genomicsnpanalyzer
Class WorkCenter

java.lang.Object
  extended by genomicsnpanalyzer.WorkCenter

public class WorkCenter
extends java.lang.Object


Constructor Summary
WorkCenter()
           
WorkCenter(Main parent)
          Creates a new instance of WorkCenter
 
Method Summary
 int BP2Byte(java.lang.String b)
           
 int BP2ByteLastBP(java.lang.String b)
           
 java.lang.String Byte2BP(int i)
           
 java.lang.String ByteChrToStr(byte byteChr)
           
 java.lang.String Center_GetINDELID_FULL_gene(CNVLociFunction thisloci)
           
 java.lang.String Center_GetSNVID_gene(LociFunction thisloci)
           
 void DeleteKeywords(java.lang.String name)
           
 boolean ExportSNPIndelPedMap(java.io.File outFile, boolean showMessage, boolean SeparateSexChromosome)
           
 boolean FilterCapturedRegionForIndel(CNVLociFunction thisloci)
           
 boolean FilterCapturedRegionForLoc(byte bytechr, int loc)
           
 boolean FilterCapturedRegionForSNV(LociFunction thisloci)
           
 boolean FilterCapturedRegionForSV(SVLociFunction thisloci)
           
 int fixedGenomicLength2Int(java.lang.String s)
           
 java.lang.Object[][] GetTabulatedIndelEntry(Components components, CacheDataCenter cacheDataCenter, int col, CNVLociFunction thisf, int sn)
           
 java.lang.Object[][] GetTabulatedIndelSubjectDatails(Components components, CacheDataCenter cacheDataCenter, int sn, CNVLociFunction thisvar)
           
 java.lang.Object[][] GetTabulatedSNPEntry(Components components, CacheDataCenter cacheDataCenter, int col, LociFunction thisf, int sn)
           
 java.lang.Object[][] GetTabulatedSNVSubjectDatails(Components components, CacheDataCenter cacheDataCenter, int sn, LociFunction thisvar)
           
 java.lang.Object[][] GetTabulatedSVEntry(Components components, CacheDataCenter cacheDataCenter, int col, SVLociFunction thisf, int sn)
           
 java.lang.Object[][] GetTabulatedSVSubjectDatails(Components components, CacheDataCenter cacheDataCenter, int sn, SVLociFunction thisvar)
           
 void handleAbout()
           
 void handleAnalysisDominantSearchMenuItem()
           
 void handleAnalysisExcessHomHwMenuItem()
           
 void handleAnalysisFisherMenuItem()
           
 void handleAnalysisGenePriorityMenuItem()
           
 void handleAnalysisHeteroCompoundMenu()
           
 void handleAnalysisIndelPositionMenuItem()
           
 void handleAnalysisVarPriorityMenuItem()
           
 void handleBuildPrjMenu()
           
 void handleChangeSubjectMenu()
           
 void handleDCAnnotateIntronicExonicMenuItem()
           
 void handleDCBreakdownKeyVariantsKnownOrNotMenuItem()
           
 void handleDCCheckOverlapSNPSetMenuItem()
           
 void handleDCDuplicateSNPCheckMenuItem()
           
 void handleDCExploreNovelSNPIndelGeneMenuItem()
           
 void handleDCExploreNovelSNPIndelMenuItem()
           
 void handleDCExploreNovelSNPMenuItem()
           
 void handleDCGenerateTruncateOnlyBinMenuItem()
           
 void handleDCGenVulnerableVarMenuItem()
           
 void handleDCOutputCovForFileMenuItem()
           
 void handleDCOutputIndKeyVars()
           
 void handleDCOutputOneKSNPMenuItem()
           
 void handleDCOutputTranscriptMenuItem()
           
 void handleDCProgressBarMenuItem()
           
 void handleDCProgressBarMenuItem2()
           
 void handleDCProgressBarMenuItem3()
           
 void handleDCSimDeletionGeneMenuItem()
           
 void handleDCSumCovChrRgnMenuItem()
           
 void handleDCSummarizeVarFeatureTypeMenuItem()
           
 void handleDCSumReferenceSeqMenuItem()
           
 void handleDCTryByteArrayObjectMenuItem()
           
 void handleDCTryFilterThroughByteArrayObjectMenuItem()
           
 void handleExportIndVarMenu()
           
 void handleExportVarListMenu()
           
 void handleFilterBioTypeMenu()
           
