genomicsnpanalyzer
Class CacheDataCenter

java.lang.Object
  extended by genomicsnpanalyzer.CacheDataCenter

public class CacheDataCenter
extends java.lang.Object


Field Summary
 java.awt.image.BufferedImage avgScore1HistogramImg
           
 java.awt.image.BufferedImage avgScore2HistogramImg
           
 java.awt.image.BufferedImage avgScore3HistogramImg
           
 java.awt.image.BufferedImage avgScore4HistogramImg
           
 java.awt.image.BufferedImage avgScore5HistogramImg
           
 java.awt.image.BufferedImage avgScore6HistogramImg
           
 int[][][] CapturedRegions
           
 java.util.Hashtable ctrlSubHash
           
 java.util.Hashtable EnsemblVarFunctionHash
           
 java.lang.String[] EnsemblVarFunctions
           
 int FilterCacheNum
           
 Gene[] genes
           
 java.util.Hashtable geneSelectedHash
           
 int[] geneSelectedIdx
           
 java.lang.String[] gos
           
 java.util.Hashtable goSelectedHash
           
 HGNC hgnc
           
 int IndelAnnotationParallelNum
           
 java.awt.image.BufferedImage indelAvgConsHistImg
           
 java.awt.image.BufferedImage indelAvgNumReadsHistImg
           
 java.awt.image.BufferedImage indelAvgQualityHistImg
           
 java.awt.image.BufferedImage indelAvgReads4IndelHistImg
           
 java.awt.image.BufferedImage indelAvgReads4RefHistImg
           
 java.awt.image.BufferedImage indelAvgRMSHistImg
           
 java.io.File indelDataFile
           
 java.io.File indelDataFileIdx
           
 int IndelFilterParallelNum
           
 byte[][] indelFunctionCache
           
 IndelFunctionFilter indelFunctionFilter
           
 java.util.ArrayList[] indelGeneCacheEnd
           
 java.util.ArrayList[] indelGeneCacheStart
           
 IndelHomFilter indelHomFilter
           
 long[] indelIndex
           
 int[] indelLength
           
 boolean indelLoaderInitiated
           
 int[][] indelLocationCache
           
 IndelQualityFilter indelQualityFilter
           
 IndelRMRFilter indelRMRFilter
           
 java.util.ArrayList indelSelectedIndex
           
 java.lang.String[] keggPathways
           
 java.util.Hashtable keggPathwaySelectedHash
           
 int LoadCacheNum
           
 int[] LocationCacheInterval
           
 int LocationCacheSegment
           
 java.util.Hashtable omimdiseasehash
           
 java.util.Hashtable omimDisorderSelectedHash
           
 java.util.Hashtable omimgenehash
           
 java.util.Hashtable omimgeneidhash
           
 java.util.Hashtable omimGeneSelectedHash
           
 java.util.ArrayList omims
           
 double OptionDefaultMinIndelConsensus
           
 double OptionDefaultMinIndelQuality
           
 double OptionDefaultMinIndelSupportReads
           
 double OptionDefaultMinSNPConsensus
           
 double OptionDefaultMinSNPQuality
           
 double OptionDefaultMinSNPSupportReads
           
 java.lang.String OptionDefaultQualityFilter
           
 boolean OptionDefaultQualitySexHalf
           
 boolean OptionShowAllFunctions
           
 int ParallelNum
           
 PedInf[] pedinf
           
 Project prj
           
 java.io.File prjFile
           
 RegionFilter regionFilter
           
