apollo.dataadapter.analysis
Class AbstractParser

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

All Implemented Interfaces:

AnalysisParserI

Direct Known Subclasses:

AlignmentParser, GeneFinderParser, RpMaskerParser, tRNA_Parser

public abstract class AbstractParser
extends java.lang.Object
implements AnalysisParserI

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

AbstractParser()

Method Summary

protected java.lang.String	getAnalysisType()
abstract java.lang.String	getProgram()
protected FeatureSetI	initAnalysis(StrandedFeatureSetI analyses, int strand, java.lang.String type)
protected void	initCuration(CurationSet curation, SequenceI focal_seq)
protected SeqFeatureI	initFeature()
protected void	initLoad(CurationSet curation, boolean new_curation, java.io.InputStream data_stream, AnalysisInput input)
protected SequenceI	initSequence(CurationSet curation, java.lang.String header, int length)
protected FeatureSetI	initSet(java.lang.String id, int strand)
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 int	parseInteger(java.util.StringTokenizer tokens, java.lang.String msg)
protected java.lang.String	parseToken(java.util.StringTokenizer tokens, java.lang.String msg)
protected void	readLine()
abstract boolean	recognizedInput()
protected void	setHitScore(FeatureSetI hit, SeqFeatureI span)

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

AbstractParser

public AbstractParser()

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

recognizedInput

public abstract boolean recognizedInput()

getProgram

public abstract java.lang.String getProgram()

setHitScore

protected void setHitScore(FeatureSetI hit,
                           SeqFeatureI span)

initSequence

protected SequenceI initSequence(CurationSet curation,
                                 java.lang.String header,
                                 int length)

initSet

protected FeatureSetI initSet(java.lang.String id,
                              int strand)

getAnalysisType

protected java.lang.String getAnalysisType()

initAnalysis

protected FeatureSetI initAnalysis(StrandedFeatureSetI analyses,
                                   int strand,
                                   java.lang.String type)

initFeature

protected SeqFeatureI initFeature()

initCuration

protected void initCuration(CurationSet curation,
                            SequenceI focal_seq)

initLoad

protected void initLoad(CurationSet curation,
                        boolean new_curation,
                        java.io.InputStream data_stream,
                        AnalysisInput input)

readLine

protected void readLine()
                 throws java.text.ParseException

Throws:

java.text.ParseException

parseToken

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

parseInteger

protected int parseInteger(java.util.StringTokenizer tokens,
                           java.lang.String msg)

parseDouble

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