uk.ac.ebi.intact.model
Class AnnotatedObjectImpl

java.lang.Object
  |
  +--uk.ac.ebi.intact.model.IntactObjectImpl
        |
        +--uk.ac.ebi.intact.model.BasicObjectImpl
              |
              +--uk.ac.ebi.intact.model.AnnotatedObjectImpl

All Implemented Interfaces:

AnnotatedObject, BasicObject, IntactObject, java.io.Serializable

Direct Known Subclasses:

BioSource, CvObject, Experiment, InteractorImpl

public abstract class AnnotatedObjectImpl

extends BasicObjectImpl

implements AnnotatedObject

Represents an object with biological annotation.

Author:

hhe

See Also:

Serialized Form

Field Summary

java.util.Collection	annotations
Person	curator The curator who has last edited the object.
protected java.lang.String	curatorAc
protected java.lang.String	fullName The full name or a minimal description of the object.
java.util.Collection	references
protected java.lang.String	shortLabel Short name for the object, not necessarily unique.
java.util.Collection	xrefs

Fields inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

ac, NEW_LINE

Constructor Summary

protected	AnnotatedObjectImpl() no-arg constructor provided for compatibility with subclasses that have no-arg constructors.
protected	AnnotatedObjectImpl(java.lang.String shortLabel, Institution owner) Constructor for subclass use only.

Method Summary

void	addAlias(Alias alias) Adds an alias to the object.
void	addAnnotation(Annotation annotation)
void	addReference(Reference reference)
void	addXref(Xref aXref) Adds an xref to the object.
boolean	equals(java.lang.Object o) Equality for AnnotatedObjects is currently based on equality for Xrefs, shortLabels and fullNames.
java.util.Collection	getAliases()
java.util.Collection	getAnnotations()
Person	getCurator()
java.lang.String	getCuratorAc()
java.lang.String	getFullName()
java.util.Collection	getReferences()
java.lang.String	getShortLabel()
java.util.Collection	getXrefs()
int	hashCode() This class overwrites equals.
void	removeAlias(Alias alias)
void	removeAnnotation(Annotation annotation)
void	removeReference(Reference reference)
void	removeXref(Xref xref)
void	setAliases(java.util.Collection someAliases)
void	setAnnotation(java.util.Collection someAnnotation)
void	setCurator(Person person)
void	setCuratorAc(java.lang.String ac)
void	setFullName(java.lang.String fullName)
void	setReferences(java.util.Collection someReferences)
void	setShortLabel(java.lang.String shortLabel)
void	setXrefs(java.util.Collection someXrefs)
java.lang.String	toString()
AnnotatedObject	update(IntactHelper helper) Update an annotated object in the database.
Annotation	updateUniqueAnnotation(CvTopic topic, java.lang.String description, Institution owner) Create or update an annotation.

Methods inherited from class uk.ac.ebi.intact.model.BasicObjectImpl

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.ebi.intact.model.BasicObject

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from interface uk.ac.ebi.intact.model.IntactObject

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Field Detail

curatorAc

protected java.lang.String curatorAc

shortLabel

protected java.lang.String shortLabel

Short name for the object, not necessarily unique. To be used for example in minimised displays of the object.

fullName

protected java.lang.String fullName

The full name or a minimal description of the object.

annotations

public java.util.Collection annotations

curator

public Person curator

The curator who has last edited the object.

xrefs

public java.util.Collection xrefs

references

public java.util.Collection references

Constructor Detail

AnnotatedObjectImpl

protected AnnotatedObjectImpl()

no-arg constructor provided for compatibility with subclasses that have no-arg constructors.

AnnotatedObjectImpl

protected AnnotatedObjectImpl(java.lang.String shortLabel,
                              Institution owner)

Constructor for subclass use only. Ensures that AnnotatedObjects cannot be created without at least a shortLabel and an owner specified.

