apollo.dataadapter.analysis
Class BlatParser

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

All Implemented Interfaces:

AnalysisParserI

public class BlatParser
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

BlatParser()

Method Summary

FeatureSetI	createFP()
void	errorCheck()
java.lang.String	getProgram()
java.lang.String	load(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
boolean	recognizedInput()

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

BlatParser

public BlatParser()

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

recognizedInput

public boolean recognizedInput()

Specified by:

recognizedInput in class AbstractParser

createFP

public FeatureSetI createFP()

errorCheck

public void errorCheck()