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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.AvgCondProbAnalysis
Analysis class which calculates the high scoring path in a clustered sequence using the average conditional probability
PredAccuracy
Field Summary |
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis |
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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 |
public AvgCondProbAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
_arrListOfGMRegions
- ArrayList of genemodel regions_allArguments
- object which contains all command line
parametersMethod Detail |
public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
If one genemodel overlaps another, the genemodel with the higher overlap is taken. For further details consult the documentation.
getHighScoringGmRegArr
in interface BasicFeatureAnalysisAble
getHighScoringGmRegArr
in class BasicFeatureAnalysis
_arrListOfGMRegionsToAnalyze
- ArrayList of genemodel regions
GeneModel
,
GFMergeRegion
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