Package org.biojavax.bio

Class SimpleBioEntry

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.SimpleBioEntry

All Implemented Interfaces:

Comparable, Annotatable, Changeable, BioEntry, RankedCrossRefable, RichAnnotatable

Direct Known Subclasses:

ThinRichSequence

public class SimpleBioEntry
extends AbstractChangeable
implements BioEntry

Reference implementation of a BioEntry object which has no features or sequence. Equality is the combination of namespace, name, accession and version.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, George Waldon

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojavax.bio.BioEntry

COMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXON

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleBioEntry()
	SimpleBioEntry(Namespace ns, String name, String accession, int version)	Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version.

Method Summary

Modifier and Type	Method	Description
void	addComment(Comment comment)	Adds a comment instance to this bioentry.
void	addRankedCrossRef(RankedCrossRef crossref)	Adds a ranked cross reference to the existing set.
void	addRankedDocRef(RankedDocRef docref)	Adds a ranked docref instance to this bioentry.
void	addRelationship(BioEntryRelationship relation)	Adds a relation instance to this bioentry.
int	compareTo(Object o)	Bioentries are ordered first by namespace, then name, accession, and finally version.
boolean	equals(Object obj)	Two bioentries are equal if they share the same namespace, name, accession and version.
String	getAccession()	Returns the accession of this bioentry.
Annotation	getAnnotation()	Should return the associated annotation object.
Set<Comment>	getComments()	Returns a set of all comments associated with this bioentry.
String	getDescription()	Returns a description of this sequence.
String	getDivision()	Returns the division of this bioentry.
Integer	getId()	Gets the Hibernate ID.
String	getIdentifier()	Returns the identifier of this bioentry.
String	getName()	Returns the name of this bioentry.
Namespace	getNamespace()	Returns the namespace of this bioentry.
Set<Note>	getNoteSet()	Returns the set of notes associated with this object.
Set<RankedCrossRef>	getRankedCrossRefs()	Returns the set of all ranked cross references associated with an object.
Set<RankedDocRef>	getRankedDocRefs()	Returns a set of all bioentrydocrefs associated with this bioentry.
Set<BioEntryRelationship>	getRelationships()	Returns a set of all relationships associated with this bioentry.
RichAnnotation	getRichAnnotation()	Return the associated annotation object.
NCBITaxon	getTaxon()	Gets the taxon associated with this bioentry.
int	getVersion()	Gets the version of this bioentry.
int	hashCode()
void	removeComment(Comment comment)	Removes a comment instance from this bioentry.
void	removeRankedCrossRef(RankedCrossRef crossref)	Removes a ranked cross reference from the existing set.
void	removeRankedDocRef(RankedDocRef docref)	Removes a ranked docref instance from this bioentry.
void	removeRelationship(BioEntryRelationship relation)	Removes a relation instance from this bioentry.
void	setDescription(String description)	Sets the description for this bioentry.
void	setDivision(String division)	Sets the division of this bioentry.
void	setId(Integer id)	Sets the Hibernate ID.
void	setIdentifier(String identifier)	Sets the identifier of this bioentry.
void	setNoteSet(Set<Note> notes)	Clears the notes associated with this object and replaces them with the contents of this set.
void	setRankedCrossRefs(Set<RankedCrossRef> rankedcrossrefs)	Sets the ranked cross references associated with an object.
void	setTaxon(NCBITaxon taxon)	Sets the taxon for this bioentry.
String	toString()	Form: namespace:name/accession.version

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleBioEntry

public SimpleBioEntry(Namespace ns,
                      String name,
                      String accession,
                      int version)

Creates a new bioentry representing the sequence in the given namespace with the given name, accession and version. These properties are all immutable and non-nullable.

Parameters:

ns - The namespace for this new bioentry (not null).

name - The name for this new bioentry (not null).

accession - The accession for this new bioentry (not null).

version - The version for this new bioentry.

