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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.GeneModelLengthAnalysis
Analysis class which calculates the high scoring path in a clustered sequence using the genemodel length (exon + intron length) as a scoring system
Field Summary |
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis |
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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 |
public GeneModelLengthAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
_arrListOfGMRegions
- ArrayList of genemodel regions_allArguments
- SimpleArg object which contains all command
line argumentsMethod Detail |
public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
Genemodel score is calculated by using the genemodel length (exon + intron length) favoring multiple equal genemodels. For further details consult the documentation.
getHighScoringGmRegArr
in interface BasicFeatureAnalysisAble
getHighScoringGmRegArr
in class BasicFeatureAnalysis
_arrListOfGMRegionsToAnalyze
- ArrayList of genemodel regions
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