uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis
Class FeatureOverlapAnalysis

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
        |
        +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
              |
              +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
All Implemented Interfaces:
BasicFeatureAnalysisAble
Direct Known Subclasses:
BlastOverlapAnalysis, CDnaOverlapAnalysis

public abstract class FeatureOverlapAnalysis
extends FeatureAnalysis

Abstract class which contains partial implementation of derived overlap analysis classes

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
private  SimpleArg allArguments
          SimpleArg object which contains all command line arguments
private  java.util.ArrayList arrListOfFeatRegions
          ArrayList of SimFeature regions
private  java.util.ArrayList arrListOfGMRegions
          ArrayList of genemodel regions
 
Constructor Summary
FeatureOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfFeatRegions, SimpleArg _allArguments)
          constructor of abstract FeatureOverlapAnalysis class, contains partial implementation of constructors of derived overlap analysis classes
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
getArrListOfFeatRegions
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
getAllArguments, getArrListOfGMRegions, getClassName, getHighScoringGmRegArr
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

arrListOfGMRegions

private java.util.ArrayList arrListOfGMRegions
ArrayList of genemodel regions


arrListOfFeatRegions

private java.util.ArrayList arrListOfFeatRegions
ArrayList of SimFeature regions


allArguments

private SimpleArg allArguments
SimpleArg object which contains all command line arguments

Constructor Detail

FeatureOverlapAnalysis

public FeatureOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions,
                              java.util.ArrayList _arrListOfFeatRegions,
                              SimpleArg _allArguments)
constructor of abstract FeatureOverlapAnalysis class, contains partial implementation of constructors of derived overlap analysis classes

Parameters:
_arrListOfGMRegions - ArrayList of genemodel regions
_arrListOfFeatRegions - ArrayList of SimFeature regions
_allArguments - SimpleArg object which contains all command line arguments