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

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

public abstract class FeatureAnalysis
extends BasicFeatureAnalysis

Abstract class which contains partial implementation of derived analysis classes

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 (cDNA, Blast)
private  java.util.ArrayList arrListOfGMRegions
          ArrayList of genemodels
 
Constructor Summary
FeatureAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions, SimpleArg _allArguments)
          constructor of abstract FeatureAnalysis class, contains partial implementation of constructors of derived analysis classes
 
Method Summary
protected  java.util.ArrayList getArrListOfFeatRegions()
          accessor method which gets ArrayList of SimFeature regions (cDNA, Blast)
private  void setArrListOfFeatRegions(java.util.ArrayList _arrListOfFeatRegions)
          accessor method which sets ArrayList of SimFeature regions (cDNA, Blast)
 
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 genemodels


arrListOfFeatRegions

private java.util.ArrayList arrListOfFeatRegions
ArrayList of SimFeature regions (cDNA, Blast)


allArguments

private SimpleArg allArguments
SimpleArg object which contains all command line arguments

Constructor Detail

FeatureAnalysis

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

Parameters:
_arrListOfGMRegions - ArrayList of genemodels
_arrListOfCDnaRegions - ArrayList of cDNA regions
_allArguments - SimpleArg object which contains all commad line arguments
Method Detail

getArrListOfFeatRegions

protected java.util.ArrayList getArrListOfFeatRegions()
accessor method which gets ArrayList of SimFeature regions (cDNA, Blast)

Returns:
ArrayList of SimFeature regions (cDNA, Blast)

setArrListOfFeatRegions

private void setArrListOfFeatRegions(java.util.ArrayList _arrListOfFeatRegions)
accessor method which sets ArrayList of SimFeature regions (cDNA, Blast)

Parameters:
_arrListOfFeatRegions - ArrayList of SimFeature regions (cDNA, Blast)