apollo.dataadapter.analysis
Class GenieParser

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

All Implemented Interfaces:

AnalysisParserI

public class GenieParser
extends GeneFinderParser

Field Summary

Fields inherited from class apollo.dataadapter.analysis.AbstractParser

logger

Constructor Summary

GenieParser()

Method Summary

protected void	grabDate(FeatureSetI forward_analysis, FeatureSetI reverse_analysis)
protected SequenceI	grabDNA()
protected boolean	grabGenes(CurationSet curation, FeatureSetI forward_analysis, FeatureSetI reverse_analysis)
protected boolean	isCommentary()
java.lang.String	load(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
protected boolean	parseLine()
boolean	recognizedInput()

Methods inherited from class apollo.dataadapter.analysis.GeneFinderParser

addGene, getProgram, parseProgram

Methods inherited from class apollo.dataadapter.analysis.AbstractParser

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

Methods inherited from class java.lang.Object

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

Constructor Detail

GenieParser

public GenieParser()

Method Detail

load

public java.lang.String load(CurationSet curation,
                             boolean new_curation,
                             java.io.InputStream data_stream,
                             AnalysisInput input)

Specified by:

load in interface AnalysisParserI

Overrides:

load in class AbstractParser

isCommentary

protected boolean isCommentary()

Specified by:

isCommentary in class GeneFinderParser

recognizedInput

public boolean recognizedInput()

Specified by:

recognizedInput in class AbstractParser

parseLine

protected boolean parseLine()

grabGenes

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

Specified by:

grabGenes in class GeneFinderParser

grabDate

protected void grabDate(FeatureSetI forward_analysis,
                        FeatureSetI reverse_analysis)

grabDNA

protected SequenceI grabDNA()
                     throws java.text.ParseException

Throws:

java.text.ParseException