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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.FeatureOverlapAnalysis | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BlastOverlapAnalysis
Analysis class which calculates the high scoring path in a clustered sequence using the Blast overlap on the exon level
Field Summary |
Fields inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis |
|
Constructor Summary | |
BlastOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions,
java.util.ArrayList _arrListOfBlastRegions,
SimpleArg _allArguments)
constructor for BlastOverlapAnalysis 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 Blast overlap on the exon level. |
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 BlastOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfBlastRegions, SimpleArg _allArguments)
_arrListOfGMRegions
- ArrayList of genemodel regions_arrListOfBlastRegions
- ArrayList of blast regions_allArguments
- SimpleArg object which contains all command
line argumentsGeneModel
,
SimFeature
,
GFMergeRegion
Method Detail |
public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
Blast hits from the same protein to a genemodel are treated as one hit. Longest protein hit is chosen for scoring the genemodel. For further details consult the documentation.
getHighScoringGmRegArr
in interface BasicFeatureAnalysisAble
getHighScoringGmRegArr
in class BasicFeatureAnalysis
_arrListOfGMRegionsToAnalyze
- ArrayList of genemodel regions
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