcludeControl

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_buildBinCoverage extends javax.swing.JDialog implements Serializable

Serialized Fields

textCovBrowse

javax.swing.JButton textCovBrowse

textCovText

javax.swing.JTextField textCovText

binCovBrowse

javax.swing.JButton binCovBrowse

binCovText

javax.swing.JTextField binCovText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

textCovF

java.io.File textCovF

binCovPathF

java.io.File binCovPathF

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_buildBinRef extends javax.swing.JDialog implements Serializable

Serialized Fields

refSeqBrowse

javax.swing.JButton refSeqBrowse

refSeqDirText

javax.swing.JTextField refSeqDirText

refSeqFSelected

javax.swing.JTextField refSeqFSelected

refSeqList

javax.swing.JList refSeqList

refSeqListModel

javax.swing.DefaultListModel refSeqListModel

filelistsc

javax.swing.JScrollPane filelistsc

removeRefSeq

javax.swing.JButton removeRefSeq

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

refPathF

java.io.File refPathF

refPath

java.lang.String refPath

refSeqF

java.util.ArrayList<E> refSeqF

done

boolean done

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_checkSNP1M extends javax.swing.JDialog implements Serializable

Serialized Fields

inputButton

javax.swing.JButton inputButton

outputButton

javax.swing.JButton outputButton

inputText

javax.swing.JTextField inputText

sampleidText

javax.swing.JTextField sampleidText

sampleidChipText

javax.swing.JTextField sampleidChipText

outputText

javax.swing.JTextField outputText

chrColText

javax.swing.JTextField chrColText

chrSelector

javax.swing.JCheckBox[] chrSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

selectedChromosomes

java.util.ArrayList<E> selectedChromosomes

inputFile

java.io.File inputFile

outputFile

java.io.File outputFile

chrs

java.lang.String[] chrs

sampleid

java.lang.String sampleid

sampleidChip

java.lang.String sampleidChip

useDefault1mRadio

javax.swing.JRadioButton useDefault1mRadio

useUserFinalReportRadio

javax.swing.JRadioButton useUserFinalReportRadio

done

boolean done

useDefault1m

boolean useDefault1m

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_checkSVrawcnv extends javax.swing.JDialog implements Serializable

Serialized Fields

inputButton

javax.swing.JButton inputButton

outputButton

javax.swing.JButton outputButton

inputText

javax.swing.JTextField inputText

sampleidText

javax.swing.JTextField sampleidText

outputText

javax.swing.JTextField outputText

chrColText

javax.swing.JTextField chrColText

overlapthresholdtext

javax.swing.JTextField overlapthresholdtext

chrSelector

javax.swing.JCheckBox[] chrSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

selectedChromosomes

java.util.ArrayList<E> selectedChromosomes

inputFile

java.io.File inputFile

outputFile

java.io.File outputFile

chrs

java.lang.String[] chrs

sampleid

java.lang.String sampleid

overlapthreshold

double overlapthreshold

done

boolean done

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_comparePrjSNPs extends javax.swing.JDialog implements Serializable

Serialized Fields

inputButton

javax.swing.JButton inputButton

outputButton

javax.swing.JButton outputButton

inputText

javax.swing.JTextField inputText

sampleidText

javax.swing.JTextField sampleidText

outputText

javax.swing.JTextField outputText

chrColText

javax.swing.JTextField chrColText

cDNACheck

javax.swing.JCheckBox cDNACheck

chrSelector

javax.swing.JCheckBox[] chrSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

selectedChromosomes

java.util.ArrayList<E> selectedChromosomes

inputFile

java.io.File inputFile

outputFile

java.io.File outputFile

chrs

java.lang.String[] chrs

sampleid

java.lang.String sampleid

iscDNA

boolean iscDNA

done

boolean done

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_createChrWisePrj extends javax.swing.JDialog implements Serializable

Serialized Fields

outputButton

javax.swing.JButton outputButton

outputText

javax.swing.JTextField outputText

chrSelector

javax.swing.JCheckBox[] chrSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

selectedChromosomes

java.util.ArrayList<E> selectedChromosomes

outputFile

java.io.File outputFile

chrs

java.lang.String[] chrs

done

boolean done

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_createInputSubset extends javax.swing.JDialog implements Serializable

Serialized Fields

inputButton

javax.swing.JButton inputButton

outputButton

javax.swing.JButton outputButton

inputText

javax.swing.JTextField inputText

outputText

javax.swing.JTextField outputText

chrColText

javax.swing.JTextField chrColText

chrSelector

javax.swing.JCheckBox[] chrSelector

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

selectedChromosomes

java.util.ArrayList<E> selectedChromosomes

inputFile

java.io.File inputFile

outputFile

java.io.File outputFile

chrs

java.lang.String[] chrs

chrColumn

int chrColumn

done

boolean done

buttonsize

java.awt.Dimension buttonsize

textsize

java.awt.Dimension textsize

panelsize

java.awt.Dimension panelsize

Class genomicsnpanalyzer.gui.Dialog_ExtractSubjects extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

javax.swing.JTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

loadListButton

javax.swing.JButton loadListButton

selectAllButton

javax.swing.JButton selectAllButton

deselectAllButton

javax.swing.JButton deselectAllButton

outFileButton

javax.swing.JButton outFileButton

outFileText

javax.swing.JTextField outFileText

selectedText

ColorTextPane selectedText

removeIndex

java.util.ArrayList<E> removeIndex

changeCaseControl

boolean[] changeCaseControl

outFile

java.io.File outFile

Class genomicsnpanalyzer.gui.Dialog_FilterHapmapFreq extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

lessButton

javax.swing.JRadioButton lessButton

greatButton

javax.swing.JRadioButton greatButton

valueText

javax.swing.JTextField valueText

done

boolean done

value

double value

less

boolean less

Class genomicsnpanalyzer.gui.Dialog_FilterRegion extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

browseButton

javax.swing.JButton browseButton

inputFileText

javax.swing.JTextField inputFileText

done

boolean done

inputFile

java.io.File inputFile

Class genomicsnpanalyzer.gui.Dialog_FilterSubject extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

javax.swing.JTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

loadListButton

javax.swing.JButton loadListButton

selectAllButton

javax.swing.JButton selectAllButton

deselectAllButton

javax.swing.JButton deselectAllButton

selectedText

ColorTextPane selectedText

removeIndex

java.util.ArrayList<E> removeIndex

Class genomicsnpanalyzer.gui.Dialog_GBdisplayItem extends javax.swing.JDialog implements Serializable

Serialized Fields

geneCheck

javax.swing.JCheckBox geneCheck

repeatCheck

javax.swing.JCheckBox repeatCheck

snpCheck

javax.swing.JCheckBox snpCheck

snprsCheck

javax.swing.JCheckBox snprsCheck

refSNPCheck

javax.swing.JCheckBox refSNPCheck

hapmapSNPCheck

javax.swing.JCheckBox hapmapSNPCheck

illuSNPCheck

javax.swing.JCheckBox illuSNPCheck

indelCheck

javax.swing.JCheckBox indelCheck

svCheck

javax.swing.JCheckBox svCheck

dgvCheck

javax.swing.JCheckBox dgvCheck

snptagcnvCheck

javax.swing.JCheckBox snptagcnvCheck

Score1Check

javax.swing.JCheckBox Score1Check

Score2Check

javax.swing.JCheckBox Score2Check

Score3Check

javax.swing.JCheckBox Score3Check

onekCheck

javax.swing.JCheckBox onekCheck

ventersnp

javax.swing.JCheckBox ventersnp

venterindel

javax.swing.JCheckBox venterindel

selectall

javax.swing.JButton selectall

deselectall

javax.swing.JButton deselectall

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

displaySectionSwitch

DisplaySectionSwitch displaySectionSwitch

Class genomicsnpanalyzer.gui.Dialog_geneBiotypeFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

biotypeCheck

javax.swing.JCheckBox[] biotypeCheck

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

selectedIndex

java.util.ArrayList<E> selectedIndex

deselectall

javax.swing.JButton deselectall

selectall

javax.swing.JButton selectall

allNonPseudoGenes

javax.swing.JButton allNonPseudoGenes

hgncCheckBox

javax.swing.JCheckBox hgncCheckBox

Class genomicsnpanalyzer.gui.Dialog_geneFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

HighlightTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

loadListButton

javax.swing.JButton loadListButton

deselectAllButton

javax.swing.JButton deselectAllButton

geneText

Java2sAutoTextField geneText

geneCombo

Java2sAutoComboBox geneCombo

selectGeneButton

javax.swing.JButton selectGeneButton

defaultgenesearchtest

java.lang.String defaultgenesearchtest

selectedIndex

java.util.ArrayList<E> selectedIndex

sortedGene

SortedGene[] sortedGene

sortedGeneSyms

java.util.ArrayList<E> sortedGeneSyms

selectedText

ColorTextPane selectedText

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowDGVCNV extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowDGVCNV.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedDGVCNV

java.util.ArrayList<E> SortedDGVCNV

done

boolean done

col

java.util.ArrayList<E> col

number

int number

start

int start

end

int end

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndels extends javax.swing.JDialog implements Serializable

Serialized Fields

indelTableModel

IndelTableModel indelTableModel

indelTable

IndelTable indelTable

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

IndelTableHeaders

java.lang.String[] IndelTableHeaders

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndIndel extends javax.swing.JFrame implements Serializable

Serialized Fields

indelTableModel

IndelTableModel indelTableModel

indelTable

IndelTable indelTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

left

javax.swing.JButton left

right

javax.swing.JButton right

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

IndelTableHeaders

java.lang.String[] IndelTableHeaders

oldx

int oldx

oldy

int oldy

x

int x

y

int y

indelidx

int indelidx

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSNP extends javax.swing.JFrame implements Serializable

Serialized Fields

snpTableModel

SNPTableModel snpTableModel

snpTable

SNPTable snpTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

left

javax.swing.JButton left

right

javax.swing.JButton right

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

SNPTableHeaders

java.lang.String[] SNPTableHeaders

oldx

int oldx

oldy

int oldy

x

int x

y

int y

snpidx

int snpidx

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowIndSV extends javax.swing.JFrame implements Serializable

Serialized Fields

svTableModel

SVTableModel svTableModel

svTable

SVTable svTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

left

javax.swing.JButton left

right

javax.swing.JButton right

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

SVTableHeaders

java.lang.String[] SVTableHeaders

oldx

int oldx

oldy

int oldy

x

int x

y

int y

indelidx

int indelidx

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowOneKSNP extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowOneKSNP.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedSNPs

java.util.ArrayList<E> SortedSNPs

done

boolean done

col

java.util.ArrayList<E> col

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSimpleSNPs extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSimpleSNPs.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedSimpleSNPs

java.util.ArrayList<E> SortedSimpleSNPs

done

boolean done

col

java.util.ArrayList<E> col

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSNPs extends javax.swing.JDialog implements Serializable

Serialized Fields

snpTableModel

SNPTableModel snpTableModel

snpTable

SNPTable snpTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

SNPTableHeaders

java.lang.String[] SNPTableHeaders

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowSVs extends javax.swing.JDialog implements Serializable

Serialized Fields

svTableModel

SVTableModel svTableModel

svTable

SVTable svTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

done

boolean done

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

SVTableHeaders

java.lang.String[] SVTableHeaders

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTaggedCNV extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTaggedCNV.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedTaggedCNV

java.util.ArrayList<E> SortedTaggedCNV

done

boolean done

col

java.util.ArrayList<E> col

number

int number

start

int start

end

int end

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTrans extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowTrans.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedTranscripts

java.util.ArrayList<E> SortedTranscripts

done

boolean done

col

java.util.ArrayList<E> col

displayTrans

java.util.ArrayList<E> displayTrans

number

int number

chrIdx

int chrIdx

start

int start

end

int end

transcripts

java.util.ArrayList<E> transcripts

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVarFeatures extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVarFeatures.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedVarFeatures

java.util.ArrayList<E> SortedVarFeatures

done

boolean done

col

java.util.ArrayList<E> col

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterIndels extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterIndels.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

parent

Main parent

SortedVarFeatures

java.util.ArrayList<E> SortedVarFeatures

done

boolean done

col

java.util.ArrayList<E> col

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

venterindels

java.util.ArrayList<E> venterindels

header

java.lang.String[] header

Class genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterSNPs extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_GenomeBrowserShowVenterSNPs.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

label

javax.swing.JLabel label

parent

Main parent

SortedVarFeatures

java.util.ArrayList<E> SortedVarFeatures

done

boolean done

col

java.util.ArrayList<E> col

number

int number

chrIdx

int chrIdx

start

int start

end

int end

colNumber

int colNumber

ventersnpidx

java.util.ArrayList<E> ventersnpidx

header

java.lang.String[] header

Class genomicsnpanalyzer.gui.Dialog_goFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

HighlightTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

keyworksearch

javax.swing.JButton keyworksearch

loadListButton

javax.swing.JButton loadListButton

deselectAllButton

javax.swing.JButton deselectAllButton

parent

Main parent

done

boolean done

selectedIndex

java.util.ArrayList<E> selectedIndex

sortedGO

SortedGO[] sortedGO

selectedText

ColorTextPane selectedText

Class genomicsnpanalyzer.gui.Dialog_IndelQualityFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

