uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools
Class BasicFeatureAnalysisTools

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
Direct Known Subclasses:
CDnaSpliceSiteAnalysisTools, FeatureOverlapAnalysisTools

public class BasicFeatureAnalysisTools
extends java.lang.Object

class which contains basic computing tools which are used by derived classes

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
BasicFeatureAnalysisTools()
           
 
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

BasicFeatureAnalysisTools

public BasicFeatureAnalysisTools()
Method Detail

getGmHashOfOverlappedFeat

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 !!!)

Parameters:
debug - debugging mode
considerStrand - switch for strand consideration
_arrListOfGMRegions - ArrayList of genemodel regions
_arrListOfFeatRegions - ArrayList of SimFeature regions
Returns:
HashMap of genemodels pointing to ArrayList of overlapping features

getFeatOverlapArr

private static java.util.ArrayList getFeatOverlapArr(boolean considerStrand,
                                                     GeneModel gm,
                                                     java.util.ArrayList _arrListOfFeatRegions)
method which gets overlapping features for genemodel

Parameters:
considerStrand - switch for strand consideration
gm - genemodel
_arrListOfFeatRegions - ArrayList of SimFeature regions
Returns:
ArrayList of overlapping features

findOverlappingFeatInFeatReg

private static java.util.ArrayList findOverlappingFeatInFeatReg(boolean considerStrand,
                                                                GeneModel gm,
                                                                GFMergeRegion featReg)
method wich finds overlapping features for gm in feature region

Parameters:
considerStrand - switch for strand consideration
gm - genemodel
featReg - region of SimFeature objects
Returns:
ArrayList of overlapping features in feature region

isFeatureOverlappingGm

public static boolean isFeatureOverlappingGm(boolean considerStrand,
                                             GeneModel gm,
                                             SimFeature feature)
method wich finds out if given feature is overlapping genemodel

Parameters:
considerStrand - switch for strand consideration
gm - genemodel
feature - SimFeature object
Returns:
is overlapping / is not overlapping (true/false)