java.lang.Object
- psidev.psi.mi.jami.xml.model.extension.xml253.AbstractXmlInteraction<T>

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Interaction<T>, NamedInteraction<T>

Direct Known Subclasses:

AbstractPsiXmlInteraction
```
public abstract class AbstractXmlInteraction<T extends Participant>
extends Object
implements FileSourceContext, com.sun.xml.bind.Locatable, NamedInteraction<T>
```
Abstract class for xml interactions
Since:
```
09/07/13
```
Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`AbstractXmlInteraction.JAXBAttributeWrapper`
`static class`	`AbstractXmlInteraction.JAXBParticipantWrapper<T extends Participant>`

Constructor Summary

Constructors
Constructor	Description
`AbstractXmlInteraction()`	Constructor for AbstractXmlInteraction.
`AbstractXmlInteraction(String shortName)`	Constructor for AbstractXmlInteraction.
`AbstractXmlInteraction(String shortName, CvTerm type)`	Constructor for AbstractXmlInteraction.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`addAllParticipants(Collection<? extends T> participants)`	This method will add all the participant and set the interaction of the new participant to this current interaction
`boolean`	`addParticipant(T part)`	addParticipant.
`void`	`assignComplexAc(String value)`	Sets the value of the complexAc property
`void`	`assignImexId(String value)`	Sets the value of the imexId property
`List<Alias>`	`getAliases()`	Collection of aliases for an interaction.
`Collection<Annotation>`	`getAnnotations()`	getAnnotations.
`protected AbstractXmlInteraction.JAXBAttributeWrapper`	`getAttributeWrapper()`	getAttributeWrapper.
`Collection<Checksum>`	`getChecksums()`	getChecksums.
`String`	`getComplexAc()`	Gets the value of the complexAc property.
`String`	`getComplexVersion()`	Gets the value of the complexVersion property.
`Date`	`getCreatedDate()`	Getter for the field `createdDate`.
`Entry`	`getEntry()`	Getter for the field `entry`.
`String`	`getFullName()`	The full name of the interaction.
`int`	`getId()`	Gets the value of the id property.
`Collection<Xref>`	`getIdentifiers()`	getIdentifiers.
`String`	`getImexId()`	Gets the value of the imexId property.
`protected NamesContainer`	`getInteractionNamesContainer()`	Getter for the field `interactionNamesContainer`.
`abstract CvTerm`	`getInteractionType()`	getInteractionType.
`protected InteractionXrefContainer`	`getInteractionXrefContainer()`	getInteractionXrefContainer.
`Collection<T>`	`getParticipants()`	getParticipants.
`String`	`getRigid()`	getRigid.
`String`	`getShortName()`	getShortName.
`FileSourceLocator`	`getSourceLocator()`	Getter for the field `sourceLocator`.
`Date`	`getUpdatedDate()`	Getter for the field `updatedDate`.
`Collection<Xref>`	`getXrefs()`	getXrefs.
`protected void`	`initialiseAnnotationWrapper()`	initialiseAnnotationWrapper.
`protected void`	`initialiseNamesContainer()`	initialiseNamesContainer.
`protected void`	`initialiseParticipantWrapper()`	initialiseParticipantWrapper.
`boolean`	`isIntraMolecular()`	isIntraMolecular.
`protected void`	`processAddedParticipant(T participant)`	processAddedParticipant.
`boolean`	`removeAllParticipants(Collection<? extends T> participants)`	This method will remove the participant and set the interaction of the removed participant to null.
`boolean`	`removeParticipant(T part)`	removeParticipant.
`void`	`setCreatedDate(Date created)`	Sets the created date
`void`	`setEntry(Entry entry)`	Setter for the field `entry`.
`void`	`setFullName(String name)`	Sets the full name of the interaction
`void`	`setId(int value)`	Sets the value of the id property.
`void`	`setInteractionNamesContainer(NamesContainer value)`	Sets the value of the names property.
`abstract void`	`setInteractionType(CvTerm term)`	Sets the interaction type.
`void`	`setInteractionXrefContainer(InteractionXrefContainer value)`	Sets the value of the interactionXrefContainer property.
`void`	`setIntraMolecular(boolean value)`	Sets the value of the intraMolecular property.
`void`	`setJAXBAttributeWrapper(AbstractXmlInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)`	setJAXBAttributeWrapper.
`void`	`setParticipantWrapper(AbstractXmlInteraction.JAXBParticipantWrapper<T> jaxbParticipantWrapper)`	setParticipantWrapper.
`void`	`setRigid(String rigid)`	Sets the rigid of this interaction.
`void`	`setShortName(String name)`	Sets the short name of the interaction
`void`	`setSourceLocator(FileSourceLocator sourceLocator)`	Sets the source locator
`void`	`setUpdatedDate(Date updated)`	Sets the last update date
`Locator`	`sourceLocation()`
`String`	`toString()`	toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - AbstractXmlInteraction
```
public AbstractXmlInteraction()
```
    Constructor for AbstractXmlInteraction.
  - AbstractXmlInteraction
```
public AbstractXmlInteraction(String shortName)
```
    Constructor for AbstractXmlInteraction.
    