numreadsHistL

javax.swing.JLabel numreadsHistL

numreadsGreatThanRadio

javax.swing.JRadioButton numreadsGreatThanRadio

numreadsLessThanRadio

javax.swing.JRadioButton numreadsLessThanRadio

numreadsBetweenRadio

javax.swing.JRadioButton numreadsBetweenRadio

numreadsGreatThanText

javax.swing.JTextField numreadsGreatThanText

numreadsLessThanText

javax.swing.JTextField numreadsLessThanText

numreadsBetweenText1

javax.swing.JTextField numreadsBetweenText1

numreadsBetweenText2

javax.swing.JTextField numreadsBetweenText2

consensusHistL

javax.swing.JLabel consensusHistL

consensusGreatThanRadio

javax.swing.JRadioButton consensusGreatThanRadio

consensusLessThanRadio

javax.swing.JRadioButton consensusLessThanRadio

consensusBetweenRadio

javax.swing.JRadioButton consensusBetweenRadio

consensusGreatThanText

javax.swing.JTextField consensusGreatThanText

consensusLessThanText

javax.swing.JTextField consensusLessThanText

consensusBetweenText1

javax.swing.JTextField consensusBetweenText1

consensusBetweenText2

javax.swing.JTextField consensusBetweenText2

RMSHistL

javax.swing.JLabel RMSHistL

RMSGreatThanRadio

javax.swing.JRadioButton RMSGreatThanRadio

RMSLessThanRadio

javax.swing.JRadioButton RMSLessThanRadio

RMSBetweenRadio

javax.swing.JRadioButton RMSBetweenRadio

RMSGreatThanText

javax.swing.JTextField RMSGreatThanText

RMSLessThanText

javax.swing.JTextField RMSLessThanText

RMSBetweenText1

javax.swing.JTextField RMSBetweenText1

RMSBetweenText2

javax.swing.JTextField RMSBetweenText2

reads4indelHistL

javax.swing.JLabel reads4indelHistL

reads4indelGreatThanRadio

javax.swing.JRadioButton reads4indelGreatThanRadio

reads4indelLessThanRadio

javax.swing.JRadioButton reads4indelLessThanRadio

reads4indelBetweenRadio

javax.swing.JRadioButton reads4indelBetweenRadio

reads4indelGreatThanText

javax.swing.JTextField reads4indelGreatThanText

reads4indelLessThanText

javax.swing.JTextField reads4indelLessThanText

reads4indelBetweenText1

javax.swing.JTextField reads4indelBetweenText1

reads4indelBetweenText2

javax.swing.JTextField reads4indelBetweenText2

reads4refHistL

javax.swing.JLabel reads4refHistL

reads4refGreatThanRadio

javax.swing.JRadioButton reads4refGreatThanRadio

reads4refLessThanRadio

javax.swing.JRadioButton reads4refLessThanRadio

reads4refBetweenRadio

javax.swing.JRadioButton reads4refBetweenRadio

reads4refGreatThanText

javax.swing.JTextField reads4refGreatThanText

reads4refLessThanText

javax.swing.JTextField reads4refLessThanText

reads4refBetweenText1

javax.swing.JTextField reads4refBetweenText1

reads4refBetweenText2

javax.swing.JTextField reads4refBetweenText2

qualityHistL

javax.swing.JLabel qualityHistL

qualityGreatThanRadio

javax.swing.JRadioButton qualityGreatThanRadio

qualityLessThanRadio

javax.swing.JRadioButton qualityLessThanRadio

qualityBetweenRadio

javax.swing.JRadioButton qualityBetweenRadio

qualityGreatThanText

javax.swing.JTextField qualityGreatThanText

qualityLessThanText

javax.swing.JTextField qualityLessThanText

qualityBetweenText1

javax.swing.JTextField qualityBetweenText1

qualityBetweenText2

javax.swing.JTextField qualityBetweenText2

halfSexBox

javax.swing.JCheckBox halfSexBox

l

javax.swing.JLabel l

indelQualityFilter

IndelQualityFilter indelQualityFilter

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_keywordsearch extends javax.swing.JDialog implements Serializable

Serialized Fields

keywordtext

javax.swing.JTextArea keywordtext

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

saveKeywords

javax.swing.JButton saveKeywords

deleteKeywords

javax.swing.JButton deleteKeywords

parent

Main parent

done

boolean done

precombo

javax.swing.JComboBox precombo

keywords

java.lang.String[] keywords

defaulttext

java.lang.String defaulttext

defaultcombotext

java.lang.String defaultcombotext

comboready

boolean comboready

Class genomicsnpanalyzer.gui.Dialog_list_het extends javax.swing.JDialog implements Serializable

Serialized Fields

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

excludeVenter

boolean excludeVenter

maxCtrlFreqText

javax.swing.JTextField maxCtrlFreqText

minCaseFreqText

javax.swing.JTextField minCaseFreqText

maxCtrlFreq

int maxCtrlFreq

minCaseFreq

int minCaseFreq

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_list_hom extends javax.swing.JDialog implements Serializable

Serialized Fields

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

excludeVenter

boolean excludeVenter

maxCtrlFreqTextDom

javax.swing.JTextField maxCtrlFreqTextDom

minCaseFreqTextDom

javax.swing.JTextField minCaseFreqTextDom

maxCtrlFreqDom

int maxCtrlFreqDom

minCaseFreqDom

int minCaseFreqDom

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_list_homhet extends javax.swing.JDialog implements Serializable

Serialized Fields

excludeControlCheck

javax.swing.JCheckBox excludeControlCheck

excludeVenterCheck

javax.swing.JCheckBox excludeVenterCheck

excludeVenter

boolean excludeVenter

maxCtrlFreqText

javax.swing.JTextField maxCtrlFreqText

minCaseFreqText

javax.swing.JTextField minCaseFreqText

maxCtrlFreq

int maxCtrlFreq

minCaseFreq

int minCaseFreq

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_omimDisorder extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

HighlightTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

loadListButton

javax.swing.JButton loadListButton

deselectAllButton

javax.swing.JButton deselectAllButton

selectedText

ColorTextPane selectedText

selectedIndex

java.util.ArrayList<E> selectedIndex

Class genomicsnpanalyzer.gui.Dialog_openProject extends javax.swing.JDialog implements Serializable

Serialized Fields

ok

gButton ok

cancel

gButton cancel

load

gButton load

saveScript

gButton saveScript

startGBCheck

javax.swing.JCheckBox startGBCheck

defaultQualityFilterCheck

javax.swing.JCheckBox defaultQualityFilterCheck

parent

Main parent

prjFile

java.io.File prjFile

done

boolean done

panelsize

java.awt.Dimension panelsize

warning

boolean warning

warningText

ColorTextPane warningText

scriptText

ColorTextPane scriptText

prj

Project prj

commentC

java.awt.Color commentC

scriptC

java.awt.Color scriptC

scriptCommandC

java.awt.Color scriptCommandC

scriptEC

java.awt.Color scriptEC

warnC

java.awt.Color warnC

cmdC

java.awt.Color cmdC

Class genomicsnpanalyzer.gui.Dialog_OptionFunctionDisplay extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

noteText

ColorTextPane noteText

displayAllButton

javax.swing.JRadioButton displayAllButton

displayOneRowButton

javax.swing.JRadioButton displayOneRowButton

done

boolean done

OptionShowAllFunctions

boolean OptionShowAllFunctions

Class genomicsnpanalyzer.gui.Dialog_OptionGenomeBrowser extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

noteText

ColorTextPane noteText

curWidthText

javax.swing.JTextField curWidthText

newWidthText

javax.swing.JTextField newWidthText

done

boolean done

newwidthint

int newwidthint

gbcfgFile

java.io.File gbcfgFile

genomeBrowserOptions

GenomeBrowserOptions genomeBrowserOptions

Class genomicsnpanalyzer.gui.Dialog_OptionMemory extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

noteText

ColorTextPane noteText

curMemText

javax.swing.JTextField curMemText

newMemText

javax.swing.JTextField newMemText

done

boolean done

newmemint

int newmemint

ramFile

java.io.File ramFile

Class genomicsnpanalyzer.gui.Dialog_OptionThreadsAnnotation extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

noteText

ColorTextPane noteText

curSNVThreadsText

javax.swing.JTextField curSNVThreadsText

newSNVThreadsText

javax.swing.JTextField newSNVThreadsText

curIndelThreadsText

javax.swing.JTextField curIndelThreadsText

newIndelThreadsText

javax.swing.JTextField newIndelThreadsText

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_outputRegionCov extends javax.swing.JDialog implements Serializable