 java.lang.String[] repeatFamilies
           
 java.lang.String[] repeatMatches
           
 Repeat[][] repeats
           
 SNPFunctionFilter snpFunctionFilter
           
 SNPHapmapFreqFilter snpHapmapFreqFilter
           
 SNPHomFilter snpHomFilter
           
 SNPNSIntoleranceFilter snpNSIntoleranceFilter
           
 SNPQualityFilter snpQualityFilter
           
 SNPRefFilter snpRefFilter
           
 SNPRMRFilter snpRMRFilter
           
 int SNVAnnotationParallelNum
           
 java.io.File snvDataFile
           
 java.io.File snvDataFileIdx
           
 int SNVFilterParallelNum
           
 byte[][] snvFunctionCache
           
 java.util.ArrayList[] snvGeneCacheEnd
           
 java.util.ArrayList[] snvGeneCacheStart
           
 long[] snvIndex
           
 int[] snvLength
           
 boolean snvLoaderInitiated
           
 int[][] snvLocationCache
           
 java.util.ArrayList snvSelectedIndex
           
 SortedOmimDisorder[] sortedOmimDisoder
           
 SortedOmimGene[] sortedOmimGene
           
 java.util.Hashtable subjectFilterHash
           
 Subject[] subjects
           
 java.awt.image.BufferedImage svAvgNumReadsHistImg
           
 java.io.File svDataFile
           
 java.io.File svDataFileIdx
           
 byte[][] svFunctionCache
           
 SVFunctionFilter svFunctionFilter
           
 java.util.ArrayList[] svGeneCacheEnd
           
 java.util.ArrayList[] svGeneCacheStart
           
 long[] svIndex
           
 int[] svLength
           
 boolean svLoaderInitiated
           
 int[][] svLocationCache
           
 SVMethodFilter svMethodFilter
           
 SVQualityFilter svQualityFilter
           
 java.util.ArrayList svSelectedIndex
           
 SVTypeFilter svTypeFilter
           
 TranscriptSave[] transcriptSaves
           
 VenterIndel[] venterIndels
           
 VenterSNP[] venterSNPs
           
 
Constructor Summary
CacheDataCenter()
          Creates a new instance of DataCenter
 
Method Summary
 void CloseDataLoader()
           
 boolean CloseIndelLoader()
           
 boolean CloseSNVLoader()
           
 boolean CloseSVLoader()
           
 CNVLociFunction[] getINDEL(java.util.ArrayList idxs)
           
 CNVLociFunction[] getINDEL(java.util.ArrayList idxs, int loaderi)
           
 CNVLociFunction getINDEL(int i)
           
 CNVLociFunction getINDEL(int i, int loaderI)
           
 int getINDELLocationStartSearchIndex(byte bytechr, int startLocation)
           
 LociFunction[] getSNV(java.util.ArrayList idxs)
           
 LociFunction[] getSNV(java.util.ArrayList idxs, int loaderi)
           
 LociFunction getSNV(int i)
           
 LociFunction getSNV(int i, int loaderI)
           
 int getSNVLocationStartSearchIndex(byte bytechr, int startLocation)
           
 SVLociFunction[] getSV(java.util.ArrayList idxs)
           
 SVLociFunction getSV(int i)
           
 SVLociFunction getSV(int i, int loaderI)
           
 int getSVLocationStartSearchIndex(byte bytechr, int startLocation)
           
 void InitiateGeneSelectedIdx()
           
 boolean InitiateIndelLoader()
           
 void InitiateLocationCache(int chrnum, int[] chrLength)
           
 boolean InitiateSNVLoader()
           
 boolean InitiateSVLoader()
           
 void resetProjectInfo()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

prjFile

public java.io.File prjFile

prj

public Project prj

snvDataFile

public java.io.File snvDataFile

snvDataFileIdx

public java.io.File snvDataFileIdx

indelDataFile

public java.io.File indelDataFile

indelDataFileIdx

public java.io.File indelDataFileIdx

svDataFile

public java.io.File svDataFile

svDataFileIdx

public java.io.File svDataFileIdx

FilterCacheNum

public int FilterCacheNum

LoadCacheNum

public int LoadCacheNum

ParallelNum

public int ParallelNum

SNVFilterParallelNum

public int SNVFilterParallelNum

IndelFilterParallelNum

public int IndelFilterParallelNum

SNVAnnotationParallelNum

public int SNVAnnotationParallelNum

IndelAnnotationParallelNum

public int IndelAnnotationParallelNum

snvIndex

public long[] snvIndex

snvLength

public int[] snvLength

indelIndex

public long[] indelIndex

indelLength

public int[] indelLength

svIndex

public long[] svIndex

svLength

public int[] svLength

snvLoaderInitiated

public boolean snvLoaderInitiated

indelLoaderInitiated

public boolean indelLoaderInitiated

svLoaderInitiated

public boolean svLoaderInitiated

snvFunctionCache

public byte[][] snvFunctionCache

indelFunctionCache

public byte[][] indelFunctionCache

svFunctionCache

public byte[][] svFunctionCache

LocationCacheSegment

public int LocationCacheSegment

snvLocationCache

public int[][] snvLocationCache

indelLocationCache

public int[][] indelLocationCache

svLocationCache

public int[][] svLocationCache

LocationCacheInterval

public int[] LocationCacheInterval

snvGeneCacheStart

public java.util.ArrayList[] snvGeneCacheStart

snvGeneCacheEnd

public java.util.ArrayList[] snvGeneCacheEnd

indelGeneCacheStart

public java.util.ArrayList[] indelGeneCacheStart

indelGeneCacheEnd

public java.util.ArrayList[] indelGeneCacheEnd

svGeneCacheStart

public java.util.ArrayList[] svGeneCacheStart

svGeneCacheEnd

public java.util.ArrayList[] svGeneCacheEnd

subjects

public Subject[] subjects

pedinf

public PedInf[] pedinf

ctrlSubHash

public java.util.Hashtable ctrlSubHash

transcriptSaves

public TranscriptSave[] transcriptSaves

genes

public Gene[] genes

keggPathways

public java.lang.String[] keggPathways

gos

public java.lang.String[] gos

CapturedRegions

public int[][][] CapturedRegions

venterSNPs

public VenterSNP[] venterSNPs

venterIndels

public VenterIndel[] venterIndels

repeats

public Repeat[][] repeats

repeatMatches

public java.lang.String[] repeatMatches

repeatFamilies

public java.lang.String[] repeatFamilies

avgScore1HistogramImg

public java.awt.image.BufferedImage avgScore1HistogramImg

avgScore2HistogramImg

public java.awt.image.BufferedImage avgScore2HistogramImg

avgScore3HistogramImg

public java.awt.image.BufferedImage avgScore3HistogramImg

avgScore4HistogramImg

public java.awt.image.BufferedImage avgScore4HistogramImg

avgScore5HistogramImg

public java.awt.image.BufferedImage avgScore5HistogramImg

avgScore6HistogramImg

public java.awt.image.BufferedImage avgScore6HistogramImg

indelAvgNumReadsHistImg

public java.awt.image.BufferedImage indelAvgNumReadsHistImg

indelAvgConsHistImg

public java.awt.image.BufferedImage indelAvgConsHistImg

indelAvgRMSHistImg

public java.awt.image.BufferedImage indelAvgRMSHistImg

indelAvgReads4IndelHistImg

public java.awt.image.BufferedImage indelAvgReads4IndelHistImg

indelAvgReads4RefHistImg

public java.awt.image.BufferedImage indelAvgReads4RefHistImg

indelAvgQualityHistImg

public java.awt.image.BufferedImage indelAvgQualityHistImg

svAvgNumReadsHistImg

public java.awt.image.BufferedImage svAvgNumReadsHistImg

EnsemblVarFunctions

public java.lang.String[] EnsemblVarFunctions

EnsemblVarFunctionHash

public java.util.Hashtable EnsemblVarFunctionHash

hgnc

public HGNC hgnc

omims

public java.util.ArrayList omims

omimgenehash

public java.util.Hashtable omimgenehash

omimdiseasehash

public java.util.Hashtable omimdiseasehash

omimgeneidhash

public java.util.Hashtable omimgeneidhash

sortedOmimDisoder

public SortedOmimDisorder[] sortedOmimDisoder

sortedOmimGene

public SortedOmimGene[] sortedOmimGene

omimDisorderSelectedHash

