Package psidev.psi.mi.jami.xml.model.extension.binary

Class AbstractXmlBinaryInteraction<P extends Participant>

java.lang.Object

psidev.psi.mi.jami.model.impl.AbstractInteraction<T>

psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction<P>

psidev.psi.mi.jami.xml.model.extension.binary.AbstractXmlBinaryInteraction<P>

All Implemented Interfaces:

BinaryInteraction<P>, FileSourceContext, Interaction<P>, NamedInteraction<P>, PsiXmlInteraction<P>

Direct Known Subclasses:

XmlModelledBinaryInteraction

public abstract class AbstractXmlBinaryInteraction<P extends Participant>
extends AbstractBinaryInteraction<P>
implements PsiXmlInteraction<P>, FileSourceContext

Abstract class for xml binary interactions

Since:

29/10/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractXmlBinaryInteraction()	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, P participantA, P participantB)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, CvTerm type)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(P participantA, P participantB)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractXmlBinaryInteraction.
AbstractXmlBinaryInteraction(CvTerm complexExpansion)	Constructor for AbstractXmlBinaryInteraction.

Method Summary

Modifier and Type	Method	Description
Collection<Alias>	getAliases()	getAliases.
Entry	getEntry()	getEntry.
String	getFullName()	The full name of the interaction.
int	getId()	getId.
FileSourceLocator	getSourceLocator()	Getter for the field sourceLocator.
boolean	isIntraMolecular()	isIntraMolecular.
void	setEntry(Entry entry)	setEntry.
void	setFullName(String name)	Sets the full name of the interaction
void	setId(int id)	setId.
void	setIntraMolecular(boolean value)	setIntraMolecular.
void	setSourceLocator(FileSourceLocator sourceLocator)	Sets the source locator
String	toString()

Methods inherited from class psidev.psi.mi.jami.binary.impl.AbstractBinaryInteraction

addAllParticipants, addParticipant, getCausalRegulatoryMechanism, getComplexExpansion, getParticipantA, getParticipantB, getParticipants, removeAllParticipants, removeParticipant, setCausalRegulatoryMechanism, setComplexExpansion, setParticipantA, setParticipantB

Methods inherited from class psidev.psi.mi.jami.model.impl.AbstractInteraction

clearPropertiesLinkedToChecksums, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefs, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface psidev.psi.mi.jami.model.Interaction

addAllParticipants, addParticipant, getAnnotations, getChecksums, getCreatedDate, getIdentifiers, getInteractionType, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, removeAllParticipants, removeParticipant, setCreatedDate, setInteractionType, setRigid, setShortName, setUpdatedDate

Constructor Detail

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction()

Constructor for AbstractXmlBinaryInteraction.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    CvTerm type)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(P participantA,
                                    P participantB)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

participantA - a P object.

participantB - a P object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    P participantA,
                                    P participantB)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a P object.

participantB - a P object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    CvTerm type,
                                    P participantA,
                                    P participantB)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a P object.

participantB - a P object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    CvTerm type,
                                    CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(P participantA,
                                    P participantB,
                                    CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

participantA - a P object.

participantB - a P object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    P participantA,
                                    P participantB,
                                    CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a P object.

participantB - a P object.

complexExpansion - a CvTerm object.

AbstractXmlBinaryInteraction

public AbstractXmlBinaryInteraction(String shortName,
                                    CvTerm type,
                                    P participantA,
                                    P participantB,
                                    CvTerm complexExpansion)

Constructor for AbstractXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a P object.

participantB - a P object.

complexExpansion - a CvTerm object.

Method Detail

getSourceLocator

public FileSourceLocator getSourceLocator()

Getter for the field sourceLocator.

Specified by:

getSourceLocator in interface FileSourceContext

Returns:

a FileSourceLocator object.

setSourceLocator

public void setSourceLocator(FileSourceLocator sourceLocator)

Sets the source locator

Specified by:

setSourceLocator in interface FileSourceContext

Parameters:

sourceLocator - : the file locator

isIntraMolecular

public boolean isIntraMolecular()

isIntraMolecular.

Specified by:

isIntraMolecular in interface PsiXmlInteraction<P extends Participant>

Returns:

a boolean.

setIntraMolecular

public void setIntraMolecular(boolean value)

setIntraMolecular.

Sets the value of the intraMolecular property.

Specified by:

setIntraMolecular in interface PsiXmlInteraction<P extends Participant>

Parameters:

value - a boolean.

getFullName

public String getFullName()

The full name of the interaction. It can be null

Specified by:

getFullName in interface NamedInteraction<P extends Participant>

Returns:

the full name

setFullName

public void setFullName(String name)

Sets the full name of the interaction

Specified by:

setFullName in interface NamedInteraction<P extends Participant>

Parameters:

name - : full name

getAliases

public Collection<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface NamedInteraction<P extends Participant>

Specified by:

getAliases in interface PsiXmlInteraction<P extends Participant>

Returns:

a Collection object.

getEntry

public Entry getEntry()

getEntry.

Specified by:

getEntry in interface PsiXmlInteraction<P extends Participant>

Returns:

a Entry object.

setEntry

public void setEntry(Entry entry)

setEntry.

Specified by:

setEntry in interface PsiXmlInteraction<P extends Participant>

Parameters:

entry - a Entry object.

getId

public int getId()

getId.

Specified by:

getId in interface PsiXmlInteraction<P extends Participant>

Returns:

a int.

setId

public void setId(int id)

setId.

Specified by:

setId in interface PsiXmlInteraction<P extends Participant>

Parameters:

id - a int.

toString

public String toString()

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractBinaryInteraction<P extends Participant>

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties