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

Class AbstractLightInteractionLineParser<T extends Interaction>

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<T>

All Implemented Interfaces:

MitabLineParserConstants

Direct Known Subclasses:

BinaryLineParser, InteractionLineParser

public abstract class AbstractLightInteractionLineParser<T extends Interaction>
extends AbstractInteractionLineParser<T,Participant,Feature>

Abstract class for InteractionLine parsers

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

Method Summary

Modifier and Type	Method	Description
protected abstract void	addParticipant(Participant participant, T interaction)	addParticipant.
protected abstract T	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

AbstractLightInteractionLineParser

public AbstractLightInteractionLineParser(InputStream stream)

Constructor for AbstractLightInteractionLineParser.

Parameters:

stream - a InputStream object.

AbstractLightInteractionLineParser

public AbstractLightInteractionLineParser(InputStream stream,
                                          String encoding)

Constructor for AbstractLightInteractionLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

AbstractLightInteractionLineParser

public AbstractLightInteractionLineParser(Reader stream)

Constructor for AbstractLightInteractionLineParser.

Parameters:

stream - a Reader object.

AbstractLightInteractionLineParser

public AbstractLightInteractionLineParser(MitabLineParserTokenManager tm)

Constructor for AbstractLightInteractionLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

addParticipant

protected abstract void addParticipant(Participant participant,
                                       T interaction)

addParticipant.

Parameters:

participant - a Participant object.

interaction - a T object.

createInteraction

protected abstract T createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractInteractionLineParser<T extends Interaction,Participant,Feature>

Returns:

a T object.