apollo.dataadapter.analysis
Class GenscanParser

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

All Implemented Interfaces:

AnalysisParserI

public class GenscanParser
extends GeneFinderParser

Field Summary

Fields inherited from class apollo.dataadapter.analysis.AbstractParser

logger

Constructor Summary

GenscanParser()

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 void	grabMatrix(FeatureSetI forward_analysis, FeatureSetI reverse_analysis)
protected void	grabSequence(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 double	parseDouble(java.util.StringTokenizer tokens, java.lang.String msg)
protected boolean	parseLine()
protected double	parseScore(java.lang.String value)
protected java.lang.String	parseVersion()
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, parseInteger, parseToken, readLine, setHitScore

Methods inherited from class java.lang.Object

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

Constructor Detail

GenscanParser

public GenscanParser()

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

parseVersion

protected java.lang.String parseVersion()

parseLine

protected boolean parseLine()

parseDouble

protected double parseDouble(java.util.StringTokenizer tokens,
                             java.lang.String msg)

Overrides:

parseDouble in class AbstractParser

parseScore

protected double parseScore(java.lang.String value)
                     throws java.text.ParseException

Throws:

java.text.ParseException

grabGenes

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

Specified by:

grabGenes in class GeneFinderParser

grabSequence

protected void grabSequence(FeatureSetI forward_analysis,
                            FeatureSetI reverse_analysis)

grabMatrix

protected void grabMatrix(FeatureSetI forward_analysis,
                          FeatureSetI reverse_analysis)

grabDate

protected void grabDate(FeatureSetI forward_analysis,
                        FeatureSetI reverse_analysis)

grabDNA

protected SequenceI grabDNA()
                     throws java.text.ParseException

Throws:

java.text.ParseException