Package org.biojavax
Class SimpleCrossRef
java.lang.Object
org.biojava.utils.Unchangeable
org.biojavax.SimpleCrossRef
- All Implemented Interfaces:
Comparable
,Annotatable
,Changeable
,CrossRef
,RichAnnotatable
A basic CrossRef implementation.
- Since:
- 1.5
- Author:
- Richard Holland, Mark Schreiber, George Waldon (made Unchangeable)
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
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 TypeMethodDescriptionint
Compares cross references first by database name, then by accession, then by version.boolean
Equality is defined as having the same database name, accession and version.Returns the accession of the object that the crossref refers to.Should return the associated annotation object.Returns the name of the database the cross reference refers to.getId()
Gets the Hibernate ID.Returns the set of notes associated with this object.Return the associated annotation object.int
Returns the version of the object that the crossref refers to.int
hashCode()
void
Sets the Hibernate ID.void
setNoteSet
(Set notes) Clears the notes associated with this object and replaces them with the contents of this set.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
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Constructor Details
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SimpleCrossRef
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.
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SimpleCrossRef
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.
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SimpleCrossRef
protected SimpleCrossRef()
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Method Details
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getAnnotation
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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getRichAnnotation
Return the associated annotation object.- Specified by:
getRichAnnotation
in interfaceRichAnnotatable
- Returns:
- a RichAnnotation object, never null
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getNoteSet
Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance.- Specified by:
getNoteSet
in interfaceRichAnnotatable
- Returns:
- set a set of Note objects.
- See Also:
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setNoteSet
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 interfaceRichAnnotatable
- Parameters:
notes
- the set of Note objects to replace the existing ones with.- See Also:
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getAccession
Returns the accession of the object that the crossref refers to.- Specified by:
getAccession
in interfaceCrossRef
- Returns:
- Value of property accession.
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getDbname
Returns the name of the database the cross reference refers to. This would normally be a namespace name, eg. 'gb' for GenBank. -
getVersion
Returns the version of the object that the crossref refers to.- Specified by:
getVersion
in interfaceCrossRef
- Returns:
- Value of property version.
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compareTo
Compares cross references first by database name, then by accession, then by version.- Specified by:
compareTo
in interfaceComparable
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equals
Equality is defined as having the same database name, accession and version. -
hashCode
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toString
Form: "dbname:accession.version" -
getId
Gets the Hibernate ID. Should be used with caution.- Returns:
- the Hibernate ID, if using Hibernate.
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setId
Sets the Hibernate ID. Should be used with caution.- Parameters:
id
- the Hibernate ID, if using Hibernate.
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