genomicsnpanalyzer
Class longTask_genomeBrowse

java.lang.Object
  extended by genomicsnpanalyzer.longTask_genomeBrowse

public class longTask_genomeBrowse
extends java.lang.Object


Field Summary
 java.util.Hashtable dbsnpHash
           
 java.util.ArrayList dbsnps
           
 java.util.ArrayList dgvcnvs
           
 int[] geneBioTypeCount
           
 java.lang.String[] geneBioTypes
           
 AGene[] genes
           
 java.util.ArrayList hapmapsnps
           
 java.util.ArrayList illumina1msnps
           
 Gene[] OneKHumGenomeGenes
           
 OneKHumGenomeLoci[] oneKHumGenomeLoci
           
 TranscriptSave[] OneKHumGenomeTranscriptSaves
           
 java.util.ArrayList taggedcnvs
           
 Transcript[][] transcripts
           
 
Constructor Summary
longTask_genomeBrowse(Main par, GenomeBrowserPane caller)
           
 
Method Summary
 void BrowseGene(java.lang.String genesym)
           
 void BrowseRegion(java.lang.String chr, int start, int end)
           
 void BrowseSNP(java.lang.String targetSNP)
           
 void BrowseTranscript(java.lang.String transcriptstableid)
           
 boolean isInitialized()
           
 void SetDataSet(java.util.ArrayList dbsnps)
           
 void SetHighlightCNVLociFunction(int sn)
           
 void SetHighlightLociFunction(int sn)
           
 void SetHighlightSVLociFunction(int sn)
           
 void SetHighlightTranscript(java.lang.String id)
           
 void StartupGenomeBrowser()
           
 void update()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

oneKHumGenomeLoci

public OneKHumGenomeLoci[] oneKHumGenomeLoci

OneKHumGenomeTranscriptSaves

public TranscriptSave[] OneKHumGenomeTranscriptSaves

OneKHumGenomeGenes

public Gene[] OneKHumGenomeGenes

genes

public AGene[] genes

geneBioTypes

public java.lang.String[] geneBioTypes

geneBioTypeCount

public int[] geneBioTypeCount

dbsnpHash

public java.util.Hashtable dbsnpHash

dbsnps

public java.util.ArrayList dbsnps

transcripts

public Transcript[][] transcripts

hapmapsnps

public java.util.ArrayList hapmapsnps

illumina1msnps

public java.util.ArrayList illumina1msnps

dgvcnvs

public java.util.ArrayList dgvcnvs

taggedcnvs

public java.util.ArrayList taggedcnvs
Constructor Detail

longTask_genomeBrowse

public longTask_genomeBrowse(Main par,
                             GenomeBrowserPane caller)
Method Detail

isInitialized

public boolean isInitialized()

SetDataSet

public void SetDataSet(java.util.ArrayList dbsnps)

BrowseRegion

public void BrowseRegion(java.lang.String chr,
                         int start,
                         int end)

BrowseGene

public void BrowseGene(java.lang.String genesym)

BrowseTranscript

public void BrowseTranscript(java.lang.String transcriptstableid)

BrowseSNP

public void BrowseSNP(java.lang.String targetSNP)

StartupGenomeBrowser

public void StartupGenomeBrowser()

SetHighlightLociFunction

public void SetHighlightLociFunction(int sn)

SetHighlightCNVLociFunction

public void SetHighlightCNVLociFunction(int sn)

SetHighlightSVLociFunction

public void SetHighlightSVLociFunction(int sn)

SetHighlightTranscript

public void SetHighlightTranscript(java.lang.String id)

update

public void update()