apollo.dataadapter.analysis
Class AlignmentParser

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

All Implemented Interfaces:

AnalysisParserI

Direct Known Subclasses:

BlastParser, BlatParser, Sim4Parser

public abstract class AlignmentParser
extends AbstractParser

Field Summary

protected java.lang.String	align_seq
protected java.lang.String	coord_seq
protected static org.apache.log4j.Logger	logger

Constructor Summary

AlignmentParser()

Method Summary

protected void	addAlignPair(FeaturePairI span, FeatureSetI hit)
protected FeatureSetI	initAlignment(SequenceI aligned_seq, int strand)
protected FeaturePairI	initAlignPair()
java.lang.String	load(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
protected void	rollCigar(FeaturePairI span)

Methods inherited from class apollo.dataadapter.analysis.AbstractParser

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

coord_seq

protected java.lang.String coord_seq

align_seq

protected java.lang.String align_seq

Constructor Detail

AlignmentParser

public AlignmentParser()

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

addAlignPair

protected void addAlignPair(FeaturePairI span,
                            FeatureSetI hit)

rollCigar

protected void rollCigar(FeaturePairI span)

initAlignment

protected FeatureSetI initAlignment(SequenceI aligned_seq,
                                    int strand)

initAlignPair

protected FeaturePairI initAlignPair()