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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
class which contains basic overlap computing tools which are used by derived overlap analysis classes (cDNA, Blast)
Constructor Summary | |
FeatureOverlapAnalysisTools()
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Method Summary | |
private static long |
calcExonTotalOverlap(Exon exon,
java.util.HashMap hashFeatOverlappedExons)
method which calculates total cDNA overlap on genemodel exon level. |
private static long |
calcGmCompTotalOverlap(FeatureComponentAble gmComp,
java.util.HashMap hashFeatOverlappedGmComps,
boolean isExon)
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private static long |
calcGmLongestOverlap(int debug,
boolean considerStrand,
GeneModel gm,
java.util.ArrayList overlappingFeatArr,
boolean considerIntrons)
method which calculates longest overlap for a single genemodel. |
private static long |
calcGmTotalExIntOverlap(int debug,
boolean considerStrand,
GeneModel gm,
java.util.ArrayList featArr,
boolean considerIntrons)
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private static long |
calcGmTotalOverlap(int debug,
boolean considerStrand,
GeneModel gm,
java.util.ArrayList featArr)
method which calculates total cDNA/single Blast protein overlap for a single genemodel. |
private static java.util.HashMap |
calcHashOfLongestFeatOverlap(int debug,
boolean considerStrand,
java.util.HashMap hashFeatOverlappedGms,
boolean considerIntrons)
method which calculates hash of longest feature overlap. |
private static java.util.HashMap |
calcHashOfScoredOverlap(java.util.HashMap gmHashOfTotalFeatOverlap,
boolean isPercentage)
method which calculates scored overlap of genemodels. |
private static java.util.HashMap |
calcHashOfTotalOverlap(int debug,
boolean considerStrand,
java.util.HashMap gmHashOfOverlappedFeat,
boolean considerIntrons)
method which calculates hash of total cDNA overlap for genemodels. |
private static long |
calcTotalLocationLength(org.biojava.bio.symbol.Location mergedSubLocs)
method which accumulates total overlap length of exons/introns by aggregating sublocations of a compound overlap. |
private static java.util.HashMap |
findLongestProteinOverlap(java.util.HashMap proteinOverlapLength)
method which finds longest protein overlap. |
private static java.util.HashMap |
getExonHashOfOverlappedFeat(int debug,
boolean considerStrand,
GeneModel gm,
java.util.ArrayList overlappingFeatArr)
method which returns hash of exons pointing to ArrayList of overlapping features. |
private static java.util.ArrayList |
getFeatOverlapArrForExon(Exon exon,
java.util.ArrayList featArr)
method which returns overlapping features for a single exon. |
private static java.util.ArrayList |
getFeatOverlapArrForGmComp(FeatureComponentAble gmComp,
java.util.ArrayList featArr)
|
private static java.util.HashMap |
getGmCompHashOfOverlappedFeat(int debug,
boolean considerStrand,
java.util.ArrayList gmCompArr,
java.util.ArrayList overlappingFeatArr)
method which returns hash of gm features (exons or introns) pointing to ArrayList of overlapping features (Blast or cDNA). |
static java.util.HashMap |
getGmHashOfAbsoluteFeatOverlap(int debug,
boolean considerStrand,
boolean isPercentage,
java.util.ArrayList arrListOfGMRegions,
java.util.ArrayList arrListOfFeatRegions,
boolean considerIntrons)
method which returns hash of genemodels pointing to their ABSOLUTE overlap (CDNA). |
static java.util.HashMap |
getGmHashOfLongestAbsoluteFeatOverlap(int debug,
boolean considerStrand,
boolean isPercentage,
java.util.ArrayList arrListOfGMRegions,
java.util.ArrayList arrListOfFeatRegions,
boolean considerIntrons)
method which returns hash of gms pointing to their longest absolute overlap (BLAST). |
private static java.util.HashMap |
getProteinHash(int debug,
GeneModel gm,
java.util.ArrayList overlappingFeatArr)
method which returns protein hash. |
private static java.lang.String |
getProteinID(GFMergeFeature feature)
method which returns the protein ID of a feature. |
private static java.util.HashMap |
getProteinOverlapHash(int debug,
boolean considerStrand,
GeneModel gm,
java.util.HashMap proteinHash,
boolean considerIntrons)
method which returns hash map of proteins pointing to overlap length. |
private static long |
getSingleProteinOverlap(int debug,
boolean considerStrand,
GeneModel gm,
java.util.ArrayList arrFeat,
boolean considerIntrons)
method which returns single protein overlap for a genemodel. |
private static java.util.HashMap |
putFeatureInProteinHash(java.lang.String proteinID,
SimFeature feature,
java.util.HashMap proteinHash)
method which stores feature in protein hash. |
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools |
getGmHashOfOverlappedFeat, isFeatureOverlappingGm |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public FeatureOverlapAnalysisTools()
Method Detail |
