Package psidev.psi.mi.jami.tab.io.parser

Class BinaryEvidenceLineParser

java.lang.Object

psidev.psi.mi.jami.tab.io.parser.MitabLineParser<T,P,F>

psidev.psi.mi.jami.tab.io.parser.AbstractInteractionLineParser<T,ParticipantEvidence,FeatureEvidence>

psidev.psi.mi.jami.tab.io.parser.AbstractInteractionEvidenceLineParser<BinaryInteractionEvidence>

psidev.psi.mi.jami.tab.io.parser.BinaryEvidenceLineParser

All Implemented Interfaces:

MitabLineParserConstants

public class BinaryEvidenceLineParser
extends AbstractInteractionEvidenceLineParser<BinaryInteractionEvidence>

An extension of MitabLineParser that returns binary interactions evidences only.

Since:

04/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.tab.io.parser.MitabLineParser

jj_nt, token, token_source

Fields inherited from interface psidev.psi.mi.jami.tab.io.parser.MitabLineParserConstants

CLOSE_PAREN, COLON, COLUMN_SEPARATOR, COMMENT, DASH, DEFAULT, EOF, FIELD_SEPARATOR, LINE_SEPARATOR, OPEN_PAREN, QUOTED_STRING, RANGE_SEPARATOR, tokenImage, UNRESERVED_STRING

Constructor Summary

Constructors

Constructor	Description
BinaryEvidenceLineParser(InputStream stream)	Constructor for BinaryEvidenceLineParser.
BinaryEvidenceLineParser(InputStream stream, String encoding)	Constructor for BinaryEvidenceLineParser.
BinaryEvidenceLineParser(Reader stream)	Constructor for BinaryEvidenceLineParser.
BinaryEvidenceLineParser(MitabLineParserTokenManager tm)	Constructor for BinaryEvidenceLineParser.

Method Summary

Modifier and Type	Method	Description
protected MitabBinaryInteractionEvidence	createInteraction()	createInteraction.
protected void	initialiseExpansionMethod(Collection<MitabCvTerm> expansion, BinaryInteractionEvidence interaction)	initialiseExpansionMethod.

Methods inherited from class psidev.psi.mi.jami.tab.io.parser.AbstractInteractionEvidenceLineParser

createExperimentFrom, createPublicationFrom, initialiseAuthorAndPublicationDate, initialiseHostOrganism, initialiseInteractionAnnotations, initialisePublicationIdentifiers

Methods inherited from class psidev.psi.mi.jami.tab.io.parser.AbstractInteractionLineParser

createAliasFromAltId, createChecksumFromAlias, createChecksumFromAltId, createChecksumFromId, createInteractorFrom, fillInteractorWithAliases, fillInteractorWithAlternativeIdentifiers, findInteractorShortNameAndFullNameFrom, getInteractorFactory, getParserListener, hasFinished, initialiseInteractionIdentifiers, initialiseOrganism, processInteractorPool, processTextFor, ReInit, ReInit, ReInit, ReInit, setInteractorFactory, setParserListener

Methods inherited from class psidev.psi.mi.jami.tab.io.parser.MitabLineParser

alias, aliases, annotation, annotations, author, checksum, checksums, complexExpansion, confidence, confidences, cvTerm, cvTerms, date, dates, disable_tracing, enable_tracing, expansion, feature, features, firstAuthors, generateParseException, getNextToken, getToken, id, ids, MitabLine, negative, organism, parameter, parameters, range, safeFreeText, safePosition, safeStoichiometry, safeString, source, sourceDbs, stoichiometry, stoichiometryList, taxId

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BinaryEvidenceLineParser

public BinaryEvidenceLineParser(InputStream stream)

Constructor for BinaryEvidenceLineParser.

Parameters:

stream - a InputStream object.

BinaryEvidenceLineParser

public BinaryEvidenceLineParser(InputStream stream,
                                String encoding)

Constructor for BinaryEvidenceLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

BinaryEvidenceLineParser

public BinaryEvidenceLineParser(Reader stream)

Constructor for BinaryEvidenceLineParser.

Parameters:

stream - a Reader object.

BinaryEvidenceLineParser

public BinaryEvidenceLineParser(MitabLineParserTokenManager tm)

Constructor for BinaryEvidenceLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

createInteraction

protected MitabBinaryInteractionEvidence createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractInteractionLineParser<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Returns:

a T object.

initialiseExpansionMethod

protected void initialiseExpansionMethod(Collection<MitabCvTerm> expansion,
                                         BinaryInteractionEvidence interaction)

initialiseExpansionMethod.

Overrides:

initialiseExpansionMethod in class AbstractInteractionLineParser<BinaryInteractionEvidence,ParticipantEvidence,FeatureEvidence>

Parameters:

expansion - a Collection object.

interaction - a T object.