SimpleBioEntry

protected SimpleBioEntry()

Method Detail

getRankedCrossRefs

public Set<RankedCrossRef> getRankedCrossRefs()

Returns the set of all ranked cross references associated with an object. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getRankedCrossRefs in interface RankedCrossRefable

Returns:

a set of RankedCrossRef objects.

setTaxon

public void setTaxon(NCBITaxon taxon)
              throws ChangeVetoException

Sets the taxon for this bioentry. It may be null, in which case the taxon is unset.

Specified by:

setTaxon in interface BioEntry

Parameters:

taxon - New value of property taxon.

Throws:

ChangeVetoException - in case of objections.

getAnnotation

public Annotation getAnnotation()

Should return the associated annotation object.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

getRichAnnotation

public RichAnnotation getRichAnnotation()

Return the associated annotation object.

Specified by:

getRichAnnotation in interface RichAnnotatable

Returns:

a RichAnnotation object, never null

getNoteSet

public Set<Note> getNoteSet()

Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getNoteSet in interface RichAnnotatable

Returns:

set a set of Note objects.

See Also:

Note

setNoteSet

public void setNoteSet(Set<Note> notes)
                throws ChangeVetoException

Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

setNoteSet in interface RichAnnotatable

Parameters:

notes - the set of Note objects to replace the existing ones with.

Throws:

ChangeVetoException - if the set is null or contains any objects that are not Note objects.

See Also:

Note

getComments

public Set<Comment> getComments()

Returns a set of all comments associated with this bioentry. This set is not mutable. If no comments are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getComments in interface BioEntry

Returns:

a set of Comment objects.

See Also:

Comment

getRankedDocRefs

public Set<RankedDocRef> getRankedDocRefs()

Returns a set of all bioentrydocrefs associated with this bioentry. This set is not mutable. If no docrefs are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getRankedDocRefs in interface BioEntry

Returns:

a set of RankedDocRef objects.

See Also:

RankedDocRef

getRelationships

public Set<BioEntryRelationship> getRelationships()

Returns a set of all relationships associated with this bioentry. This set is not mutable. If no relationships are associated, you will get back an empty set. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

Specified by:

getRelationships in interface BioEntry

Returns:

a set of BioEntryRelationship objects.

See Also:

BioEntryRelationship

setIdentifier

public void setIdentifier(String identifier)
                   throws ChangeVetoException

Sets the identifier of this bioentry. Null is allowable.

Specified by:

setIdentifier in interface BioEntry

Parameters:

identifier - New value of property identifier.

Throws:

ChangeVetoException - in case of objections.

setDivision

public void setDivision(String division)
                 throws ChangeVetoException

Sets the division of this bioentry. Null is allowable.

Specified by:

setDivision in interface BioEntry

Parameters:

division - New value of property division.

Throws:

ChangeVetoException - in case of objections.

setDescription

public void setDescription(String description)
                    throws ChangeVetoException

Sets the description for this bioentry.

Specified by:

setDescription in interface BioEntry

Parameters:

description - New value of property description.

Throws:

ChangeVetoException - in case of objections.

getAccession

public String getAccession()

Returns the accession of this bioentry. The accession is supposed to be an immutable property set by the constructor.

Specified by:

getAccession in interface BioEntry

Returns:

Value of property accession.

getDescription

public String getDescription()

Returns a description of this sequence.

Specified by:

getDescription in interface BioEntry

Returns:

Value of property description.

getDivision

public String getDivision()

Returns the division of this bioentry. Division relates to a division of the parent namespace.

Specified by:

getDivision in interface BioEntry

Returns:

Value of property division.

getIdentifier

public String getIdentifier()

Returns the identifier of this bioentry.

Specified by:

getIdentifier in interface BioEntry

Returns:

Value of property identifier.

getName

public String getName()

Returns the name of this bioentry. The name is supposed to be an immutable property set by the constructor.

Specified by:

getName in interface BioEntry

Returns:

Value of property name.

getNamespace

public Namespace getNamespace()

Returns the namespace of this bioentry. The namespace is supposed to be an immutable property set by the constructor.

