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

Class ModelledBinaryLineParser

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<ModelledBinaryInteraction>

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

All Implemented Interfaces:

MitabLineParserConstants

public class ModelledBinaryLineParser
extends AbstractModelledInteractionLineParser<ModelledBinaryInteraction>

An extension of MitabLineParser which parses only ModelledBinaryInteraction

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

Method Summary

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

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

ModelledBinaryLineParser

public ModelledBinaryLineParser(InputStream stream)

Constructor for ModelledBinaryLineParser.

Parameters:

stream - a InputStream object.

ModelledBinaryLineParser

public ModelledBinaryLineParser(InputStream stream,
                                String encoding)

Constructor for ModelledBinaryLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

ModelledBinaryLineParser

public ModelledBinaryLineParser(Reader stream)

Constructor for ModelledBinaryLineParser.

Parameters:

stream - a Reader object.

ModelledBinaryLineParser

public ModelledBinaryLineParser(MitabLineParserTokenManager tm)

Constructor for ModelledBinaryLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

createInteraction

protected MitabModelledBinaryInteraction createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractInteractionLineParser<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Returns:

a T object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Overrides:

initialiseExpansionMethod in class AbstractInteractionLineParser<ModelledBinaryInteraction,ModelledParticipant,ModelledFeature>

Parameters:

expansion - a Collection object.

interaction - a T object.