 void handleFilterGeneMenu()
           
 void handleFilterGeneResetMenu()
           
 void handleFilterGOMenu()
           
 void handleFilterIndelScoreMenu()
           
 void handleFilterIndQCMenu()
           
 void handleFilterOmimDisorderMenu()
           
 void handleFilterOmimGeneMenu()
           
 void handleFilterPathwayMenu()
           
 void handleFilterRegionMenu()
           
 void handleFilterResetMenu()
           
 void handleFilterScoreMenu()
           
 void handleFilterSubjectMenu()
           
 void handleFilterSVScoreMenu()
           
 void handleListMenuCompoundHets()
           
 void handleListMenuHet()
           
 void handleListMenuHom()
           
 void handleListMenuNoCtrl()
           
 void handleListMenuSVCompoundHets()
           
 void handleListMenuSVGenes()
           
 void handleOpenExampleMenu()
           
 void handleOpenMenu()
           
 void handleOptionAnnotationThreadsMenu()
           
 void handleOptionFunctionDisplayMenu()
           
 void handleOptionGenomeBrowserMenu()
           
 void handleOptionMemoryMenu()
           
 void handleOutputFilteredGeneMenu()
           
 void handleSearchGeneMenu()
           
 void handleSearchSNPMenu()
           
 void handleStartupGenomeBrowserMenu()
           
 void handleSumCompPrjSNPsMenu()
           
 void handleSumCovHisMenu()
           
 void handleSumCovMenu()
           
 void handleSumCovRegionsMenu()
           
 void handleSumCovSelectedGeneMenu()
           
 void handleSumIndelLengthMenu()
           
 void handleSumIndelMenu()
           
 void handleSumSNPbyDatabaseMenu()
           
 void handleSumSNPbyMafMenu()
           
 void handleSumSVLengthMenu()
           
 void handleSumSvMenu()
           
 void handleToolAnalyzeRefSeqMenu()
           
 void handleToolBuildBinChrMenu()
           
 void handleToolBuildBinCoverageMenu()
           
 void handleToolCheck1MGenoMenu()
           
 void handleToolCheckRawcnvMenu()
           
 void handleToolCreateChrWisePrjMenu()
           
 void handleToolCreateSubsetInputMenu()
           
 void handleToolOutputRegionCovMenu()
           
 void handleToolOutputSNPINDELPedMenu()
           
 void handleToolScanLowConsensusMenu()
           
 void handleWinDensityMenu()
           
 void handleWinFilterMenu()
           
 void handleWinGenomeBrowserMenu()
           
 void handleWinIndelMenu()
           
 void handleWinListMenu()
           
 void handleWinLogMenu()
           
 void handleWinProjectMenu()
           
 void handleWinSummaryMenu_indel_nonrs()
           
 void handleWinSummaryMenu_indel_rs()
           
 void handleWinSummaryMenu_indel()
           
 void handleWinSummaryMenu_nonrs()
           
 void handleWinSummaryMenu_rs()
           
 void handleWinSummaryMenu()
           
 void handleWinSVMenu()
           
 void LoadKeywords()
           
 java.io.File OpenFile(java.lang.String ext, java.lang.String title)
           
 void OpenProject(java.io.File prjFile)
           
 void OpenProjectFile(Project prj, java.io.File prjFile, Components components, ColorTextPane scriptText, ColorTextPane warningText, java.awt.Color commentC, java.awt.Color scriptC, java.awt.Color scriptCommandC, java.awt.Color scriptEC, java.awt.Color warnC, java.awt.Color cmdC)
           
 void readCfgFile()
           
 void resetProject()
           
 void restartApplication()
           
 java.io.File SaveFile(java.lang.String ext, java.lang.String title)
           
 void SaveKeywords(java.lang.String name, java.lang.String list)
           
 void setMainLoadingStatus(boolean isLoading)
           
 boolean StopForAnotherProcess()
           
 byte StrChrToByte(java.lang.String strChr)
           
 void testJAVAEtc()
           
 void updateDefaultPath(java.io.File path)
           
 void updateJavaVersion()
           
 void updateJavaVersionErr(java.lang.String version)
           
 java.util.ArrayList UpdateOneKSNPTableByIndex(javax.swing.table.DefaultTableModel snpTableModel, java.util.ArrayList SortedSNPs)
           
 void writeRecentFiles(java.io.File curFile)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

