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

Class AbstractInteractionEvidenceLineParser<T extends InteractionEvidence>

java.lang.Object

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

psidev.psi.mi.jami.tab.io.parser.AbstractInteractionLineParser<T,ParticipantEvidence,FeatureEvidence>

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

All Implemented Interfaces:

MitabLineParserConstants

Direct Known Subclasses:

BinaryEvidenceLineParser, InteractionEvidenceLineParser

public abstract class AbstractInteractionEvidenceLineParser<T extends InteractionEvidence>
extends AbstractInteractionLineParser<T,ParticipantEvidence,FeatureEvidence>

Abstract class for Interaction evidence 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
AbstractInteractionEvidenceLineParser(InputStream stream)	Constructor for AbstractInteractionEvidenceLineParser.
AbstractInteractionEvidenceLineParser(InputStream stream, String encoding)	Constructor for AbstractInteractionEvidenceLineParser.
AbstractInteractionEvidenceLineParser(Reader stream)	Constructor for AbstractInteractionEvidenceLineParser.
AbstractInteractionEvidenceLineParser(MitabLineParserTokenManager tm)	Constructor for AbstractInteractionEvidenceLineParser.

Method Summary

Modifier and Type	Method	Description
protected MitabExperiment	createExperimentFrom(MitabPublication publication, Collection<MitabCvTerm> detMethod, Collection<MitabOrganism> host)	createExperimentFrom.
protected MitabPublication	createPublicationFrom(Collection<MitabAuthor> firstAuthor, Collection<MitabXref> pubId, Collection<MitabSource> source)	createPublicationFrom.
protected void	initialiseAuthorAndPublicationDate(MitabPublication publication, MitabAuthor author)	initialiseAuthorAndPublicationDate.
protected void	initialiseHostOrganism(Collection<MitabOrganism> organisms, MitabExperiment exp)	initialiseHostOrganism.
protected void	initialiseInteractionAnnotations(Collection<MitabAnnotation> annots, T interaction)	initialiseInteractionAnnotations.
protected boolean	initialisePublicationIdentifiers(Collection<MitabXref> pubId, MitabPublication publication, boolean hasInitialisedLocator)	initialisePublicationIdentifiers.

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

AbstractInteractionEvidenceLineParser

public AbstractInteractionEvidenceLineParser(InputStream stream)

Constructor for AbstractInteractionEvidenceLineParser.

Parameters:

stream - a InputStream object.

AbstractInteractionEvidenceLineParser

public AbstractInteractionEvidenceLineParser(InputStream stream,
                                             String encoding)

Constructor for AbstractInteractionEvidenceLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

AbstractInteractionEvidenceLineParser

public AbstractInteractionEvidenceLineParser(Reader stream)

Constructor for AbstractInteractionEvidenceLineParser.

Parameters:

stream - a Reader object.

AbstractInteractionEvidenceLineParser

public AbstractInteractionEvidenceLineParser(MitabLineParserTokenManager tm)

Constructor for AbstractInteractionEvidenceLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

initialiseInteractionAnnotations

protected void initialiseInteractionAnnotations(Collection<MitabAnnotation> annots,
                                                T interaction)

initialiseInteractionAnnotations.

Parameters:

annots - a Collection object.

interaction - a T object.

createExperimentFrom

protected MitabExperiment createExperimentFrom(MitabPublication publication,
                                               Collection<MitabCvTerm> detMethod,
                                               Collection<MitabOrganism> host)

createExperimentFrom.

Parameters:

publication - a MitabPublication object.

detMethod - a Collection object.

host - a Collection object.

Returns:

a MitabExperiment object.

initialiseHostOrganism

protected void initialiseHostOrganism(Collection<MitabOrganism> organisms,
                                      MitabExperiment exp)

initialiseHostOrganism.

Parameters:

organisms - a Collection object.

exp - a MitabExperiment object.

createPublicationFrom

protected MitabPublication createPublicationFrom(Collection<MitabAuthor> firstAuthor,
                                                 Collection<MitabXref> pubId,
                                                 Collection<MitabSource> source)

createPublicationFrom.

Parameters:

firstAuthor - a Collection object.

pubId - a Collection object.

source - a Collection object.

Returns:

a MitabPublication object.

initialisePublicationIdentifiers

protected boolean initialisePublicationIdentifiers(Collection<MitabXref> pubId,
                                                   MitabPublication publication,
                                                   boolean hasInitialisedLocator)

initialisePublicationIdentifiers.

Parameters:

pubId - a Collection object.

publication - a MitabPublication object.

hasInitialisedLocator - a boolean.

Returns:

a boolean.

initialiseAuthorAndPublicationDate

protected void initialiseAuthorAndPublicationDate(MitabPublication publication,
                                                  MitabAuthor author)

initialiseAuthorAndPublicationDate.

Parameters:

publication - a MitabPublication object.

author - a MitabAuthor object.