Serialized Fields

chrCombo

javax.swing.JComboBox chrCombo

startText

javax.swing.JTextField startText

endText

javax.swing.JTextField endText

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

chr

java.lang.String chr

start

int start

end

int end

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_pathwayFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

table

HighlightTable table

totalL

javax.swing.JLabel totalL

selectedL

javax.swing.JLabel selectedL

totalN

int totalN

selectedN

int selectedN

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

keyworksearch

javax.swing.JButton keyworksearch

loadListButton

javax.swing.JButton loadListButton

deselectAllButton

javax.swing.JButton deselectAllButton

parent

Main parent

done

boolean done

selectedIndex

java.util.ArrayList<E> selectedIndex

sortedPathway

SortedPathway[] sortedPathway

selectedText

ColorTextPane selectedText

Class genomicsnpanalyzer.gui.Dialog_searchGene extends javax.swing.JDialog implements Serializable

Serialized Fields

geneCombo

Java2sAutoComboBox geneCombo

searchGeneButton

gButton searchGeneButton

defaultgenesearchtest

java.lang.String defaultgenesearchtest

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_searchSNP extends javax.swing.JDialog implements Serializable

Serialized Fields

snptext

javax.swing.JTextField snptext

searchSNPButton

gButton searchSNPButton

defaultsnpsearchtest

java.lang.String defaultsnpsearchtest

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_selectIndelTableHeaders extends javax.swing.JDialog implements Serializable

Serialized Fields

headerCheck

javax.swing.JCheckBox[] headerCheck

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

include

boolean[] include

deselectall

javax.swing.JButton deselectall

selectall

javax.swing.JButton selectall

Class genomicsnpanalyzer.gui.Dialog_selectSNPTableHeaders extends javax.swing.JDialog implements Serializable

Serialized Fields

headerCheck

javax.swing.JCheckBox[] headerCheck

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

include

boolean[] include

deselectall

javax.swing.JButton deselectall

selectall

javax.swing.JButton selectall

Class genomicsnpanalyzer.gui.Dialog_showIndelSubjectDetails extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_showIndelSubjectDetails.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

SortedCNVLociFunctionSubjectInfs

java.util.ArrayList<E> SortedCNVLociFunctionSubjectInfs

done

boolean done

col

java.util.ArrayList<E> col

chrIdx

int chrIdx

start

int start

end

int end

CNVLociFunctionSubjectTableHeaders

java.lang.String[] CNVLociFunctionSubjectTableHeaders

colNumber

int colNumber

rowNumber

int rowNumber

sn

int sn

thisvar

CNVLociFunction thisvar

Class genomicsnpanalyzer.gui.Dialog_showSNPSubjectDetails extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_showSNPSubjectDetails.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

done

boolean done

col

java.util.ArrayList<E> col

chrIdx

int chrIdx

start

int start

end

int end

LociFunctionSubjectTableHeaders

java.lang.String[] LociFunctionSubjectTableHeaders

colNumber

int colNumber

rowNumber

int rowNumber

sn

int sn

thisvar

LociFunction thisvar

Class genomicsnpanalyzer.gui.Dialog_showSVSubjectDetails extends javax.swing.JDialog implements Serializable

Serialized Fields

tableModel

javax.swing.table.DefaultTableModel tableModel

snpFoundTable

genomicsnpanalyzer.gui.Dialog_showSVSubjectDetails.hyperlinkTable snpFoundTable

sortby

javax.swing.JButton sortby

ok

javax.swing.JButton ok

copyToClip

javax.swing.JButton copyToClip

save

javax.swing.JButton save

compSelector

javax.swing.JComboBox compSelector

label

javax.swing.JLabel label

parent

Main parent

done

boolean done

col

java.util.ArrayList<E> col

chrIdx

int chrIdx

start

int start

end

int end

SVLociFunctionSubjectTableHeaders

java.lang.String[] SVLociFunctionSubjectTableHeaders

colNumber

int colNumber

rowNumber

int rowNumber

sn

int sn

thisvar

SVLociFunction thisvar

Class genomicsnpanalyzer.gui.Dialog_SNPQualityFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

score1HistL

javax.swing.JLabel score1HistL

score2HistL

javax.swing.JLabel score2HistL

score3HistL

javax.swing.JLabel score3HistL

score4HistL

javax.swing.JLabel score4HistL

score5HistL

javax.swing.JLabel score5HistL

score6HistL

javax.swing.JLabel score6HistL

score1GreatThanRadio

javax.swing.JRadioButton score1GreatThanRadio

score1LessThanRadio

javax.swing.JRadioButton score1LessThanRadio

score1BetweenRadio

javax.swing.JRadioButton score1BetweenRadio

score1GreatThanText

javax.swing.JTextField score1GreatThanText

score1LessThanText

javax.swing.JTextField score1LessThanText

score1BetweenText1

javax.swing.JTextField score1BetweenText1

score1BetweenText2

javax.swing.JTextField score1BetweenText2

score2GreatThanRadio

javax.swing.JRadioButton score2GreatThanRadio

score2LessThanRadio

javax.swing.JRadioButton score2LessThanRadio

score2BetweenRadio

javax.swing.JRadioButton score2BetweenRadio

score2GreatThanText

javax.swing.JTextField score2GreatThanText

score2LessThanText

javax.swing.JTextField score2LessThanText

score2BetweenText1

javax.swing.JTextField score2BetweenText1

score2BetweenText2

javax.swing.JTextField score2BetweenText2

score3GreatThanRadio

javax.swing.JRadioButton score3GreatThanRadio

score3LessThanRadio

javax.swing.JRadioButton score3LessThanRadio

score3BetweenRadio

javax.swing.JRadioButton score3BetweenRadio

score3GreatThanText

javax.swing.JTextField score3GreatThanText

score3LessThanText

javax.swing.JTextField score3LessThanText

score3BetweenText1

javax.swing.JTextField score3BetweenText1

score3BetweenText2

javax.swing.JTextField score3BetweenText2

score4GreatThanRadio

javax.swing.JRadioButton score4GreatThanRadio

score4LessThanRadio

javax.swing.JRadioButton score4LessThanRadio

score4BetweenRadio

javax.swing.JRadioButton score4BetweenRadio

score4GreatThanText

javax.swing.JTextField score4GreatThanText

score4LessThanText

javax.swing.JTextField score4LessThanText

score4BetweenText1

javax.swing.JTextField score4BetweenText1

score4BetweenText2

javax.swing.JTextField score4BetweenText2

score5GreatThanRadio

javax.swing.JRadioButton score5GreatThanRadio

score5LessThanRadio

javax.swing.JRadioButton score5LessThanRadio

score5BetweenRadio

javax.swing.JRadioButton score5BetweenRadio

score5GreatThanText

javax.swing.JTextField score5GreatThanText

score5LessThanText

javax.swing.JTextField score5LessThanText

score5BetweenText1

javax.swing.JTextField score5BetweenText1

score5BetweenText2

javax.swing.JTextField score5BetweenText2

score6GreatThanRadio

javax.swing.JRadioButton score6GreatThanRadio

score6LessThanRadio

javax.swing.JRadioButton score6LessThanRadio

score6BetweenRadio

javax.swing.JRadioButton score6BetweenRadio

score6GreatThanText

javax.swing.JTextField score6GreatThanText

score6LessThanText

javax.swing.JTextField score6LessThanText

score6BetweenText1

javax.swing.JTextField score6BetweenText1

score6BetweenText2

javax.swing.JTextField score6BetweenText2

l

javax.swing.JLabel l

sNPQualityFilter

SNPQualityFilter sNPQualityFilter

halfSexBox

javax.swing.JCheckBox halfSexBox

done

boolean done

Class genomicsnpanalyzer.gui.Dialog_summary_indelsFun extends javax.swing.JDialog implements Serializable

