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

Class AbstractExtendedXmlBinaryInteraction<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.AbstractExtendedXmlBinaryInteraction<P>

All Implemented Interfaces:

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

Direct Known Subclasses:

AbstractXmlBinaryInteractionEvidence, XmlBinaryInteraction, XmlModelledBinaryInteraction

public abstract class AbstractExtendedXmlBinaryInteraction<P extends Participant>
extends AbstractBinaryInteraction<P>
implements ExtendedPsiXmlInteraction<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
AbstractExtendedXmlBinaryInteraction()	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, P participantA, P participantB)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(String shortName, CvTerm type, CvTerm complexExpansion)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(P participantA, P participantB)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(P participantA, P participantB, CvTerm complexExpansion)	Constructor for AbstractExtendedXmlBinaryInteraction.
AbstractExtendedXmlBinaryInteraction(CvTerm complexExpansion)	Constructor for AbstractExtendedXmlBinaryInteraction.

Method Summary

Modifier and Type	Method	Description
List<Alias>	getAliases()	getAliases.
Entry	getEntry()	getEntry.
String	getFullName()	The full name of the interaction.
int	getId()	getId.
List<AbstractInferredInteraction>	getInferredInteractions()	getInferredInteractions.
CvTerm	getInteractionType()	Getter for the field interactionType.
List<CvTerm>	getInteractionTypes()	getInteractionTypes.
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	setInteractionType(CvTerm term)	Sets the interaction type.
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, getRigid, getShortName, getUpdatedDate, getXrefs, initialiseAnnotations, initialiseAnnotationsWith, initialiseChecksums, initialiseChecksumWith, initialiseIdentifiers, initialiseIdentifiersWith, initialiseParticipants, initialiseParticipantsWith, initialiseXrefs, initialiseXrefsWith, processAddedChecksumEvent, processRemovedChecksumEvent, setCreatedDate, 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, getParticipants, getRigid, getShortName, getUpdatedDate, getXrefs, removeAllParticipants, removeParticipant, setCreatedDate, setRigid, setShortName, setUpdatedDate

Constructor Detail

AbstractExtendedXmlBinaryInteraction

public AbstractExtendedXmlBinaryInteraction()

Constructor for AbstractExtendedXmlBinaryInteraction.

AbstractExtendedXmlBinaryInteraction

public AbstractExtendedXmlBinaryInteraction(String shortName)

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

AbstractExtendedXmlBinaryInteraction

public AbstractExtendedXmlBinaryInteraction(String shortName,
                                            CvTerm type)

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

AbstractExtendedXmlBinaryInteraction

public AbstractExtendedXmlBinaryInteraction(P participantA,
                                            P participantB)

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

participantA - a P object.

participantB - a P object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a P object.

participantB - a P object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

participantA - a P object.

participantB - a P object.

AbstractExtendedXmlBinaryInteraction

public AbstractExtendedXmlBinaryInteraction(CvTerm complexExpansion)

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

complexExpansion - a CvTerm object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

type - a CvTerm object.

complexExpansion - a CvTerm object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

participantA - a P object.

participantB - a P object.

complexExpansion - a CvTerm object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

Parameters:

shortName - a String object.

participantA - a P object.

participantB - a P object.

complexExpansion - a CvTerm object.

AbstractExtendedXmlBinaryInteraction

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

Constructor for AbstractExtendedXmlBinaryInteraction.

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 List<Alias> getAliases()

getAliases.

Specified by:

getAliases in interface ExtendedPsiXmlInteraction<P extends Participant>

Specified by:

getAliases in interface NamedInteraction<P extends Participant>

Specified by:

getAliases in interface PsiXmlInteraction<P extends Participant>

Returns:

a Collection object.

getInteractionType

public CvTerm getInteractionType()

Getter for the field interactionType.

Specified by:

getInteractionType in interface Interaction<P extends Participant>

Overrides:

getInteractionType in class AbstractInteraction<P extends Participant>

Returns:

a CvTerm object.

setInteractionType

public void setInteractionType(CvTerm term)

Sets the interaction type.

Specified by:

setInteractionType in interface Interaction<P extends Participant>

Overrides:

setInteractionType in class AbstractInteraction<P extends Participant>

Parameters:

term - : interaction type

getInteractionTypes

public List<CvTerm> getInteractionTypes()

getInteractionTypes.

Specified by:

getInteractionTypes in interface ExtendedPsiXmlInteraction<P extends Participant>

Returns:

a List 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.

getInferredInteractions

public List<AbstractInferredInteraction> getInferredInteractions()

getInferredInteractions.

Specified by:

getInferredInteractions in interface ExtendedPsiXmlInteraction<P extends Participant>

Returns:

a List 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