WorkCenter

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


WorkCenter

public WorkCenter()
Method Detail

testJAVAEtc

public void testJAVAEtc()

restartApplication

public void restartApplication()

setMainLoadingStatus

public void setMainLoadingStatus(boolean isLoading)

updateJavaVersionErr

public void updateJavaVersionErr(java.lang.String version)

updateJavaVersion

public void updateJavaVersion()

handleAbout

public void handleAbout()

handleBuildPrjMenu

public void handleBuildPrjMenu()

OpenProjectFile

public void OpenProjectFile(Project prj,
                            java.io.File prjFile,
                            Components components,
                            ColorTextPane scriptText,
                            ColorTextPane warningText,
                            java.awt.Color commentC,
                            java.awt.Color scriptC,
                            java.awt.Color scriptCommandC,
                            java.awt.Color scriptEC,
                            java.awt.Color warnC,
                            java.awt.Color cmdC)

handleOpenMenu

public void handleOpenMenu()

handleOpenExampleMenu

public void handleOpenExampleMenu()

handleChangeSubjectMenu

public void handleChangeSubjectMenu()

handleExportVarListMenu

public void handleExportVarListMenu()

handleExportIndVarMenu

public void handleExportIndVarMenu()

OpenProject

public void OpenProject(java.io.File prjFile)

OpenFile

public java.io.File OpenFile(java.lang.String ext,
                             java.lang.String title)

SaveFile

public java.io.File SaveFile(java.lang.String ext,
                             java.lang.String title)

handleWinListMenu

public void handleWinListMenu()

handleWinIndelMenu

public void handleWinIndelMenu()

handleWinSVMenu

public void handleWinSVMenu()

handleWinGenomeBrowserMenu

public void handleWinGenomeBrowserMenu()

handleStartupGenomeBrowserMenu

public void handleStartupGenomeBrowserMenu()

handleWinFilterMenu

public void handleWinFilterMenu()

handleWinDensityMenu

public void handleWinDensityMenu()

handleWinLogMenu

public void handleWinLogMenu()

handleWinSummaryMenu

public void handleWinSummaryMenu()

handleWinSummaryMenu_nonrs

public void handleWinSummaryMenu_nonrs()

handleWinSummaryMenu_rs

public void handleWinSummaryMenu_rs()

handleWinSummaryMenu_indel

public void handleWinSummaryMenu_indel()

handleWinSummaryMenu_indel_nonrs

public void handleWinSummaryMenu_indel_nonrs()

handleWinSummaryMenu_indel_rs

public void handleWinSummaryMenu_indel_rs()

handleWinProjectMenu

public void handleWinProjectMenu()

handleFilterPathwayMenu

public void handleFilterPathwayMenu()

handleFilterGeneMenu

public void handleFilterGeneMenu()

handleFilterBioTypeMenu

public void handleFilterBioTypeMenu()

handleFilterGOMenu

public void handleFilterGOMenu()

handleFilterOmimGeneMenu

public void handleFilterOmimGeneMenu()

handleFilterOmimDisorderMenu

public void handleFilterOmimDisorderMenu()

handleFilterSubjectMenu

public void handleFilterSubjectMenu()

handleFilterRegionMenu

public void handleFilterRegionMenu()

handleFilterScoreMenu

public void handleFilterScoreMenu()

handleFilterIndelScoreMenu

public void handleFilterIndelScoreMenu()

handleFilterSVScoreMenu

public void handleFilterSVScoreMenu()

handleFilterIndQCMenu

public void handleFilterIndQCMenu()

handleFilterResetMenu

public void handleFilterResetMenu()

handleFilterGeneResetMenu

public void handleFilterGeneResetMenu()

handleOutputFilteredGeneMenu

public void handleOutputFilteredGeneMenu()

handleSearchGeneMenu

public void handleSearchGeneMenu()

handleSearchSNPMenu

public void handleSearchSNPMenu()

handleAnalysisHeteroCompoundMenu

public void handleAnalysisHeteroCompoundMenu()

handleAnalysisGenePriorityMenuItem

public void handleAnalysisGenePriorityMenuItem()

handleAnalysisVarPriorityMenuItem

public void handleAnalysisVarPriorityMenuItem()

handleAnalysisDominantSearchMenuItem

public void handleAnalysisDominantSearchMenuItem()

handleAnalysisExcessHomHwMenuItem

public void handleAnalysisExcessHomHwMenuItem()