Serialized Fields

homCoverageText

javax.swing.JTextField homCoverageText

homCoverageTextSex

javax.swing.JTextField homCoverageTextSex

mafText

javax.swing.JTextField mafText

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

homCov

int homCov

homCovSex

int homCovSex

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_summary_snpsFunMaf extends javax.swing.JDialog implements Serializable

Serialized Fields

homCoverageText

javax.swing.JTextField homCoverageText

homCoverageTextSex

javax.swing.JTextField homCoverageTextSex

mafText

javax.swing.JTextField mafText

browseButton

javax.swing.JButton browseButton

outputText

javax.swing.JTextField outputText

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

homCov

int homCov

homCovSex

int homCovSex

maf

double maf

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_summaryCoverageRegions extends javax.swing.JDialog implements Serializable

Serialized Fields

chrCombo

javax.swing.JComboBox chrCombo

browseInButton

javax.swing.JButton browseInButton

browseOutButton

javax.swing.JButton browseOutButton

inputText

javax.swing.JTextField inputText

outputText

javax.swing.JTextField outputText

thresholdText

javax.swing.JTextField thresholdText

thresholdTextRegion

javax.swing.JTextField thresholdTextRegion

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

parent

Main parent

done

boolean done

coverThreshold

int coverThreshold

coverThresholdRegion

double coverThresholdRegion

inputFile

java.io.File inputFile

outputFile

java.io.File outputFile

Class genomicsnpanalyzer.gui.Dialog_SVQualityFilter extends javax.swing.JDialog implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

numreadsHistL

javax.swing.JLabel numreadsHistL

numreadsGreatThanRadio

javax.swing.JRadioButton numreadsGreatThanRadio

numreadsLessThanRadio

javax.swing.JRadioButton numreadsLessThanRadio

numreadsBetweenRadio

javax.swing.JRadioButton numreadsBetweenRadio

numreadsGreatThanText

javax.swing.JTextField numreadsGreatThanText

numreadsLessThanText

javax.swing.JTextField numreadsLessThanText

numreadsBetweenText1

javax.swing.JTextField numreadsBetweenText1

numreadsBetweenText2

javax.swing.JTextField numreadsBetweenText2

l

javax.swing.JLabel l

svQualityFilter

SVQualityFilter svQualityFilter

done

boolean done

Class genomicsnpanalyzer.gui.FilterSummaryPane extends javax.swing.JPanel implements Serializable

Serialized Fields

parent

Main parent

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

mainText

ColorTextPane mainText

MaxGeneDisplayed

int MaxGeneDisplayed

Class genomicsnpanalyzer.gui.gButton extends javax.swing.JButton implements Serializable

Serialized Fields

fg

java.awt.Color fg

Creates a new instance of gButton

Class genomicsnpanalyzer.gui.GenomeBrowserPane extends javax.swing.JPanel implements Serializable

Serialized Fields

Parent

Main Parent

handCursor

java.awt.Cursor handCursor

defaultCursor

java.awt.Cursor defaultCursor

upperTool1

javax.swing.JToolBar upperTool1

upperTool2

javax.swing.JToolBar upperTool2

upperTool3

javax.swing.JToolBar upperTool3

selectedColor

java.awt.Color selectedColor

highlightColor

java.awt.Color highlightColor

solidHighlightColor

java.awt.Color solidHighlightColor

plotPane

genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPane

plotPaneTop

genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPaneTop

centerPlotPanel

javax.swing.JSplitPane centerPlotPanel

plotSc

javax.swing.JScrollPane plotSc

plotScTop

javax.swing.JScrollPane plotScTop

saveImgButton

gButton saveImgButton

chrCombo

javax.swing.JComboBox chrCombo

chrComboReady

boolean chrComboReady

startText

javax.swing.JTextField startText

endText

javax.swing.JTextField endText

browseButton

gButton browseButton

ChrLength

int[] ChrLength

leftButton

javax.swing.JButton leftButton

rightButton

javax.swing.JButton rightButton

zoominButton

javax.swing.JButton zoominButton

zoomoutButton

javax.swing.JButton zoomoutButton

x2Button

javax.swing.JButton x2Button

x05Button

javax.swing.JButton x05Button

zoomStepCombo

javax.swing.JComboBox zoomStepCombo

zoomSteps

java.lang.String[] zoomSteps

geneText

Java2sAutoTextField geneText

geneCombo

Java2sAutoComboBox geneCombo

searchGeneButton

gButton searchGeneButton

defaultgenesearchtest

java.lang.String defaultgenesearchtest

genelist

java.util.ArrayList<E> genelist

genetranslist

java.util.ArrayList<E> genetranslist

selectDisplaySectionButton

gButton selectDisplaySectionButton

displaySectionSwitch

DisplaySectionSwitch displaySectionSwitch

wholeImg

java.awt.image.BufferedImage wholeImg

refSNPText

javax.swing.JTextField refSNPText

searchRefSNPButton

gButton searchRefSNPButton

defaultrefsnpsearchtest

java.lang.String defaultrefsnpsearchtest

l

javax.swing.JLabel l

genomeBrowserStatusLabel

javax.swing.JLabel genomeBrowserStatusLabel

MouseXYLabel

javax.swing.JLabel MouseXYLabel

MouseX

int MouseX

MouseY

int MouseY

MouseCoordLineRadioOn

javax.swing.JRadioButton MouseCoordLineRadioOn

MouseCoordLineRadioOff

javax.swing.JRadioButton MouseCoordLineRadioOff

defaultW

int defaultW

defaultH

int defaultH

GenomeBrowse

longTask_genomeBrowse GenomeBrowse

ltskbrowserControl

longTask_BrowserControl ltskbrowserControl

ltskGetCDS

longTask_RetrieveCDS ltskGetCDS

windowSequence

WindowSequence windowSequence

MouseCoordinateSwitch

boolean MouseCoordinateSwitch

Class genomicsnpanalyzer.gui.HighlightTable extends javax.swing.JTable implements Serializable

Serialized Fields

model

javax.swing.table.DefaultTableModel model

SelectionCol

int SelectionCol

Class genomicsnpanalyzer.gui.IconTableCellRenderer extends javax.swing.JLabel implements Serializable

Serialized Fields

icon

javax.swing.ImageIcon icon

Creates a new instance of IconTableCellRenderer

msg

java.lang.String msg

f

java.awt.Font f

Class genomicsnpanalyzer.gui.IndelListTablePane extends javax.swing.JPanel implements Serializable