public static java.util.HashMap getGmHashOfLongestAbsoluteFeatOverlap(int debug, boolean considerStrand, boolean isPercentage, java.util.ArrayList arrListOfGMRegions, java.util.ArrayList arrListOfFeatRegions, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationarrListOfGMRegions
- ArrayList of genemodel regionsarrListOfFeatRegions
- ArrayList of SimFeature regions (Blast)
private static java.util.HashMap calcHashOfLongestFeatOverlap(int debug, boolean considerStrand, java.util.HashMap hashFeatOverlappedGms, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationhashFeatOverlappedGms
- hash of genemodels pointing to an
ArrayList of overlapping features
private static long calcGmLongestOverlap(int debug, boolean considerStrand, GeneModel gm, java.util.ArrayList overlappingFeatArr, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationgm
- genemodeloverlappingFeatArr
- ArrayList of overlapping features
private static java.util.HashMap findLongestProteinOverlap(java.util.HashMap proteinOverlapLength)
proteinOverlapLength
- hash of proteins (protein ID) pointing to
their overlap length
private static java.util.HashMap getProteinOverlapHash(int debug, boolean considerStrand, GeneModel gm, java.util.HashMap proteinHash, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationgm
- genemodelproteinHash
- hash of proteins (protein ID) pointing to their
overlapping feature hits
private static long getSingleProteinOverlap(int debug, boolean considerStrand, GeneModel gm, java.util.ArrayList arrFeat, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationgm
- genemodelarrFeat
- ArrayList of different hits from the same protein
private static java.util.HashMap getProteinHash(int debug, GeneModel gm, java.util.ArrayList overlappingFeatArr)
debug
- debugging modegm
- genemodeloverlappingFeatArr
- ArrayList of genemodel overlapping
features
private static java.lang.String getProteinID(GFMergeFeature feature)
feature
- overlapping feature
private static java.util.HashMap putFeatureInProteinHash(java.lang.String proteinID, SimFeature feature, java.util.HashMap proteinHash)
proteinID
- ID of the proteinfeature
- overlapping SimFeatureproteinHash
- protein hash
public static java.util.HashMap getGmHashOfAbsoluteFeatOverlap(int debug, boolean considerStrand, boolean isPercentage, java.util.ArrayList arrListOfGMRegions, java.util.ArrayList arrListOfFeatRegions, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationarrListOfGMRegions
- ArrayList of genemodel regionsarrListOfFeatRegions
- ArrayList of feature regions (cDNA)
private static java.util.HashMap calcHashOfTotalOverlap(int debug, boolean considerStrand, java.util.HashMap gmHashOfOverlappedFeat, boolean considerIntrons)
debug
- debugging modeconsiderStrand
- switch for strand considerationgmHashOfOverlappedFeat
- hash of genemodels pointing to
ArrayList of overlapping cDNA features
private static long calcGmTotalOverlap(int debug, boolean considerStrand, GeneModel gm, java.util.ArrayList featArr)
debug
- debugging modeconsiderStrand
- switch for strand considerationgm
- genemodelfeatArr
- ArrayList of genemodel overlapping cDNA features
private static long calcGmTotalExIntOverlap(int debug, boolean considerStrand, GeneModel gm, java.util.ArrayList featArr, boolean considerIntrons)
private static long calcExonTotalOverlap(Exon exon, java.util.HashMap hashFeatOverlappedExons)
exon
- Exon objecthashFeatOverlappedExons
- hash of exons pointing to their
overlapping cDNA / Blast features
private static long calcGmCompTotalOverlap(FeatureComponentAble gmComp, java.util.HashMap hashFeatOverlappedGmComps, boolean isExon)
private static long calcTotalLocationLength(org.biojava.bio.symbol.Location mergedSubLocs)
mergedSubLocs
- merged Locations of all htis at exon level
private static java.util.HashMap calcHashOfScoredOverlap(java.util.HashMap gmHashOfTotalFeatOverlap, boolean isPercentage)
gmHashOfTotalFeatOverlap
- hash genemodels pointing to their
absolute overlap [Long]isPercentage
- switch for percentage overlap otherwise absolute
overlap [Double]
private static java.util.HashMap getExonHashOfOverlappedFeat(int debug, boolean considerStrand, GeneModel gm, java.util.ArrayList overlappingFeatArr)
debug
- debugging modeconsiderStrand
- switch for strand considerationgm
- genemodeloverlappingFeatArr
- ArrayList of genemodel overlapping
features
private static java.util.HashMap getGmCompHashOfOverlappedFeat(int debug, boolean considerStrand, java.util.ArrayList gmCompArr, java.util.ArrayList overlappingFeatArr)
debug
- debugging modeconsiderStrand
- switch for strand considerationgmCompArr
- ArrayList of genemodel components (exons or introns)overlappingFeatArr
- ArrayList of genemodel overlapping
features
private static java.util.ArrayList getFeatOverlapArrForExon(Exon exon, java.util.ArrayList featArr)
exon
- Exon objectfeatArr
- ArrayList of genemodel overlapping features
private static java.util.ArrayList getFeatOverlapArrForGmComp(FeatureComponentAble gmComp, java.util.ArrayList featArr)
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