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java.lang.Object | +--uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
abstract class from which feature analysis class are derived
Field Summary | |
private SimpleArg |
allArguments
Object which contains all command line arguments |
private java.util.ArrayList |
arrListOfGMRegions
ArrayList of genemodel regions |
Constructor Summary | |
BasicFeatureAnalysis(java.util.ArrayList _arrListOfGMRegions,
SimpleArg _allArguments)
constructor of abstract BasicFeatureClass, contains partial implementation of constructors of derived classes |
Method Summary | |
protected SimpleArg |
getAllArguments()
accessor method which returns object which contains all command line arguments |
protected java.util.ArrayList |
getArrListOfGMRegions()
accessor method which returns ArrayList of genemodel regions |
java.lang.String |
getClassName()
accessor method which retrieves the class name without package information |
abstract java.util.ArrayList |
getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
stub for high scoring method which returns the high scoring path of genemodels on a sequence |
private void |
setAllArguments(SimpleArg _allArguments)
accessor method which sets object of command line arguments |
private void |
setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
accessor method which sets ArrayList of genemodel regions |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
private java.util.ArrayList arrListOfGMRegions
GeneModel
private SimpleArg allArguments
Constructor Detail |
public BasicFeatureAnalysis(java.util.ArrayList _arrListOfGMRegions, SimpleArg _allArguments)
_arrListOfGMRegions
- ArrayList of genemodel regions_allArguments
- SimpleArg object which contains all command
line argumentsMethod Detail |
public abstract java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
getHighScoringGmRegArr
in interface BasicFeatureAnalysisAble
_arrListOfGMRegionsToAnalyze
- ArrayList of genemodel regions
public java.lang.String getClassName()
getClassName
in interface BasicFeatureAnalysisAble
protected java.util.ArrayList getArrListOfGMRegions()
protected SimpleArg getAllArguments()
private void setArrListOfGMRegions(java.util.ArrayList _arrListOfGMRegions)
_arrListOfGMRegions
- ArrayList of genemodel regionsprivate void setAllArguments(SimpleArg _allArguments)
_allArguments
- SimpleArg object which contains all command line
arguments
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