Serialized Fields

indelTableModel

IndelTableModel indelTableModel

indelTable

IndelTable indelTable

IndelTableHeaders

java.lang.String[] IndelTableHeaders

columnToolTips

java.lang.String[] columnToolTips

col

int col

cols

java.util.ArrayList<E> cols

indexCombo

javax.swing.JComboBox indexCombo

indexLocCombo

javax.swing.JComboBox indexLocCombo

indexComboReady

boolean indexComboReady

indexLocComboReady

boolean indexLocComboReady

indexComboBoxLength

int indexComboBoxLength

functionCombo

javax.swing.JComboBox functionCombo

functionComboReady

boolean functionComboReady

toolbar2

javax.swing.JToolBar toolbar2

pathwayButton

gButton pathwayButton

genefilterButton

gButton genefilterButton

gofilterButton

gButton gofilterButton

homFilterButton

gButton homFilterButton

rmrFilterButton

gButton rmrFilterButton

qualityButton

gButton qualityButton

homPopup

javax.swing.JPopupMenu homPopup

homMenuItem

javax.swing.JMenuItem homMenuItem

Parent

Main Parent

saveListButton

gButton saveListButton

selectColumnButton

gButton selectColumnButton

saveTask

longTask_saveList saveTask

saveTask_subdetails

longTask_saveList_subDetails saveTask_subdetails

selectedIndex

java.util.ArrayList<E> selectedIndex

totalCountLabel

javax.swing.JLabel totalCountLabel

selectedCountLabel

javax.swing.JLabel selectedCountLabel

selectedFunctionMethodLabel

javax.swing.JLabel selectedFunctionMethodLabel

selectedGeneMethodLabel

javax.swing.JLabel selectedGeneMethodLabel

selectedQualityLabel

javax.swing.JLabel selectedQualityLabel

selectedHomLabel

javax.swing.JLabel selectedHomLabel

selectRmrLabel

javax.swing.JLabel selectRmrLabel

selectedSubjectLabel

javax.swing.JLabel selectedSubjectLabel

statusC

java.awt.Color statusC

rmrPopup

javax.swing.JPopupMenu rmrPopup

rmrOnlyMenuItem

javax.swing.JMenuItem rmrOnlyMenuItem

nonrmrOnlyMenuItem

javax.swing.JMenuItem nonrmrOnlyMenuItem

Class genomicsnpanalyzer.gui.IndelTable extends javax.swing.JTable implements Serializable

Serialized Fields

IndelTableHeaders

java.lang.String[] IndelTableHeaders

columnToolTips

java.lang.String[] columnToolTips

col

int col

totalCol

int totalCol

SelectedColIdx

int[] SelectedColIdx

cols

java.util.ArrayList<E> cols

Parent

Main Parent

indelPopup

javax.swing.JPopupMenu indelPopup

snpGenomeBrowserMenuItem

javax.swing.JMenuItem snpGenomeBrowserMenuItem

subjectPopup

javax.swing.JPopupMenu subjectPopup

subjectShowDetailMenuItem

javax.swing.JMenuItem subjectShowDetailMenuItem

transcriptPopup

javax.swing.JPopupMenu transcriptPopup

transcriptGenomeBrowserMenuItem

javax.swing.JMenuItem transcriptGenomeBrowserMenuItem

defaultGenomeBrowseMenuItemText

java.lang.String defaultGenomeBrowseMenuItemText

defaultShowDetailsMenuItemText

java.lang.String defaultShowDetailsMenuItemText

indelTableModel

IndelTableModel indelTableModel

Class genomicsnpanalyzer.gui.IndelTableModel extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

headers

java.lang.String[] headers

Class genomicsnpanalyzer.gui.Java2sAutoComboBox extends javax.swing.JComboBox implements Serializable

Serialized Fields

autoTextFieldEditor

genomicsnpanalyzer.gui.Java2sAutoComboBox.AutoTextFieldEditor autoTextFieldEditor

isFired

boolean isFired

Class genomicsnpanalyzer.gui.Java2sAutoTextField extends javax.swing.JTextField implements Serializable

Serialized Fields

dataList

java.util.List<E> dataList

isCaseSensitive

boolean isCaseSensitive

isStrict

boolean isStrict

autoComboBox

Java2sAutoComboBox autoComboBox

Class genomicsnpanalyzer.gui.MainContentPane extends javax.swing.JSplitPane implements Serializable

Serialized Fields

Parent

Main Parent

maintab

ClosableTabbedPane maintab

logTab

ClosableTabbedPane logTab

navigatorTab

ClosableTabbedPane navigatorTab

infotab

ClosableTabbedPane infotab

logScorll

javax.swing.JScrollPane logScorll

summaryPanel

javax.swing.JPanel summaryPanel

summaryPane

ColorTextPane summaryPane

summaryImg

java.awt.image.BufferedImage summaryImg

summmarySaveImgButton

javax.swing.JButton summmarySaveImgButton

summaryPanel_nonrs

javax.swing.JPanel summaryPanel_nonrs

summaryPane_nonrs

ColorTextPane summaryPane_nonrs

summaryImg_nonrs

java.awt.image.BufferedImage summaryImg_nonrs

summmarySaveImgButton_nonrs

javax.swing.JButton summmarySaveImgButton_nonrs

summaryPanel_rs

javax.swing.JPanel summaryPanel_rs

summaryPane_rs

ColorTextPane summaryPane_rs

summaryImg_rs

java.awt.image.BufferedImage summaryImg_rs

summmarySaveImgButton_rs

javax.swing.JButton summmarySaveImgButton_rs

logScorll_indel

javax.swing.JScrollPane logScorll_indel

summaryPanel_indel

javax.swing.JPanel summaryPanel_indel

summaryPane_indel

ColorTextPane summaryPane_indel

summaryImg_indel

java.awt.image.BufferedImage summaryImg_indel

summmarySaveImgButton_indel

javax.swing.JButton summmarySaveImgButton_indel

summaryPanel_indel_nonrs

javax.swing.JPanel summaryPanel_indel_nonrs

summaryPane_indel_nonrs

ColorTextPane summaryPane_indel_nonrs

summaryImg_indel_nonrs

java.awt.image.BufferedImage summaryImg_indel_nonrs

summmarySaveImgButton_indel_nonrs

javax.swing.JButton summmarySaveImgButton_indel_nonrs

summaryPanel_indel_rs

javax.swing.JPanel summaryPanel_indel_rs

summaryPane_indel_rs

ColorTextPane summaryPane_indel_rs

summaryImg_indel_rs

java.awt.image.BufferedImage summaryImg_indel_rs

summmarySaveImgButton_indel_rs

javax.swing.JButton summmarySaveImgButton_indel_rs

startText

javax.swing.JTextField startText

endText

javax.swing.JTextField endText

geneText

javax.swing.JTextField geneText

snpText

javax.swing.JTextField snpText

saveImageButton1

javax.swing.JButton saveImageButton1

saveImageButton2

javax.swing.JButton saveImageButton2

info

ColorTextPane info

plotPaneToolBar

javax.swing.JToolBar plotPaneToolBar

overviewPaneToolBar

javax.swing.JToolBar overviewPaneToolBar

bg

java.awt.Color bg

defaultw

int defaultw

defaulth

int defaulth

w

int w

h

int h

snppane

SNPListTablePane snppane

indelpane

IndelListTablePane indelpane

svpane

SVListTablePane svpane

densitypane

DensityOverviewPane densitypane

filterpane

FilterSummaryPane filterpane

genomeBrowserPane

GenomeBrowserPane genomeBrowserPane

filterTask

longTaskPar_filter filterTask

tabHighlightColor

java.awt.Color tabHighlightColor

Class genomicsnpanalyzer.gui.MainLowerToolbar extends javax.swing.JToolBar implements Serializable

Serialized Fields

datal

javax.swing.JLabel datal

database

javax.swing.JLabel database

javal

javax.swing.JLabel javal

javaversion

javax.swing.JLabel javaversion

internetl

javax.swing.JLabel internetl

internet

javax.swing.JLabel internet

loadLabel

javax.swing.JLabel loadLabel

peakMLabel

javax.swing.JLabel peakMLabel

internetTip

java.lang.String internetTip

memTip

java.lang.String memTip

slide

javax.swing.JProgressBar slide

rt

java.lang.Runtime rt

parent

Main parent

timer

javax.swing.Timer timer

maxM

double maxM

totalM

double totalM

MaxMThisSession

double MaxMThisSession

Class genomicsnpanalyzer.gui.MainUpperToolbar extends javax.swing.JPanel implements Serializable

