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

Class AbstractInteractionLineParser<T extends Interaction,P extends Participant,F extends Feature>

java.lang.Object

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

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

All Implemented Interfaces:

MitabLineParserConstants

Direct Known Subclasses:

AbstractInteractionEvidenceLineParser, AbstractLightInteractionLineParser, AbstractModelledInteractionLineParser

public abstract class AbstractInteractionLineParser<T extends Interaction,P extends Participant,F extends Feature>
extends MitabLineParser<T,P,F>

Abstract mitab line parser

Since:

20/06/13

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

Method Summary

Modifier and Type	Method	Description
protected void	createAliasFromAltId(Interactor interactor, MitabXref ref)	createAliasFromAltId.
protected void	createChecksumFromAlias(Interactor interactor, MitabAlias alias)	createChecksumFromAlias.
protected void	createChecksumFromAltId(Interactor interactor, MitabXref ref)	createChecksumFromAltId.
protected void	createChecksumFromId(Interaction interaction, MitabXref ref)	createChecksumFromId.
protected abstract T	createInteraction()	createInteraction.
protected Interactor	createInteractorFrom(Collection<MitabXref> uniqueId, Collection<MitabXref> altid, Collection<MitabAlias> aliases, Collection<MitabOrganism> taxid, Collection<MitabCvTerm> type, Collection<MitabXref> xref, Collection<MitabChecksum> checksum, int line, int column, int mitabColumn)	createInteractorFrom.
protected void	fillInteractorWithAliases(Collection<MitabAlias> aliases, Interactor interactor)	fillInteractorWithAliases.
protected void	fillInteractorWithAlternativeIdentifiers(Collection<MitabXref> altid, Interactor interactor)	fillInteractorWithAlternativeIdentifiers.
protected String[]	findInteractorShortNameAndFullNameFrom(Collection<MitabXref> uniqueId, Collection<MitabXref> altid, Collection<MitabAlias> aliases, int line, int column, int mitabColumn)	findInteractorShortNameAndFullNameFrom.
InteractorFactory	getInteractorFactory()	Getter for the field interactorFactory.
MitabParserListener	getParserListener()
boolean	hasFinished()	hasFinished.
protected void	initialiseExpansionMethod(Collection<MitabCvTerm> expansion, T interaction)	initialiseExpansionMethod.
protected void	initialiseInteractionIdentifiers(Collection<MitabXref> interactionIds, T interaction)	initialiseInteractionIdentifiers.
protected void	initialiseOrganism(Collection<MitabOrganism> organisms, Interactor interactor)	initialiseOrganism.
protected void	processInteractorPool(Collection<MitabXref> xref, InteractorPool interactor)	processInteractorPool.
protected void	processTextFor(MitabFeature feature, String text)	processTextFor.
void	ReInit(InputStream stream)	Reinitialise.
void	ReInit(InputStream stream, String encoding)	Reinitialise.
void	ReInit(Reader stream)	Reinitialise.
void	ReInit(MitabLineParserTokenManager tm)	Reinitialise.
void	setInteractorFactory(InteractorFactory interactorFactory)	Setter for the field interactorFactory.
void	setParserListener(MitabParserListener listener)

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

AbstractInteractionLineParser

public AbstractInteractionLineParser(InputStream stream)

Constructor for AbstractInteractionLineParser.

Parameters:

stream - a InputStream object.

AbstractInteractionLineParser

public AbstractInteractionLineParser(InputStream stream,
                                     String encoding)

Constructor for AbstractInteractionLineParser.

Parameters:

stream - a InputStream object.

encoding - a String object.

AbstractInteractionLineParser

public AbstractInteractionLineParser(Reader stream)

Constructor for AbstractInteractionLineParser.

Parameters:

stream - a Reader object.

AbstractInteractionLineParser

public AbstractInteractionLineParser(MitabLineParserTokenManager tm)

Constructor for AbstractInteractionLineParser.

Parameters:

tm - a MitabLineParserTokenManager object.

Method Detail

getParserListener

public MitabParserListener getParserListener()

Specified by:

getParserListener in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

setParserListener

public void setParserListener(MitabParserListener listener)

Specified by:

setParserListener in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

getInteractorFactory

public InteractorFactory getInteractorFactory()

Getter for the field interactorFactory.

Returns:

a InteractorFactory object.

setInteractorFactory

public void setInteractorFactory(InteractorFactory interactorFactory)

Setter for the field interactorFactory.

Parameters:

interactorFactory - a InteractorFactory object.

ReInit

public void ReInit(InputStream stream)

Reinitialise.

