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

Class InteractionLineParser

java.lang.Object

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

psidev.psi.mi.jami.tab.io.parser.AbstractInteractionLineParser<T,Participant,Feature>

psidev.psi.mi.jami.tab.io.parser.AbstractLightInteractionLineParser<Interaction>

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

All Implemented Interfaces:

MitabLineParserConstants

public class InteractionLineParser
extends AbstractLightInteractionLineParser<Interaction>

An extension of MitabLineParser that returns simple interactions only. It ignore properties of InteractionEvidence and ModelledInteraction

Since:

20/06/13

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

Method Summary

Modifier and Type	Method	Description
protected void	addParticipant(Participant participant, Interaction interaction)	addParticipant.
protected Interaction	createInteraction()	createInteraction.

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

InteractionLineParser

public InteractionLineParser(InputStream stream)

Constructor for InteractionLineParser.

Parameters:

stream - a InputStream object.

InteractionLineParser

public InteractionLineParser(InputStream stream,
                             String encoding)

Constructor for InteractionLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

InteractionLineParser

public InteractionLineParser(Reader stream)

Constructor for InteractionLineParser.

Parameters:

stream - a Reader object.

InteractionLineParser

public InteractionLineParser(MitabLineParserTokenManager tm)

Constructor for InteractionLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

addParticipant

protected void addParticipant(Participant participant,
                              Interaction interaction)

addParticipant.

Specified by:

addParticipant in class AbstractLightInteractionLineParser<Interaction>

Parameters:

participant - a Participant object.

interaction - a T object.

createInteraction

protected Interaction createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractLightInteractionLineParser<Interaction>

Returns:

a T object.