Serialized Fields

parent

Main parent

newPrjButton

javax.swing.JButton newPrjButton

openPrjButton

javax.swing.JButton openPrjButton

openEPrjButton

javax.swing.JButton openEPrjButton

listPanelButton

javax.swing.JButton listPanelButton

indelPanelButton

javax.swing.JButton indelPanelButton

svPanelButton

javax.swing.JButton svPanelButton

genomeBrowserButton

javax.swing.JButton genomeBrowserButton

densityPanelButton

javax.swing.JButton densityPanelButton

pathwayFilterButton

javax.swing.JButton pathwayFilterButton

geneFilterButton

javax.swing.JButton geneFilterButton

goFilterButton

javax.swing.JButton goFilterButton

biotypeFilterButton

javax.swing.JButton biotypeFilterButton

omimFilterButton

javax.swing.JButton omimFilterButton

scoreFilterButton

javax.swing.JButton scoreFilterButton

indelscoreFilterButton

javax.swing.JButton indelscoreFilterButton

svscoreFilterButton

javax.swing.JButton svscoreFilterButton

subjectFilterButton

javax.swing.JButton subjectFilterButton

regionFilterButton

javax.swing.JButton regionFilterButton

resetFilterButton

javax.swing.JButton resetFilterButton

omimPopup

javax.swing.JPopupMenu omimPopup

omimDisorderMenuItem

javax.swing.JMenuItem omimDisorderMenuItem

omimGeneMenuItem

javax.swing.JMenuItem omimGeneMenuItem

Class genomicsnpanalyzer.gui.MyProgressMonitor extends javax.swing.JFrame implements Serializable

Serialized Fields

progress

javax.swing.JProgressBar progress

status

javax.swing.JLabel status

status1

javax.swing.JLabel status1

status2

javax.swing.JLabel status2

current

int current

max

int max

Class genomicsnpanalyzer.gui.MyProgressMonitor1 extends javax.swing.JDialog implements Serializable

Serialized Fields

progress

javax.swing.JProgressBar progress

status

javax.swing.JLabel status

status1

javax.swing.JLabel status1

status2

javax.swing.JLabel status2

timer

javax.swing.Timer timer

current

int current

max

int max

Class genomicsnpanalyzer.gui.ProjectPane extends javax.swing.JPanel implements Serializable

Serialized Fields

Parent

Main Parent

tree

javax.swing.JTree tree

treenode

javax.swing.tree.DefaultMutableTreeNode treenode

treeModel

javax.swing.tree.DefaultTreeModel treeModel

Class genomicsnpanalyzer.gui.SNPListTablePane extends javax.swing.JPanel implements Serializable

Serialized Fields

snpTableModel

SNPTableModel snpTableModel

snpTable

SNPTable snpTable

SNPTableHeaders

java.lang.String[] SNPTableHeaders

columnToolTips

java.lang.String[] columnToolTips

col

int col

cols

java.util.ArrayList<E> cols

indexCombo

javax.swing.JComboBox indexCombo

indexLocCombo

javax.swing.JComboBox indexLocCombo

indexComboReady

boolean indexComboReady

indexLocComboReady

boolean indexLocComboReady

indexComboBoxLength

int indexComboBoxLength

saveListButton

gButton saveListButton

selectColumnButton

gButton selectColumnButton

saveTask

longTask_saveList saveTask

saveTask_subdetails

longTask_saveList_subDetails saveTask_subdetails

functionCombo

javax.swing.JComboBox functionCombo

functionComboReady

boolean functionComboReady

toolbar1

javax.swing.JToolBar toolbar1

toolbar2

javax.swing.JToolBar toolbar2

pathwayButton

gButton pathwayButton

genefilterButton

gButton genefilterButton

gofilterButton

gButton gofilterButton

nsToleranceFilterButton

gButton nsToleranceFilterButton

homFilterButton

gButton homFilterButton

refFilterButton

gButton refFilterButton

rmrFilterButton

gButton rmrFilterButton

hapmapFreqFilterButton

gButton hapmapFreqFilterButton

qualityButton

gButton qualityButton

nsTolerancePopup

javax.swing.JPopupMenu nsTolerancePopup

nsToleranceMenuItem

javax.swing.JMenuItem nsToleranceMenuItem

homPopup

javax.swing.JPopupMenu homPopup

homMenuItem

javax.swing.JMenuItem homMenuItem

refSNPPopup

javax.swing.JPopupMenu refSNPPopup

refSNPOnlyMenuItem

javax.swing.JMenuItem refSNPOnlyMenuItem

novelSNPOnlyMenuItem

javax.swing.JMenuItem novelSNPOnlyMenuItem

rmrPopup

javax.swing.JPopupMenu rmrPopup

rmrOnlyMenuItem

javax.swing.JMenuItem rmrOnlyMenuItem

nonrmrOnlyMenuItem

javax.swing.JMenuItem nonrmrOnlyMenuItem

Parent

Main Parent

selectedIndex

java.util.ArrayList<E> selectedIndex

totalCountLabel

javax.swing.JLabel totalCountLabel

selectedCountLabel

javax.swing.JLabel selectedCountLabel

selectedFunctionMethodLabel

javax.swing.JLabel selectedFunctionMethodLabel

selectedGeneMethodLabel

javax.swing.JLabel selectedGeneMethodLabel

selectedQualityLabel

javax.swing.JLabel selectedQualityLabel

selectNSIntolerantLabel

javax.swing.JLabel selectNSIntolerantLabel

selectHomLabel

javax.swing.JLabel selectHomLabel

selectRefLabel

javax.swing.JLabel selectRefLabel

selectRmrLabel

javax.swing.JLabel selectRmrLabel

selectSubjectLabel

javax.swing.JLabel selectSubjectLabel

selectHapmapFreqLabel

javax.swing.JLabel selectHapmapFreqLabel

statusC

java.awt.Color statusC

Class genomicsnpanalyzer.gui.SNPTable extends javax.swing.JTable implements Serializable

Serialized Fields

SNPTableHeaders

java.lang.String[] SNPTableHeaders

columnToolTips

java.lang.String[] columnToolTips

col

int col

totalCol

int totalCol

SelectedColIdx

int[] SelectedColIdx

cols

java.util.ArrayList<E> cols

Parent

Main Parent

snpPopup

javax.swing.JPopupMenu snpPopup

snpGenomeBrowserMenuItem

javax.swing.JMenuItem snpGenomeBrowserMenuItem

subjectPopup

javax.swing.JPopupMenu subjectPopup

subjectShowDetailMenuItem

javax.swing.JMenuItem subjectShowDetailMenuItem

nonsymPopup

javax.swing.JPopupMenu nonsymPopup

nonsymMenuText

javax.swing.JTextArea nonsymMenuText

defaultNonsymMenuText

java.lang.String defaultNonsymMenuText

transcriptPopup

javax.swing.JPopupMenu transcriptPopup

transcriptGenomeBrowserMenuItem

javax.swing.JMenuItem transcriptGenomeBrowserMenuItem

defaultGenomeBrowseMenuItemText

java.lang.String defaultGenomeBrowseMenuItemText

defaultShowDetailsMenuItemText

java.lang.String defaultShowDetailsMenuItemText

snpTableModel

SNPTableModel snpTableModel

Class genomicsnpanalyzer.gui.SNPTableModel extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

headers

java.lang.String[] headers

Class genomicsnpanalyzer.gui.SVListTablePane extends javax.swing.JPanel implements Serializable

