Package org.biojavax

Class SimpleCrossRef

java.lang.Object

org.biojava.utils.Unchangeable

org.biojavax.SimpleCrossRef

All Implemented Interfaces:

Comparable, Annotatable, Changeable, CrossRef, RichAnnotatable

public class SimpleCrossRef
extends Unchangeable
implements CrossRef

A basic CrossRef implementation.

Since:

1.5

Author:

Richard Holland, Mark Schreiber, George Waldon (made Unchangeable)

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

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleCrossRef()
	SimpleCrossRef(String dbname, String accession, int version)	Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.
	SimpleCrossRef(String dbname, String accession, Integer version)	Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.

Method Summary

Modifier and Type	Method	Description
int	compareTo(Object o)	Compares cross references first by database name, then by accession, then by version.
boolean	equals(Object obj)	Equality is defined as having the same database name, accession and version.
String	getAccession()	Returns the accession of the object that the crossref refers to.
Annotation	getAnnotation()	Should return the associated annotation object.
String	getDbname()	Returns the name of the database the cross reference refers to.
Integer	getId()	Gets the Hibernate ID.
Set	getNoteSet()	Returns the set of notes associated with this object.
RichAnnotation	getRichAnnotation()	Return the associated annotation object.
int	getVersion()	Returns the version of the object that the crossref refers to.
int	hashCode()
void	setId(Integer id)	Sets the Hibernate ID.
void	setNoteSet(Set notes)	Clears the notes associated with this object and replaces them with the contents of this set.
String	toString()	Form: "dbname:accession.version"

Methods inherited from class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

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

SimpleCrossRef

public SimpleCrossRef(String dbname,
                      String accession,
                      int version)

Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version.

Parameters:

dbname - the dbname for this crossref.

accession - the accession for this crossref.

version - the version for this crossref.

SimpleCrossRef

public SimpleCrossRef(String dbname,
                      String accession,
                      Integer version)

Creates a new instance of SimpleCrossRef with the values to use for the immutable database name, accession and version. Identical to other dbname/accession/version constructor except the version is specified as an Integer object rather than an int primitive. Will throw an exception if version is null.

Parameters:

dbname - the dbname for this crossref.

accession - the accession for this crossref.

version - the version for this crossref.

SimpleCrossRef

protected SimpleCrossRef()

Method Detail

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 getNoteSet()

Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance.

Specified by:

getNoteSet in interface RichAnnotatable

Returns:

set a set of Note objects.

See Also:

Note

setNoteSet

public void setNoteSet(Set notes)

Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance.

Specified by:

setNoteSet in interface RichAnnotatable

Parameters:

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

See Also:

Note

getAccession

public String getAccession()

Returns the accession of the object that the crossref refers to.

Specified by:

getAccession in interface CrossRef

Returns:

Value of property accession.

getDbname

public String getDbname()

Returns the name of the database the cross reference refers to. This would normally be a namespace name, eg. 'gb' for GenBank.

Specified by:

getDbname in interface CrossRef

Returns:

Value of property dbname.

getVersion

public int getVersion()

Returns the version of the object that the crossref refers to.

Specified by:

getVersion in interface CrossRef

Returns:

Value of property version.

compareTo

public int compareTo(Object o)

Compares cross references first by database name, then by accession, then by version.

Specified by:

compareTo in interface Comparable

equals

public boolean equals(Object obj)

Equality is defined as having the same database name, accession and version.

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Form: "dbname:accession.version"

Overrides:

toString in class Object

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.