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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
class which contains basic computing tools which are used by derived classes
Constructor Summary | |
BasicFeatureAnalysisTools()
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Method Summary | |
private static java.util.ArrayList |
findOverlappingFeatInFeatReg(boolean considerStrand,
GeneModel gm,
GFMergeRegion featReg)
method wich finds overlapping features for gm in feature region |
private static java.util.ArrayList |
getFeatOverlapArr(boolean considerStrand,
GeneModel gm,
java.util.ArrayList _arrListOfFeatRegions)
method which gets overlapping features for genemodel |
protected static java.util.HashMap |
getGmHashOfOverlappedFeat(int debug,
boolean considerStrand,
java.util.ArrayList _arrListOfGMRegions,
java.util.ArrayList _arrListOfFeatRegions)
method which gets hash of gms pointing to ArrayList of overlapping features (returns only overlapped genemodels !!!) |
static boolean |
isFeatureOverlappingGm(boolean considerStrand,
GeneModel gm,
SimFeature feature)
method wich finds out if given feature is overlapping genemodel |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public BasicFeatureAnalysisTools()
Method Detail |
protected static java.util.HashMap getGmHashOfOverlappedFeat(int debug, boolean considerStrand, java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfFeatRegions)
debug
- debugging modeconsiderStrand
- switch for strand consideration_arrListOfGMRegions
- ArrayList of genemodel regions_arrListOfFeatRegions
- ArrayList of SimFeature regions
private static java.util.ArrayList getFeatOverlapArr(boolean considerStrand, GeneModel gm, java.util.ArrayList _arrListOfFeatRegions)
considerStrand
- switch for strand considerationgm
- genemodel_arrListOfFeatRegions
- ArrayList of SimFeature regions
private static java.util.ArrayList findOverlappingFeatInFeatReg(boolean considerStrand, GeneModel gm, GFMergeRegion featReg)
considerStrand
- switch for strand considerationgm
- genemodelfeatReg
- region of SimFeature objects
public static boolean isFeatureOverlappingGm(boolean considerStrand, GeneModel gm, SimFeature feature)
considerStrand
- switch for strand considerationgm
- genemodelfeature
- SimFeature object
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