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

Class BinaryLineParser

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<BinaryInteraction>

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

All Implemented Interfaces:

MitabLineParserConstants

public class BinaryLineParser
extends AbstractLightInteractionLineParser<BinaryInteraction>

An extension of MitabLineParser that returns simple binary interactions only. It ignore properties of BinaryInteractionEvidence and 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
BinaryLineParser(InputStream stream)	Constructor for BinaryLineParser.
BinaryLineParser(InputStream stream, String encoding)	Constructor for BinaryLineParser.
BinaryLineParser(Reader stream)	Constructor for BinaryLineParser.
BinaryLineParser(MitabLineParserTokenManager tm)	Constructor for BinaryLineParser.

Method Summary

Modifier and Type	Method	Description
protected void	addParticipant(Participant participant, BinaryInteraction interaction)	addParticipant.
protected MitabBinaryInteraction	createInteraction()	createInteraction.
protected void	initialiseExpansionMethod(Collection<MitabCvTerm> expansion, BinaryInteraction 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

BinaryLineParser

public BinaryLineParser(InputStream stream)

Constructor for BinaryLineParser.

Parameters:

stream - a InputStream object.

BinaryLineParser

public BinaryLineParser(InputStream stream,
                        String encoding)

Constructor for BinaryLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

BinaryLineParser

public BinaryLineParser(Reader stream)

Constructor for BinaryLineParser.

Parameters:

stream - a Reader object.

BinaryLineParser

public BinaryLineParser(MitabLineParserTokenManager tm)

Constructor for BinaryLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

createInteraction

protected MitabBinaryInteraction createInteraction()

createInteraction.

Specified by:

createInteraction in class AbstractLightInteractionLineParser<BinaryInteraction>

Returns:

a T object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Overrides:

initialiseExpansionMethod in class AbstractInteractionLineParser<BinaryInteraction,Participant,Feature>

Parameters:

expansion - a Collection object.

interaction - a T object.

addParticipant

protected void addParticipant(Participant participant,
                              BinaryInteraction interaction)

addParticipant.

Specified by:

addParticipant in class AbstractLightInteractionLineParser<BinaryInteraction>

Parameters:

participant - a Participant object.

interaction - a T object.