apollo.dataadapter.analysis
Class Sim4Parser

java.lang.Object
  apollo.dataadapter.analysis.AbstractParser
      apollo.dataadapter.analysis.AlignmentParser
          apollo.dataadapter.analysis.Sim4Parser

All Implemented Interfaces:

AnalysisParserI

public class Sim4Parser
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

Sim4Parser()

Method Summary

java.lang.String	debugName(SeqFeatureI sf)
void	extendWith(SeqFeatureI to, SeqFeatureI from)
java.lang.String	getProgram()
protected FeaturePairI	grabAlignment(int seq_length, FeatureSetI match, FeaturePairI prev_span)
protected java.lang.String	grabDatabase()
java.lang.String	load(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
protected int	parseLength(java.lang.String line)
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

Sim4Parser

public Sim4Parser()

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

parseLength

protected int parseLength(java.lang.String line)
                   throws java.text.ParseException

Throws:

java.text.ParseException

grabDatabase

protected java.lang.String grabDatabase()

grabAlignment

protected FeaturePairI grabAlignment(int seq_length,
                                     FeatureSetI match,
                                     FeaturePairI prev_span)
                              throws java.text.ParseException

Throws:

java.text.ParseException

extendWith

public void extendWith(SeqFeatureI to,
                       SeqFeatureI from)

debugName

public java.lang.String debugName(SeqFeatureI sf)