genomicsnpanalyzer.entry
Class Project

java.lang.Object
  extended by genomicsnpanalyzer.entry.Project

public class Project
extends java.lang.Object


Field Summary
static java.lang.String[] annotationFileDesc
           
static int annotationFileNumber
           
 InputObjectMultiple[] binCoverageF
           
 java.lang.String[] binRef
           
 java.lang.String[] binRefN
           
 java.io.File CapturedRegionFile
           
 java.util.Hashtable chrHash
           
 java.lang.String[] chrList
           
static int chrnumber
           
 java.util.ArrayList cmds
           
 java.io.File cnvDgvFile
           
 java.io.File cnvTaggingFile
           
 boolean controlIndluded
           
 byte dataMode
           
 boolean DetailedAnnotation
           
 double DGVCNVOverlap
           
 int DownstreamSpan
           
 java.io.File exceptionLogFile
           
 boolean ExistingOutputSkipAnnotation
           
 java.io.File exonFile
           
 java.io.File exonTranscriptFile
           
 java.io.File geneFile
           
 java.io.File geneStableIDFile
           
 java.io.File GenomeBrowserBufferFile
           
 boolean GenomeBrowserBufferSwitch
           
 java.io.File goFile
           
 java.io.File hapmapFile
           
 java.io.File hgncFile
           
 double hmmSVMinAvgLod
           
 double hmmSVMinLod
           
 java.io.File HumanGenome1000SNPBinFile
           
 java.io.File HumanGenome1000SNPTxtFile
           
 java.io.File illumina1mFile
           
 java.util.ArrayList inputObject
           
 java.util.ArrayList inputObjectCNV
           
 java.util.ArrayList inputObjectHMMSV
           
 java.util.ArrayList inputObjectSV
           
 byte InputSource
           
 int IntronicExonBoundary
           
 int IntronicExonBoundaryIntoExon
           
 java.io.File keggGenePathwayFile
           
 java.io.File keggMapTitleFile
           
 boolean NeedScreenCapturedRegion
           
 boolean needWarning
           
 java.io.File objectxrefFile
           
 java.io.File omimGenemapFile
           
 java.io.File omimGenemapFileProcessed
           
 java.io.File outFile
           
 java.io.File pedinfFile
           
 java.io.File prjFile
           
 java.io.File proteinfastaoutputfolder
           
 java.io.File proteinPolyFile
           
 long[] refLength
           
 boolean regenerateRefN
           
 java.io.File repeatFamilyFile
           
 java.io.File[] repeatMaskerFiles
           
 java.io.File repeatMaskerFolder
           
 java.io.File repeatMatchFile
           
 java.io.File seqRegionFile
           
 java.util.Hashtable strChrHash
           
 Subject[] subjects
           
 java.io.File svaDictionaryFile
           
 java.io.File transcriptFile
           
 java.io.File transcriptStableIDFile
           
 java.io.File translationFile
           
 int UpstreamSpan
           
 boolean valid
           
 java.io.File varAlleleFile1
           
 java.io.File varAlleleFile2
           
 java.io.File varFeatureFile1
           
 java.io.File varFeatureFile2
           
 java.io.File variationFile
           
 java.io.File varSampleFile
           
 java.io.File VenterIndelFile
           
 java.io.File VenterSNPFile
           
 java.lang.String version
           
 java.io.File xrefFile
           
 
Constructor Summary
Project()
          Creates a new instance of Project
 
Method Summary
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dataMode

public byte dataMode

version

public java.lang.String version

prjFile

public java.io.File prjFile

exceptionLogFile

public java.io.File exceptionLogFile

outFile

public java.io.File outFile

svaDictionaryFile

public java.io.File svaDictionaryFile

inputObject

public java.util.ArrayList inputObject