Specified by:

getNamespace in interface BioEntry

Returns:

the namespace of this bioentry.

getTaxon

public NCBITaxon getTaxon()

Gets the taxon associated with this bioentry. It may be null.

Specified by:

getTaxon in interface BioEntry

Returns:

Value of property taxon.

getVersion

public int getVersion()

Gets the version of this bioentry. Bioentries with no versions return 0. The version is supposed to be immutable and set only by the constructor.

Specified by:

getVersion in interface BioEntry

Returns:

Value of property version.

equals

public boolean equals(Object obj)

Two bioentries are equal if they share the same namespace, name, accession and version.

Overrides:

equals in class Object

compareTo

public int compareTo(Object o)

Bioentries are ordered first by namespace, then name, accession, and finally version.

Specified by:

compareTo in interface Comparable

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Form: namespace:name/accession.version

Overrides:

toString in class Object

addRankedCrossRef

public void addRankedCrossRef(RankedCrossRef crossref)
                       throws ChangeVetoException

Adds a ranked cross reference to the existing set. If already present, this call is ignored. Null values are not acceptable.

Specified by:

addRankedCrossRef in interface RankedCrossRefable

Parameters:

crossref - the ranked cross reference to add.

Throws:

ChangeVetoException - if the parameter is null.

removeRankedCrossRef

public void removeRankedCrossRef(RankedCrossRef crossref)
                          throws ChangeVetoException

Removes a ranked cross reference from the existing set. If not present, this call is ignored. Null values are not acceptable.

Specified by:

removeRankedCrossRef in interface RankedCrossRefable

Parameters:

crossref - the ranked cross reference to remove.

Throws:

ChangeVetoException - if the parameter is null.

addRankedDocRef

public void addRankedDocRef(RankedDocRef docref)
                     throws ChangeVetoException

Adds a ranked docref instance to this bioentry. Must not be null.

Specified by:

addRankedDocRef in interface BioEntry

Parameters:

docref - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeRankedDocRef

public void removeRankedDocRef(RankedDocRef docref)
                        throws ChangeVetoException

Removes a ranked docref instance from this bioentry. If it was not found, nothing happens.

Specified by:

removeRankedDocRef in interface BioEntry

Parameters:

docref - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.

addComment

public void addComment(Comment comment)
                throws ChangeVetoException

Adds a comment instance to this bioentry. Must not be null.

Specified by:

addComment in interface BioEntry

Parameters:

comment - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeComment

public void removeComment(Comment comment)
                   throws ChangeVetoException

Removes a comment instance from this bioentry. If it wasn't present, it nothing will happen.

Specified by:

removeComment in interface BioEntry

Parameters:

comment - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.

addRelationship

public void addRelationship(BioEntryRelationship relation)
                     throws ChangeVetoException

Adds a relation instance to this bioentry. It must not be null.

Specified by:

addRelationship in interface BioEntry

Parameters:

relation - the item to add.

Throws:

ChangeVetoException - if it doesn't want to add it.

removeRelationship

public void removeRelationship(BioEntryRelationship relation)
                        throws ChangeVetoException

Removes a relation instance from this bioentry. If it wasn't present, nothing will happen.

Specified by:

removeRelationship in interface BioEntry

Parameters:

relation - the item to remove.

Throws:

ChangeVetoException - if it doesn't want to remove it.

setRankedCrossRefs

public void setRankedCrossRefs(Set<RankedCrossRef> rankedcrossrefs)

Description copied from interface: RankedCrossRefable

Sets the ranked cross references associated with an object. Null will throw an exception but the empty set is fine.

Specified by:

setRankedCrossRefs in interface RankedCrossRefable

Parameters:

rankedcrossrefs - a set of RankedCrossRef objects.

getId

public Integer getId()

Gets the Hibernate ID. Should be used with caution.

Returns:

the Hibernate ID, if using Hibernate.

setId

public void setId(Integer id)

Sets the Hibernate ID. Should be used with caution.

Parameters:

id - the Hibernate ID, if using Hibernate.