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

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
        |
        +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.GeneModelLengthAnalysis
All Implemented Interfaces:
BasicFeatureAnalysisAble

public class GeneModelLengthAnalysis
extends BasicFeatureAnalysis

Analysis class which calculates the high scoring path in a clustered sequence using the genemodel length (exon + intron length) as a scoring system

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
 
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
 
Constructor Summary
GeneModelLengthAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
          constructor for GeneModelLengthAnalysis objects
 
Method Summary
 java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          method which returns the high scoring path of genemodels on a sequence.
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
getAllArguments, getArrListOfGMRegions, getClassName
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GeneModelLengthAnalysis

public GeneModelLengthAnalysis(java.util.ArrayList _arrListOfGMRegions,
                               SimpleArg _allArguments)
constructor for GeneModelLengthAnalysis objects

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

getHighScoringGmRegArr

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

Genemodel score is calculated by using the genemodel length (exon + intron length) favoring multiple equal genemodels. For further details consult the documentation.

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