public java.util.Hashtable omimDisorderSelectedHash

omimGeneSelectedHash

public java.util.Hashtable omimGeneSelectedHash

goSelectedHash

public java.util.Hashtable goSelectedHash

keggPathwaySelectedHash

public java.util.Hashtable keggPathwaySelectedHash

geneSelectedHash

public java.util.Hashtable geneSelectedHash

geneSelectedIdx

public int[] geneSelectedIdx

regionFilter

public RegionFilter regionFilter

subjectFilterHash

public java.util.Hashtable subjectFilterHash

snpQualityFilter

public SNPQualityFilter snpQualityFilter

indelQualityFilter

public IndelQualityFilter indelQualityFilter

svQualityFilter

public SVQualityFilter svQualityFilter

snpFunctionFilter

public SNPFunctionFilter snpFunctionFilter

indelFunctionFilter

public IndelFunctionFilter indelFunctionFilter

svFunctionFilter

public SVFunctionFilter svFunctionFilter

snpNSIntoleranceFilter

public SNPNSIntoleranceFilter snpNSIntoleranceFilter

snpHomFilter

public SNPHomFilter snpHomFilter

snpRefFilter

public SNPRefFilter snpRefFilter

snpRMRFilter

public SNPRMRFilter snpRMRFilter

snpHapmapFreqFilter

public SNPHapmapFreqFilter snpHapmapFreqFilter

indelHomFilter

public IndelHomFilter indelHomFilter

indelRMRFilter

public IndelRMRFilter indelRMRFilter

svTypeFilter

public SVTypeFilter svTypeFilter

svMethodFilter

public SVMethodFilter svMethodFilter

OptionShowAllFunctions

public boolean OptionShowAllFunctions

OptionDefaultMinSNPQuality

public double OptionDefaultMinSNPQuality

OptionDefaultMinSNPConsensus

public double OptionDefaultMinSNPConsensus

OptionDefaultMinSNPSupportReads

public double OptionDefaultMinSNPSupportReads

OptionDefaultMinIndelQuality

public double OptionDefaultMinIndelQuality

OptionDefaultMinIndelConsensus

public double OptionDefaultMinIndelConsensus

OptionDefaultMinIndelSupportReads

public double OptionDefaultMinIndelSupportReads

OptionDefaultQualitySexHalf

public boolean OptionDefaultQualitySexHalf

OptionDefaultQualityFilter

public java.lang.String OptionDefaultQualityFilter

snvSelectedIndex

public java.util.ArrayList snvSelectedIndex

indelSelectedIndex

public java.util.ArrayList indelSelectedIndex

svSelectedIndex

public java.util.ArrayList svSelectedIndex
Constructor Detail

CacheDataCenter

public CacheDataCenter()
Creates a new instance of DataCenter

Method Detail

resetProjectInfo

public void resetProjectInfo()

InitiateSNVLoader

public boolean InitiateSNVLoader()

InitiateIndelLoader

public boolean InitiateIndelLoader()

InitiateSVLoader

public boolean InitiateSVLoader()

CloseSNVLoader

public boolean CloseSNVLoader()

CloseIndelLoader

public boolean CloseIndelLoader()

CloseSVLoader

public boolean CloseSVLoader()

CloseDataLoader

public void CloseDataLoader()

getSNV

public LociFunction getSNV(int i)

getSNV

public LociFunction[] getSNV(java.util.ArrayList idxs)

getSNV

public LociFunction getSNV(int i,
                           int loaderI)

getSNV

public LociFunction[] getSNV(java.util.ArrayList idxs,
                             int loaderi)

getINDEL

public CNVLociFunction getINDEL(int i)

getINDEL

public CNVLociFunction[] getINDEL(java.util.ArrayList idxs)

getINDEL

public CNVLociFunction getINDEL(int i,
                                int loaderI)

getINDEL

public CNVLociFunction[] getINDEL(java.util.ArrayList idxs,
                                  int loaderi)

getSV

public SVLociFunction getSV(int i)

getSV

public SVLociFunction[] getSV(java.util.ArrayList idxs)

getSV

public SVLociFunction getSV(int i,
                            int loaderI)

getSNVLocationStartSearchIndex

public int getSNVLocationStartSearchIndex(byte bytechr,
                                          int startLocation)

getINDELLocationStartSearchIndex

public int getINDELLocationStartSearchIndex(byte bytechr,
                                            int startLocation)

getSVLocationStartSearchIndex

public int getSVLocationStartSearchIndex(byte bytechr,
                                         int startLocation)

InitiateLocationCache

public void InitiateLocationCache(int chrnum,
                                  int[] chrLength)

InitiateGeneSelectedIdx

public void InitiateGeneSelectedIdx()