    Parameters:
    
    shortName - a String object.
  - AbstractXmlInteraction
```
public AbstractXmlInteraction(String shortName,
                              CvTerm type)
```
    Constructor for AbstractXmlInteraction.
    
    Parameters:
    
    shortName - a String object.
    
    type - a CvTerm object.
- Method Detail
  - getShortName
```
public String getShortName()
```
    getShortName.
    
    Specified by:
    
    getShortName in interface Interaction<T extends Participant>
    
    Returns:
    
    a String object.
  - setShortName
```
public void setShortName(String name)
```
    Sets the short name of the interaction
    
    Specified by:
    
    setShortName in interface Interaction<T extends Participant>
    
    Parameters:
    
    name - : short name
  - getAliases
```
public List<Alias> getAliases()
```
    Collection of aliases for an interaction. The Collection cannot be null and if the interaction does not have any aliases, the method should return an empty Collection.
    
    Specified by:
    
    getAliases in interface NamedInteraction<T extends Participant>
    
    Returns:
    
    the aliases
  - setFullName
```
public void setFullName(String name)
```
    Sets the full name of the interaction
    
    Specified by:
    
    setFullName in interface NamedInteraction<T extends Participant>
    
    Parameters:
    
    name - : full name
  - getFullName
```
public String getFullName()
```
    The full name of the interaction. It can be null
    
    Specified by:
    
    getFullName in interface NamedInteraction<T extends Participant>
    
    Returns:
    
    the full name
  - getRigid
```
public String getRigid()
```
    getRigid.
    
    Specified by:
    
    getRigid in interface Interaction<T extends Participant>
    
    Returns:
    
    a String object.
  - setRigid
```
public void setRigid(String rigid)
```
    Sets the rigid of this interaction. It will remove the previous rigid from the list of checksum and add the new one. If rigid is null, it will remove all the rigid in the list of checksum
    
    Specified by:
    
    setRigid in interface Interaction<T extends Participant>
    
    Parameters:
    
    rigid - : the rigid
  - getIdentifiers
```
public Collection<Xref> getIdentifiers()
```
    getIdentifiers.
    
    Specified by:
    
    getIdentifiers in interface Interaction<T extends Participant>
    
    Returns:
    
    a Collection object.
  - getXrefs
```
public Collection<Xref> getXrefs()
```
    getXrefs.
    
    Specified by:
    
    getXrefs in interface Interaction<T extends Participant>
    
    Returns:
    
    a Collection object.
  - getChecksums
```
public Collection<Checksum> getChecksums()
```
    getChecksums.
    
    Specified by:
    
    getChecksums in interface Interaction<T extends Participant>
    
    Returns:
    
    a Collection object.
  - getAnnotations
```
public Collection<Annotation> getAnnotations()
```
    getAnnotations.
    
    Specified by:
    
    getAnnotations in interface Interaction<T extends Participant>
    
    Returns:
    
    a Collection object.
  - getUpdatedDate
```
public Date getUpdatedDate()
```
    Getter for the field updatedDate.
    
    Specified by:
    
    getUpdatedDate in interface Interaction<T extends Participant>
    
    Returns:
    
    a Date object.
  - setUpdatedDate
```
public void setUpdatedDate(Date updated)
```
    Sets the last update date
    
    Specified by:
    
    setUpdatedDate in interface Interaction<T extends Participant>
    
    Parameters:
    
    updated - : last update date
  - getCreatedDate
```
public Date getCreatedDate()
```
    Getter for the field createdDate.
    
    Specified by:
    
    getCreatedDate in interface Interaction<T extends Participant>
    
    Returns:
    
    a Date object.
  - setCreatedDate
```
public void setCreatedDate(Date created)
```
    Sets the created date
    
    Specified by:
    
    setCreatedDate in interface Interaction<T extends Participant>
    
    Parameters:
    
    created - : created date
  - getInteractionType
```
public abstract CvTerm getInteractionType()
```
    getInteractionType.
    
    Specified by:
    
    getInteractionType in interface Interaction<T extends Participant>
    
    Returns:
    
    a CvTerm object.
  - setInteractionType
```
public abstract void setInteractionType(CvTerm term)
```
    Sets the interaction type.
    
    Specified by:
    
    setInteractionType in interface Interaction<T extends Participant>
    
    Parameters:
    
    term - : interaction type
  - getParticipants
```
public Collection<T> getParticipants()
```
    getParticipants.
    
    Specified by:
    
    getParticipants in interface Interaction<T extends Participant>
    
    Returns:
    
    a Collection object.
  - addParticipant
```
public boolean addParticipant(T part)
```
    addParticipant.
    
    Specified by:
    
    addParticipant in interface Interaction<T extends Participant>
    
    Parameters:
    
    part - a T object.
    
    Returns:
    
    a boolean.
  - removeParticipant
```
public boolean removeParticipant(T part)
```
    removeParticipant.
    
    Specified by:
    
    removeParticipant in interface Interaction<T extends Participant>
    
    Parameters:
    
    part - a T object.
    
    Returns:
    
    a boolean.
  - addAllParticipants
```
public boolean addAllParticipants(Collection<? extends T> participants)
```
    This method will add all the participant and set the interaction of the new participant to this current interaction
    
    Specified by:
    
    addAllParticipants in interface Interaction<T extends Participant>
    
    Parameters:
    
    participants - : participants to add
    
    Returns:
    
    true if participant are added to the list of participants
  - removeAllParticipants
```
public boolean removeAllParticipants(Collection<? extends T> participants)
```
    This method will remove the participant and set the interaction of the removed participant to null.
    
    Specified by:
    
    removeAllParticipants in interface Interaction<T extends Participant>
    
    Parameters:
    
    participants - : participants to remove
    
    Returns:
    
    true if participant are removed from the list of participants
  - getInteractionNamesContainer
```
protected NamesContainer getInteractionNamesContainer()
```
    Getter for the field interactionNamesContainer.
    
    Returns:
    
    a NamesContainer object.
  - setInteractionNamesContainer
```
public void setInteractionNamesContainer(NamesContainer value)
```
    Sets the value of the names property.
    
    Parameters:
    
    value - allowed object is NamesContainer
  - getInteractionXrefContainer
```
protected InteractionXrefContainer getInteractionXrefContainer()
```
    getInteractionXrefContainer.
    
    Returns:
    
    a InteractionXrefContainer object.
  - setInteractionXrefContainer
```
public void setInteractionXrefContainer(InteractionXrefContainer value)
```
    Sets the value of the interactionXrefContainer property.
    
    Parameters:
    
    value - allowed object is InteractionXrefContainer
  - isIntraMolecular
```
public boolean isIntraMolecular()
```
    isIntraMolecular.
    
    Returns:
    
    a boolean.
  - setIntraMolecular
```
public void setIntraMolecular(boolean value)
```
    Sets the value of the intraMolecular property.
    
    Parameters:
    
    value - allowed object is Boolean
  - getId
```
public int getId()
```
    Gets the value of the id property.
    