handleAnalysisFisherMenuItem

public void handleAnalysisFisherMenuItem()

handleAnalysisIndelPositionMenuItem

public void handleAnalysisIndelPositionMenuItem()

handleListMenuHom

public void handleListMenuHom()

handleListMenuHet

public void handleListMenuHet()

handleListMenuNoCtrl

public void handleListMenuNoCtrl()

handleListMenuSVGenes

public void handleListMenuSVGenes()

handleListMenuCompoundHets

public void handleListMenuCompoundHets()

handleListMenuSVCompoundHets

public void handleListMenuSVCompoundHets()

handleOptionMemoryMenu

public void handleOptionMemoryMenu()

handleOptionAnnotationThreadsMenu

public void handleOptionAnnotationThreadsMenu()

handleOptionGenomeBrowserMenu

public void handleOptionGenomeBrowserMenu()

handleOptionFunctionDisplayMenu

public void handleOptionFunctionDisplayMenu()

handleToolBuildBinChrMenu

public void handleToolBuildBinChrMenu()

handleToolBuildBinCoverageMenu

public void handleToolBuildBinCoverageMenu()

handleToolCreateSubsetInputMenu

public void handleToolCreateSubsetInputMenu()

handleToolCreateChrWisePrjMenu

public void handleToolCreateChrWisePrjMenu()

handleToolScanLowConsensusMenu

public void handleToolScanLowConsensusMenu()

handleToolOutputRegionCovMenu

public void handleToolOutputRegionCovMenu()

handleToolOutputSNPINDELPedMenu

public void handleToolOutputSNPINDELPedMenu()

handleToolAnalyzeRefSeqMenu

public void handleToolAnalyzeRefSeqMenu()

handleToolCheck1MGenoMenu

public void handleToolCheck1MGenoMenu()

handleSumCompPrjSNPsMenu

public void handleSumCompPrjSNPsMenu()

handleToolCheckRawcnvMenu

public void handleToolCheckRawcnvMenu()

handleSumCovMenu

public void handleSumCovMenu()

handleSumCovSelectedGeneMenu

public void handleSumCovSelectedGeneMenu()

handleSumCovRegionsMenu

public void handleSumCovRegionsMenu()

handleSumCovHisMenu

public void handleSumCovHisMenu()

handleDCSumCovChrRgnMenuItem

public void handleDCSumCovChrRgnMenuItem()

handleDCDuplicateSNPCheckMenuItem

public void handleDCDuplicateSNPCheckMenuItem()

handleDCExploreNovelSNPMenuItem

public void handleDCExploreNovelSNPMenuItem()

handleDCExploreNovelSNPIndelMenuItem

public void handleDCExploreNovelSNPIndelMenuItem()

handleDCExploreNovelSNPIndelGeneMenuItem

public void handleDCExploreNovelSNPIndelGeneMenuItem()

handleDCBreakdownKeyVariantsKnownOrNotMenuItem

public void handleDCBreakdownKeyVariantsKnownOrNotMenuItem()

handleDCOutputIndKeyVars

public void handleDCOutputIndKeyVars()

handleDCCheckOverlapSNPSetMenuItem

public void handleDCCheckOverlapSNPSetMenuItem()

handleDCAnnotateIntronicExonicMenuItem

public void handleDCAnnotateIntronicExonicMenuItem()

handleDCGenerateTruncateOnlyBinMenuItem

public void handleDCGenerateTruncateOnlyBinMenuItem()

handleDCSumReferenceSeqMenuItem

public void handleDCSumReferenceSeqMenuItem()

handleDCOutputCovForFileMenuItem

public void handleDCOutputCovForFileMenuItem()

handleDCTryByteArrayObjectMenuItem

public void handleDCTryByteArrayObjectMenuItem()

handleDCTryFilterThroughByteArrayObjectMenuItem

public void handleDCTryFilterThroughByteArrayObjectMenuItem()

handleDCSummarizeVarFeatureTypeMenuItem

public void handleDCSummarizeVarFeatureTypeMenuItem()

handleDCGenVulnerableVarMenuItem

public void handleDCGenVulnerableVarMenuItem()

handleSumSNPbyDatabaseMenu

public void handleSumSNPbyDatabaseMenu()

handleSumSNPbyMafMenu

public void handleSumSNPbyMafMenu()

handleSumIndelMenu

public void handleSumIndelMenu()

handleSumIndelLengthMenu

public void handleSumIndelLengthMenu()

handleSumSVLengthMenu

public void handleSumSVLengthMenu()

handleSumSvMenu

public void handleSumSvMenu()

resetProject

public void resetProject()

updateDefaultPath

public void updateDefaultPath(java.io.File path)

