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

Class AbstractModelledInteractionLineParser<T extends ModelledInteraction>

java.lang.Object

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

psidev.psi.mi.jami.tab.io.parser.AbstractInteractionLineParser<T,ModelledParticipant,ModelledFeature>

psidev.psi.mi.jami.tab.io.parser.AbstractModelledInteractionLineParser<T>

All Implemented Interfaces:

MitabLineParserConstants

Direct Known Subclasses:

ModelledBinaryLineParser, ModelledInteractionLineParser

public abstract class AbstractModelledInteractionLineParser<T extends ModelledInteraction>
extends AbstractInteractionLineParser<T,ModelledParticipant,ModelledFeature>

Abstract class for ModelledInteraction line 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
AbstractModelledInteractionLineParser(InputStream stream)	Constructor for AbstractModelledInteractionLineParser.
AbstractModelledInteractionLineParser(InputStream stream, String encoding)	Constructor for AbstractModelledInteractionLineParser.
AbstractModelledInteractionLineParser(Reader stream)	Constructor for AbstractModelledInteractionLineParser.
AbstractModelledInteractionLineParser(MitabLineParserTokenManager tm)	Constructor for AbstractModelledInteractionLineParser.

Method Summary

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

createAliasFromAltId, createChecksumFromAlias, createChecksumFromAltId, createChecksumFromId, createInteraction, 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

AbstractModelledInteractionLineParser

public AbstractModelledInteractionLineParser(InputStream stream)

Constructor for AbstractModelledInteractionLineParser.

Parameters:

stream - a InputStream object.

AbstractModelledInteractionLineParser

public AbstractModelledInteractionLineParser(InputStream stream,
                                             String encoding)

Constructor for AbstractModelledInteractionLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

AbstractModelledInteractionLineParser

public AbstractModelledInteractionLineParser(Reader stream)

Constructor for AbstractModelledInteractionLineParser.

Parameters:

stream - a Reader object.

AbstractModelledInteractionLineParser

public AbstractModelledInteractionLineParser(MitabLineParserTokenManager tm)

Constructor for AbstractModelledInteractionLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.