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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaSpliceSiteAnalysis
Analysis class which calculates the high scoring path in a clustered sequence using a cDNA splice sites scoring system
Field Summary |
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis |
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Constructor Summary | |
CDnaSpliceSiteAnalysis(java.util.ArrayList _arrListOfGMRegions,
java.util.ArrayList _arrListOfCDnaRegions,
SimpleArg _allArguments)
constructor for CDnaSpliceSiteAnalysis objects |
Method Summary | |
java.util.ArrayList |
getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
method which returns the high scoring path of genemodels on a sequence using a cDNA splice site scoring system |
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis |
getArrListOfFeatRegions |
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 CDnaSpliceSiteAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions, SimpleArg _allArguments)
_arrListOfGMRegions
- ArrayList of genemodel regions_arrListOfCDnaRegions
- ArrayList of cDNA regions_allArguments
- SimpleArg object which contains all command
line argumentsMethod Detail |
public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
Genemodel splice sites are scored with +1 when they match a cDNA splice site, with -1 when they overlap a cDNA but do not match and 0 when they do not overlap a cDNA. The total score is calculated as the sum of all splice site scores. For further details consult the documentation.
getHighScoringGmRegArr
in interface BasicFeatureAnalysisAble
getHighScoringGmRegArr
in class BasicFeatureAnalysis
_arrListOfGMRegionsToAnalyze
- ArrayList of genemodel regions
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