apollo.dataadapter.analysis
Class GeneFinderParser

java.lang.Object
  apollo.dataadapter.analysis.AbstractParser
      apollo.dataadapter.analysis.GeneFinderParser

All Implemented Interfaces:

AnalysisParserI

Direct Known Subclasses:

FgeneshGFFParser, FgeneshParser, GenieParser, GenscanParser

public abstract class GeneFinderParser
extends AbstractParser

Field Summary

Fields inherited from class apollo.dataadapter.analysis.AbstractParser

logger

Constructor Summary

GeneFinderParser()

Method Summary

protected void	addGene(FeatureSetI gene, FeatureSetI forward_analysis, FeatureSetI reverse_analysis)
java.lang.String	getProgram()
protected abstract boolean	grabGenes(CurationSet curation, FeatureSetI forward_analysis, FeatureSetI reverse_analysis)
protected abstract boolean	isCommentary()
protected java.lang.String	parseProgram()

Methods inherited from class apollo.dataadapter.analysis.AbstractParser

getAnalysisType, initAnalysis, initCuration, initFeature, initLoad, initSequence, initSet, load, parseDouble, parseInteger, parseToken, readLine, recognizedInput, setHitScore

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneFinderParser

public GeneFinderParser()

Method Detail

grabGenes

protected abstract boolean grabGenes(CurationSet curation,
                                     FeatureSetI forward_analysis,
                                     FeatureSetI reverse_analysis)

isCommentary

protected abstract boolean isCommentary()

addGene

protected void addGene(FeatureSetI gene,
                       FeatureSetI forward_analysis,
                       FeatureSetI reverse_analysis)

parseProgram

protected java.lang.String parseProgram()

getProgram

public java.lang.String getProgram()

Specified by:

getProgram in class AbstractParser