    Returns:
    
    a int.
  - setId
```
public void setId(int value)
```
    Sets the value of the id property.
    
    Parameters:
    
    value - a int.
  - getImexId
```
public String getImexId()
```
    Gets the value of the imexId property.
    
    Returns:
    
    a String object.
  - assignImexId
```
public void assignImexId(String value)
```
    Sets the value of the imexId property
    
    Parameters:
    
    value - a String object.
  - getComplexAc
```
public String getComplexAc()
```
    Gets the value of the complexAc property.
    
    Returns:
    
    a String object.
  - getComplexVersion
```
public String getComplexVersion()
```
    Gets the value of the complexVersion property.
    
    Returns:
    
    a String object.
  - assignComplexAc
```
public void assignComplexAc(String value)
```
    Sets the value of the complexAc property
    
    Parameters:
    
    value - a String object.
  - sourceLocation
```
public Locator sourceLocation()
```
    Specified by:
    
    sourceLocation in interface com.sun.xml.bind.Locatable
  - 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
  - getEntry
```
public Entry getEntry()
```
    Getter for the field entry.
    
    Returns:
    
    a Entry object.
  - setEntry
```
public void setEntry(Entry entry)
```
    Setter for the field entry.
    
    Parameters:
    
    entry - a Entry object.
  - toString
```
public String toString()
```
    toString
    
    Specified by:
    
    toString in interface FileSourceContext
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    the file source context as a String. If the source locator is not null, it should give the source locator properties
  - setJAXBAttributeWrapper
```
public void setJAXBAttributeWrapper(AbstractXmlInteraction.JAXBAttributeWrapper jaxbAttributeWrapper)
```
    setJAXBAttributeWrapper.
    
    Parameters:
    
    jaxbAttributeWrapper - a AbstractXmlInteraction.JAXBAttributeWrapper object.
  - setParticipantWrapper
```
public void setParticipantWrapper(AbstractXmlInteraction.JAXBParticipantWrapper<T> jaxbParticipantWrapper)
```
    setParticipantWrapper.
    
    Parameters:
    
    jaxbParticipantWrapper - a AbstractXmlInteraction.JAXBParticipantWrapper object.
  - processAddedParticipant
```
protected void processAddedParticipant(T participant)
```
    processAddedParticipant.
    
    Parameters:
    
    participant - a T object.
  - initialiseAnnotationWrapper
```
protected void initialiseAnnotationWrapper()
```
    initialiseAnnotationWrapper.
  - initialiseParticipantWrapper
```
protected void initialiseParticipantWrapper()
```
    initialiseParticipantWrapper.
  - getAttributeWrapper
```
protected AbstractXmlInteraction.JAXBAttributeWrapper getAttributeWrapper()
```
    getAttributeWrapper.
    
    Returns:
    
    a AbstractXmlInteraction.JAXBAttributeWrapper object.
  - initialiseNamesContainer
```
protected void initialiseNamesContainer()
```
    initialiseNamesContainer.

Class AbstractXmlInteraction<T extends Participant>

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

AbstractXmlInteraction

AbstractXmlInteraction

AbstractXmlInteraction

Method Detail

getShortName

setShortName

getAliases

setFullName

getFullName

getRigid

setRigid

getIdentifiers

getXrefs

getChecksums

getAnnotations

getUpdatedDate

setUpdatedDate

getCreatedDate

setCreatedDate

getInteractionType

setInteractionType

getParticipants

addParticipant

removeParticipant

addAllParticipants

removeAllParticipants

getInteractionNamesContainer

setInteractionNamesContainer

getInteractionXrefContainer

setInteractionXrefContainer

isIntraMolecular

setIntraMolecular

getId

setId

getImexId

assignImexId

getComplexAc

getComplexVersion

assignComplexAc

sourceLocation

getSourceLocator

setSourceLocator

getEntry

setEntry

toString

setJAXBAttributeWrapper

setParticipantWrapper

processAddedParticipant

initialiseAnnotationWrapper

initialiseParticipantWrapper

getAttributeWrapper

initialiseNamesContainer