Overrides:

ReInit in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

Parameters:

stream - a InputStream object.

ReInit

public void ReInit(InputStream stream,
                   String encoding)

Reinitialise.

Overrides:

ReInit in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

Parameters:

stream - a InputStream object.

encoding - a String object.

ReInit

public void ReInit(Reader stream)

Reinitialise.

Overrides:

ReInit in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

Parameters:

stream - a InputStream object.

ReInit

public void ReInit(MitabLineParserTokenManager tm)

Reinitialise.

Overrides:

ReInit in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

Parameters:

tm - a MitabLineParserTokenManager object.

hasFinished

public boolean hasFinished()

hasFinished.

Specified by:

hasFinished in class MitabLineParser<T extends Interaction,P extends Participant,F extends Feature>

Returns:

a boolean.

initialiseInteractionIdentifiers

protected void initialiseInteractionIdentifiers(Collection<MitabXref> interactionIds,
                                                T interaction)

initialiseInteractionIdentifiers.

Parameters:

interactionIds - a Collection object.

interaction - a T object.

createInteractorFrom

protected Interactor createInteractorFrom(Collection<MitabXref> uniqueId,
                                          Collection<MitabXref> altid,
                                          Collection<MitabAlias> aliases,
                                          Collection<MitabOrganism> taxid,
                                          Collection<MitabCvTerm> type,
                                          Collection<MitabXref> xref,
                                          Collection<MitabChecksum> checksum,
                                          int line,
                                          int column,
                                          int mitabColumn)

createInteractorFrom.

Parameters:

uniqueId - a Collection object.

altid - a Collection object.

aliases - a Collection object.

taxid - a Collection object.

type - a Collection object.

xref - a Collection object.

checksum - a Collection object.

line - a int.

column - a int.

mitabColumn - a int.

Returns:

a Interactor object.

processInteractorPool

protected void processInteractorPool(Collection<MitabXref> xref,
                                     InteractorPool interactor)

processInteractorPool.

Parameters:

xref - a Collection object.

interactor - a InteractorPool object.

findInteractorShortNameAndFullNameFrom

protected String[] findInteractorShortNameAndFullNameFrom(Collection<MitabXref> uniqueId,
                                                          Collection<MitabXref> altid,
                                                          Collection<MitabAlias> aliases,
                                                          int line,
                                                          int column,
                                                          int mitabColumn)

findInteractorShortNameAndFullNameFrom.

Parameters:

uniqueId - a Collection object.

altid - a Collection object.

aliases - a Collection object.

line - a int.

column - a int.

mitabColumn - a int.

Returns:

an array of String objects.

fillInteractorWithAlternativeIdentifiers

protected void fillInteractorWithAlternativeIdentifiers(Collection<MitabXref> altid,
                                                        Interactor interactor)

fillInteractorWithAlternativeIdentifiers.

Parameters:

altid - a Collection object.

interactor - a Interactor object.

fillInteractorWithAliases

protected void fillInteractorWithAliases(Collection<MitabAlias> aliases,
                                         Interactor interactor)

fillInteractorWithAliases.

Parameters:

aliases - a Collection object.

interactor - a Interactor object.

initialiseOrganism

protected void initialiseOrganism(Collection<MitabOrganism> organisms,
                                  Interactor interactor)

initialiseOrganism.

Parameters:

organisms - a Collection object.

interactor - a Interactor object.

createChecksumFromId

protected void createChecksumFromId(Interaction interaction,
                                    MitabXref ref)

createChecksumFromId.

Parameters:

interaction - a Interaction object.

ref - a MitabXref object.

createChecksumFromAltId

protected void createChecksumFromAltId(Interactor interactor,
                                       MitabXref ref)

createChecksumFromAltId.

Parameters:

interactor - a Interactor object.

ref - a MitabXref object.

createAliasFromAltId

protected void createAliasFromAltId(Interactor interactor,
                                    MitabXref ref)

createAliasFromAltId.

Parameters:

interactor - a Interactor object.

ref - a MitabXref object.

createChecksumFromAlias

protected void createChecksumFromAlias(Interactor interactor,
                                       MitabAlias alias)

createChecksumFromAlias.

Parameters:

interactor - a Interactor object.

alias - a MitabAlias object.

initialiseExpansionMethod

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

initialiseExpansionMethod.

Parameters:

expansion - a Collection object.

interaction - a T object.

createInteraction

protected abstract T createInteraction()

createInteraction.

Returns:

a T object.

processTextFor

protected void processTextFor(MitabFeature feature,
                              String text)

processTextFor.

Parameters:

feature - a MitabFeature object.

text - a String object.