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

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

public class AvgCondProbAnalysis
extends BasicFeatureAnalysis

Analysis class which calculates the high scoring path in a clustered sequence using the average conditional probability

Version:
1.0
Author:
Sebastian R. Spiegler
See Also:
PredAccuracy

Field Summary
 
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
 
Constructor Summary
AvgCondProbAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
          constructor of AvgCondProbAnalysis objects
 
Method Summary
 java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          method which returns the high scoring path of genemodels on a sequence using the average conditional probability as scoring system
 
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

AvgCondProbAnalysis

public AvgCondProbAnalysis(java.util.ArrayList _arrListOfGMRegions,
                           SimpleArg _allArguments)
constructor of AvgCondProbAnalysis objects

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

getHighScoringGmRegArr

public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
method which returns the high scoring path of genemodels on a sequence using the average conditional probability as scoring system

If one genemodel overlaps another, the genemodel with the higher overlap is taken. 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
See Also:
GeneModel, GFMergeRegion