Serialized Fields

toolbar2

javax.swing.JToolBar toolbar2

svTableModel

SVTableModel svTableModel

svTable

SVTable svTable

headers

java.lang.String[] headers

columnToolTips

java.lang.String[] columnToolTips

col

int col

cols

java.util.ArrayList<E> cols

saveListButton

gButton saveListButton

saveTask

longTask_saveList saveTask

saveTask_subdetails

longTask_saveList_subDetails saveTask_subdetails

indexCombo

javax.swing.JComboBox indexCombo

indexLocCombo

javax.swing.JComboBox indexLocCombo

indexComboReady

boolean indexComboReady

indexLocComboReady

boolean indexLocComboReady

indexComboBoxLength

int indexComboBoxLength

functionCombo

javax.swing.JComboBox functionCombo

functionComboReady

boolean functionComboReady

pathwayButton

gButton pathwayButton

genefilterButton

gButton genefilterButton

gofilterButton

gButton gofilterButton

qualityButton

gButton qualityButton

selectTypeButton

gButton selectTypeButton

selectTypePopup

javax.swing.JPopupMenu selectTypePopup

selectTypeDelCheckMenu

javax.swing.JCheckBoxMenuItem selectTypeDelCheckMenu

selectTypeDupCheckMenu

javax.swing.JCheckBoxMenuItem selectTypeDupCheckMenu

selectTypeInvCheckMenu

javax.swing.JCheckBoxMenuItem selectTypeInvCheckMenu

selectMethodButton

gButton selectMethodButton

selectMethodPopup

javax.swing.JPopupMenu selectMethodPopup

selectMethodRPCheckMenu

javax.swing.JCheckBoxMenuItem selectMethodRPCheckMenu

selectMethodRDCheckMenu

javax.swing.JCheckBoxMenuItem selectMethodRDCheckMenu

Parent

Main Parent

selectedIndex

java.util.ArrayList<E> selectedIndex

totalCountLabel

javax.swing.JLabel totalCountLabel

selectedCountLabel

javax.swing.JLabel selectedCountLabel

selectedFunctionMethodLabel

javax.swing.JLabel selectedFunctionMethodLabel

selectedGeneMethodLabel

javax.swing.JLabel selectedGeneMethodLabel

selectedQualityLabel

javax.swing.JLabel selectedQualityLabel

selectedTypeLabel

javax.swing.JLabel selectedTypeLabel

selectedMethodLabel

javax.swing.JLabel selectedMethodLabel

selectedSubjectLabel

javax.swing.JLabel selectedSubjectLabel

statusC

java.awt.Color statusC

Class genomicsnpanalyzer.gui.SVTable extends javax.swing.JTable implements Serializable

Serialized Fields

Parent

Main Parent

svTableModel

SVTableModel svTableModel

svTableHeaders

java.lang.String[] svTableHeaders

columnToolTips

java.lang.String[] columnToolTips

col

int col

totalCol

int totalCol

SelectedColIdx

int[] SelectedColIdx

cols

java.util.ArrayList<E> cols

snpPopup

javax.swing.JPopupMenu snpPopup

snpGenomeBrowserMenuItem

javax.swing.JMenuItem snpGenomeBrowserMenuItem

transcriptPopup

javax.swing.JPopupMenu transcriptPopup

transcriptGenomeBrowserMenuItem

javax.swing.JMenuItem transcriptGenomeBrowserMenuItem

subjectPopup

javax.swing.JPopupMenu subjectPopup

subjectShowDetailMenuItem

javax.swing.JMenuItem subjectShowDetailMenuItem

defaultGenomeBrowseMenuItemText

java.lang.String defaultGenomeBrowseMenuItemText

defaultShowDetailsMenuItemText

java.lang.String defaultShowDetailsMenuItemText

Class genomicsnpanalyzer.gui.SVTableModel extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

headers

java.lang.String[] headers

Class genomicsnpanalyzer.gui.WindowNote extends javax.swing.JFrame implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

noteText

ColorTextPane noteText

Class genomicsnpanalyzer.gui.WindowSequence extends javax.swing.JFrame implements Serializable

Serialized Fields

parent

Main parent

ok

javax.swing.JButton ok

saveImage

javax.swing.JButton saveImage

plotPane

genomicsnpanalyzer.gui.WindowSequence.PlotPane plotPane

nsHighlightButton

gButton nsHighlightButton

protHighlightButton

gButton protHighlightButton

nsHighlightText

javax.swing.JTextField nsHighlightText

protHighlightText

javax.swing.JTextField protHighlightText

missenseSNPCombo

javax.swing.JComboBox missenseSNPCombo

introduceMissenseSNPButton

gButton introduceMissenseSNPButton

missenseIndelCombo

javax.swing.JComboBox missenseIndelCombo

introduceMissenseIndelButton

gButton introduceMissenseIndelButton

genesym

java.lang.String genesym

transcriptid

java.lang.String transcriptid

cds

char[] cds

prot

java.lang.String[] prot

strand

byte strand

missenseCDS

char[] missenseCDS

missenseProt

java.lang.String[] missenseProt

missensesnps

java.util.ArrayList<E> missensesnps

missensesnpsfunidx

java.util.ArrayList<E> missensesnpsfunidx

missenseSNPChange

char missenseSNPChange

missenseSNPcdsidx

int missenseSNPcdsidx

missenseindels

java.util.ArrayList<E> missenseindels

missenseindelsfunidx

java.util.ArrayList<E> missenseindelsfunidx

missenseindelchange

char[] missenseindelchange

missenseindelcdsidx

int missenseindelcdsidx

missenseindelDelOrIns

boolean missenseindelDelOrIns

highlightNsNum

int highlightNsNum

highlightResNum

int highlightResNum

BasePerRow

int BasePerRow

aaPerRow

int aaPerRow

charH

int charH

charW

int charW

charInterval

int charInterval

lineInterval

int lineInterval

labelInterval

int labelInterval

labelIntervalr

int labelIntervalr

lm

int lm

tm

int tm

bm

int bm

rm

int rm

fontsize

int fontsize

fontboldstyle

int fontboldstyle

fontplainstyle

int fontplainstyle

font

java.lang.String font

f

java.awt.Font f

bf

java.awt.Font bf

fm

java.awt.FontMetrics fm

rec

java.awt.geom.Rectangle2D.Double rec

line

java.awt.geom.Line2D.Double line

charSizeDetermined

boolean charSizeDetermined

defaultw

int defaultw

defaulth

int defaulth

w

int w

h

int h

bc

java.awt.Color bc

penc

java.awt.Color penc

lc

java.awt.Color lc

c1

java.awt.Color c1

c2

java.awt.Color c2

c

java.awt.Color c

mc

java.awt.Color mc

stopc

java.awt.Color stopc

highlightC

java.awt.Color highlightC

img

java.awt.image.BufferedImage img

Package nsanalyzer

Class nsanalyzer.MappResult extends java.lang.Object implements Serializable

Serialized Fields

transcriptid

java.lang.String transcriptid

AAs

java.util.ArrayList<E> AAs

Class nsanalyzer.MappResultAA extends java.lang.Object implements Serializable

Serialized Fields

pvals

float[] pvals

goodAAs

char[] goodAAs