Parameters:

shortLabel - The memorable label to identify this AnnotatedObject

owner - The Institution which owns this AnnotatedObject

Throws:

java.lang.NullPointerException - thrown if either parameters are not specified

Method Detail

getShortLabel

public java.lang.String getShortLabel()

Specified by:

getShortLabel in interface AnnotatedObject

setShortLabel

public void setShortLabel(java.lang.String shortLabel)

Specified by:

setShortLabel in interface AnnotatedObject

getFullName

public java.lang.String getFullName()

Specified by:

getFullName in interface AnnotatedObject

setFullName

public void setFullName(java.lang.String fullName)

Specified by:

setFullName in interface AnnotatedObject

setAnnotation

public void setAnnotation(java.util.Collection someAnnotation)

Specified by:

setAnnotation in interface AnnotatedObject

getAnnotations

public java.util.Collection getAnnotations()

Specified by:

getAnnotations in interface AnnotatedObject

addAnnotation

public void addAnnotation(Annotation annotation)

Specified by:

addAnnotation in interface AnnotatedObject

removeAnnotation

public void removeAnnotation(Annotation annotation)

Specified by:

removeAnnotation in interface AnnotatedObject

getCurator

public Person getCurator()

Specified by:

getCurator in interface AnnotatedObject

setCurator

public void setCurator(Person person)

Specified by:

setCurator in interface AnnotatedObject

setXrefs

public void setXrefs(java.util.Collection someXrefs)

Specified by:

setXrefs in interface AnnotatedObject

getXrefs

public java.util.Collection getXrefs()

Specified by:

getXrefs in interface AnnotatedObject

addXref

public void addXref(Xref aXref)

Adds an xref to the object. The xref will only be added if an equivalent xref is not yet part of the object.

Specified by:

addXref in interface AnnotatedObject

removeXref

public void removeXref(Xref xref)

Specified by:

removeXref in interface AnnotatedObject

setAliases

public void setAliases(java.util.Collection someAliases)

Specified by:

setAliases in interface AnnotatedObject

getAliases

public java.util.Collection getAliases()

Specified by:

getAliases in interface AnnotatedObject

addAlias

public void addAlias(Alias alias)

Adds an alias to the object. The alis will only be added if an equivalent alias is not yet part of the object.

Specified by:

addAlias in interface AnnotatedObject

removeAlias

public void removeAlias(Alias alias)

Specified by:

removeAlias in interface AnnotatedObject

setReferences

public void setReferences(java.util.Collection someReferences)

Specified by:

setReferences in interface AnnotatedObject

getReferences

public java.util.Collection getReferences()

Specified by:

getReferences in interface AnnotatedObject

addReference

public void addReference(Reference reference)

Specified by:

addReference in interface AnnotatedObject

removeReference

public void removeReference(Reference reference)

Specified by:

removeReference in interface AnnotatedObject

getCuratorAc

public java.lang.String getCuratorAc()

Specified by:

getCuratorAc in interface AnnotatedObject

setCuratorAc

public void setCuratorAc(java.lang.String ac)

Specified by:

setCuratorAc in interface AnnotatedObject

update

public AnnotatedObject update(IntactHelper helper)
                       throws IntactException

Update an annotated object in the database. Ensure subobjects are updated appropriately.

Specified by:

update in interface AnnotatedObject

IntactException

updateUniqueAnnotation

public Annotation updateUniqueAnnotation(CvTopic topic,
                                         java.lang.String description,
                                         Institution owner)

Create or update an annotation. The anntation topic may only occur once in the object.

Specified by:

updateUniqueAnnotation in interface AnnotatedObject

equals

public boolean equals(java.lang.Object o)

Equality for AnnotatedObjects is currently based on equality for Xrefs, shortLabels and fullNames.

Specified by:

equals in interface AnnotatedObject

Overrides:

equals in class java.lang.Object

Parameters:

o - The object to check

Returns:

true if the parameter equals this object, false otherwise

See Also:

Xref

hashCode

public int hashCode()

This class overwrites equals. To ensure proper functioning of HashTable, hashCode must be overwritten, too.

Specified by:

hashCode in interface AnnotatedObject

Overrides:

hashCode in class java.lang.Object

Returns:

hash code of the object.

toString

public java.lang.String toString()

Specified by:

toString in interface AnnotatedObject

Overrides:

toString in class BasicObjectImpl