apollo.dataadapter.analysis
Class BlastParser

java.lang.Object
  apollo.dataadapter.analysis.AbstractParser
      apollo.dataadapter.analysis.AlignmentParser
          apollo.dataadapter.analysis.BlastParser

All Implemented Interfaces:

AnalysisParserI

public class BlastParser
extends AlignmentParser

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.dataadapter.analysis.AlignmentParser

align_seq, coord_seq

Constructor Summary

BlastParser()

Method Summary

java.lang.String	getProgram()
java.lang.String	getVersion()
java.lang.String	load(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
boolean	recognizedInput()
protected void	setHitScore(FeatureSetI hit, FeaturePairI span)

Methods inherited from class apollo.dataadapter.analysis.AlignmentParser

addAlignPair, initAlignment, initAlignPair, rollCigar

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

BlastParser

public BlastParser()

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 AlignmentParser

getProgram

public java.lang.String getProgram()

Specified by:

getProgram in class AbstractParser

getVersion

public java.lang.String getVersion()

recognizedInput

public boolean recognizedInput()

Specified by:

recognizedInput in class AbstractParser

setHitScore

protected void setHitScore(FeatureSetI hit,
                           FeaturePairI span)