inputObjectCNV

public java.util.ArrayList inputObjectCNV

inputObjectSV

public java.util.ArrayList inputObjectSV

inputObjectHMMSV

public java.util.ArrayList inputObjectHMMSV

hmmSVMinAvgLod

public double hmmSVMinAvgLod

hmmSVMinLod

public double hmmSVMinLod

InputSource

public byte InputSource

subjects

public Subject[] subjects

controlIndluded

public boolean controlIndluded

transcriptFile

public java.io.File transcriptFile

transcriptStableIDFile

public java.io.File transcriptStableIDFile

translationFile

public java.io.File translationFile

exonFile

public java.io.File exonFile

exonTranscriptFile

public java.io.File exonTranscriptFile

xrefFile

public java.io.File xrefFile

geneFile

public java.io.File geneFile

seqRegionFile

public java.io.File seqRegionFile

variationFile

public java.io.File variationFile

varFeatureFile1

public java.io.File varFeatureFile1

varFeatureFile2

public java.io.File varFeatureFile2

hapmapFile

public java.io.File hapmapFile

illumina1mFile

public java.io.File illumina1mFile

keggMapTitleFile

public java.io.File keggMapTitleFile

keggGenePathwayFile

public java.io.File keggGenePathwayFile

goFile

public java.io.File goFile

objectxrefFile

public java.io.File objectxrefFile

geneStableIDFile

public java.io.File geneStableIDFile

cnvDgvFile

public java.io.File cnvDgvFile

cnvTaggingFile

public java.io.File cnvTaggingFile

proteinPolyFile

public java.io.File proteinPolyFile

varAlleleFile1

public java.io.File varAlleleFile1

varAlleleFile2

public java.io.File varAlleleFile2

varSampleFile

public java.io.File varSampleFile

HumanGenome1000SNPTxtFile

public java.io.File HumanGenome1000SNPTxtFile

HumanGenome1000SNPBinFile

public java.io.File HumanGenome1000SNPBinFile

VenterSNPFile

public java.io.File VenterSNPFile

VenterIndelFile

public java.io.File VenterIndelFile

repeatMaskerFolder

public java.io.File repeatMaskerFolder

repeatMaskerFiles

public java.io.File[] repeatMaskerFiles

repeatMatchFile

public java.io.File repeatMatchFile

repeatFamilyFile

public java.io.File repeatFamilyFile

omimGenemapFile

public java.io.File omimGenemapFile

omimGenemapFileProcessed

public java.io.File omimGenemapFileProcessed

pedinfFile

public java.io.File pedinfFile

CapturedRegionFile

public java.io.File CapturedRegionFile

NeedScreenCapturedRegion

public boolean NeedScreenCapturedRegion

hgncFile

public java.io.File hgncFile

annotationFileNumber

public static int annotationFileNumber

annotationFileDesc

public static java.lang.String[] annotationFileDesc

chrHash

public java.util.Hashtable chrHash

strChrHash

public java.util.Hashtable strChrHash

binRef

public java.lang.String[] binRef

binRefN

public java.lang.String[] binRefN

regenerateRefN

public boolean regenerateRefN

refLength

public long[] refLength

chrnumber

public static int chrnumber

binCoverageF

public InputObjectMultiple[] binCoverageF

chrList

public java.lang.String[] chrList

UpstreamSpan

public int UpstreamSpan

DownstreamSpan

public int DownstreamSpan

IntronicExonBoundary

public int IntronicExonBoundary

IntronicExonBoundaryIntoExon

public int IntronicExonBoundaryIntoExon

DetailedAnnotation

public boolean DetailedAnnotation

ExistingOutputSkipAnnotation

public boolean ExistingOutputSkipAnnotation

DGVCNVOverlap

public double DGVCNVOverlap

proteinfastaoutputfolder

public java.io.File proteinfastaoutputfolder

GenomeBrowserBufferSwitch

public boolean GenomeBrowserBufferSwitch

GenomeBrowserBufferFile

public java.io.File GenomeBrowserBufferFile

valid

public boolean valid

needWarning

public boolean needWarning

cmds

public java.util.ArrayList cmds
Constructor Detail

Project

public Project()
Creates a new instance of Project