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

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

public abstract class BasicFeatureAnalysis
extends java.lang.Object
implements BasicFeatureAnalysisAble

abstract class from which feature analysis class are derived

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
private  SimpleArg allArguments
          Object which contains all command line arguments
private  java.util.ArrayList arrListOfGMRegions
          ArrayList of genemodel regions
 
Constructor Summary
BasicFeatureAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
          constructor of abstract BasicFeatureClass, contains partial implementation of constructors of derived classes
 
Method Summary
protected  SimpleArg getAllArguments()
          accessor method which returns object which contains all command line arguments
protected  java.util.ArrayList getArrListOfGMRegions()
          accessor method which returns ArrayList of genemodel regions
 java.lang.String getClassName()
          accessor method which retrieves the class name without package information
abstract  java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          stub for high scoring method which returns the high scoring path of genemodels on a sequence
private  void setAllArguments(SimpleArg _allArguments)
          accessor method which sets object of command line arguments
private  void setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
          accessor method which sets ArrayList of genemodel regions
 
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

See Also:
GeneModel

allArguments

private SimpleArg allArguments
Object which contains all command line arguments

Constructor Detail

BasicFeatureAnalysis

public BasicFeatureAnalysis(java.util.ArrayList _arrListOfGMRegions,
                            SimpleArg _allArguments)
constructor of abstract BasicFeatureClass, contains partial implementation of constructors of derived classes

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

getHighScoringGmRegArr

public abstract java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
stub for high scoring method which returns the high scoring path of genemodels on a sequence

Specified by:
getHighScoringGmRegArr in interface BasicFeatureAnalysisAble
Parameters:
_arrListOfGMRegionsToAnalyze - ArrayList of genemodel regions
Returns:
ArrayList of regions with high scoring genemodels

getClassName

public java.lang.String getClassName()
accessor method which retrieves the class name without package information

Specified by:
getClassName in interface BasicFeatureAnalysisAble
Returns:
class name without package information

getArrListOfGMRegions

protected java.util.ArrayList getArrListOfGMRegions()
accessor method which returns ArrayList of genemodel regions

Returns:
ArrayList of genemodel regions

getAllArguments

protected SimpleArg getAllArguments()
accessor method which returns object which contains all command line arguments

Returns:
object which contains all command line arguments

setArrListOfGMRegions

private void setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
accessor method which sets ArrayList of genemodel regions

Parameters:
_arrListOfGMRegions - ArrayList of genemodel regions

setAllArguments

private void setAllArguments(SimpleArg _allArguments)
accessor method which sets object of command line arguments

Parameters:
_allArguments - SimpleArg object which contains all command line arguments