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

Class InteractionEvidenceLineParser

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<InteractionEvidence>

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

All Implemented Interfaces:

MitabLineParserConstants

public class InteractionEvidenceLineParser
extends AbstractInteractionEvidenceLineParser<InteractionEvidence>

An extension of MitabLineParser that returns interactions evidences only.

Since:

18/06/13

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

Method Summary

Modifier and Type	Method	Description
protected InteractionEvidence	createInteraction()	createInteraction.

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, initialiseExpansionMethod, 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

InteractionEvidenceLineParser

public InteractionEvidenceLineParser(InputStream stream)

Constructor for InteractionEvidenceLineParser.

Parameters:

stream - a InputStream object.

InteractionEvidenceLineParser

public InteractionEvidenceLineParser(InputStream stream,
                                     String encoding)

Constructor for InteractionEvidenceLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

InteractionEvidenceLineParser

public InteractionEvidenceLineParser(Reader stream)

Constructor for InteractionEvidenceLineParser.

Parameters:

stream - a Reader object.

InteractionEvidenceLineParser

public InteractionEvidenceLineParser(MitabLineParserTokenManager tm)

Constructor for InteractionEvidenceLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

createInteraction

protected InteractionEvidence createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractInteractionLineParser<InteractionEvidence,ParticipantEvidence,FeatureEvidence>

Returns:

a T object.