LoadKeywords

public void LoadKeywords()

SaveKeywords

public void SaveKeywords(java.lang.String name,
                         java.lang.String list)

DeleteKeywords

public void DeleteKeywords(java.lang.String name)

StrChrToByte

public byte StrChrToByte(java.lang.String strChr)

ByteChrToStr

public java.lang.String ByteChrToStr(byte byteChr)

BP2Byte

public int BP2Byte(java.lang.String b)

BP2ByteLastBP

public int BP2ByteLastBP(java.lang.String b)

Byte2BP

public java.lang.String Byte2BP(int i)

fixedGenomicLength2Int

public int fixedGenomicLength2Int(java.lang.String s)

readCfgFile

public void readCfgFile()

writeRecentFiles

public void writeRecentFiles(java.io.File curFile)

UpdateOneKSNPTableByIndex

public java.util.ArrayList UpdateOneKSNPTableByIndex(javax.swing.table.DefaultTableModel snpTableModel,
                                                     java.util.ArrayList SortedSNPs)
                                              throws java.lang.Throwable
Throws:
java.lang.Throwable

handleDCSimDeletionGeneMenuItem

public void handleDCSimDeletionGeneMenuItem()

handleDCOutputTranscriptMenuItem

public void handleDCOutputTranscriptMenuItem()

handleDCOutputOneKSNPMenuItem

public void handleDCOutputOneKSNPMenuItem()

GetTabulatedSNPEntry

public java.lang.Object[][] GetTabulatedSNPEntry(Components components,
                                                 CacheDataCenter cacheDataCenter,
                                                 int col,
                                                 LociFunction thisf,
                                                 int sn)

GetTabulatedIndelEntry

public java.lang.Object[][] GetTabulatedIndelEntry(Components components,
                                                   CacheDataCenter cacheDataCenter,
                                                   int col,
                                                   CNVLociFunction thisf,
                                                   int sn)

GetTabulatedSVEntry

public java.lang.Object[][] GetTabulatedSVEntry(Components components,
                                                CacheDataCenter cacheDataCenter,
                                                int col,
                                                SVLociFunction thisf,
                                                int sn)

GetTabulatedSNVSubjectDatails

public java.lang.Object[][] GetTabulatedSNVSubjectDatails(Components components,
                                                          CacheDataCenter cacheDataCenter,
                                                          int sn,
                                                          LociFunction thisvar)

GetTabulatedIndelSubjectDatails

public java.lang.Object[][] GetTabulatedIndelSubjectDatails(Components components,
                                                            CacheDataCenter cacheDataCenter,
                                                            int sn,
                                                            CNVLociFunction thisvar)

GetTabulatedSVSubjectDatails

public java.lang.Object[][] GetTabulatedSVSubjectDatails(Components components,
                                                         CacheDataCenter cacheDataCenter,
                                                         int sn,
                                                         SVLociFunction thisvar)

ExportSNPIndelPedMap

public boolean ExportSNPIndelPedMap(java.io.File outFile,
                                    boolean showMessage,
                                    boolean SeparateSexChromosome)

FilterCapturedRegionForLoc

public boolean FilterCapturedRegionForLoc(byte bytechr,
                                          int loc)

FilterCapturedRegionForSNV

public boolean FilterCapturedRegionForSNV(LociFunction thisloci)

FilterCapturedRegionForIndel

public boolean FilterCapturedRegionForIndel(CNVLociFunction thisloci)

FilterCapturedRegionForSV

public boolean FilterCapturedRegionForSV(SVLociFunction thisloci)

StopForAnotherProcess

public boolean StopForAnotherProcess()

handleDCProgressBarMenuItem

public void handleDCProgressBarMenuItem()

handleDCProgressBarMenuItem2

public void handleDCProgressBarMenuItem2()

handleDCProgressBarMenuItem3

public void handleDCProgressBarMenuItem3()

Center_GetSNVID_gene

public java.lang.String Center_GetSNVID_gene(LociFunction thisloci)

Center_GetINDELID_FULL_gene

public java.lang.String Center_GetINDELID_FULL_gene(CNVLociFunction thisloci)