Package org.biojava.utils.lsid

Class LifeScienceIdentifier

java.lang.Object

org.biojava.utils.lsid.LifeScienceIdentifier

All Implemented Interfaces:

Serializable

public final class LifeScienceIdentifier
extends Object
implements Serializable

Life Science Identifier (LSID). LSID syntax:

urn:lsid:<authorityId>:<namespaceId>:<objectId>:<revisionId>

The elements of a LSID are as follows:

• authorityId = <authorityId> identifies the organization
• namespaceId = <namespaceId> namespace to scope the identifier value
• objectId = <objectId> identifier of the object within namespace
• revisionId = <revisionId> optional version information

Examples:

 urn:lsid:ebi.ac.uk:SWISS-PROT/accession:P34355:3
 urn:lsid:rcsb.org:PDB:1D4X:22
 urn:lsid:ncbi.nlm.nih.gov:Genbank/accession:NT_001063:2
 

As described in the memo URN Namespace for Life Science Identifiers
> http://www.i3c.org/workgroups/technical_architecture/resources/lsid/docs/LSIDSyntax9-20-02.htm

TODO:
Should this class support the spec definition of "lexical equivalence" in the equals(Object) method, or by the introduction of a new method boolean lexicallyEquivalent(LifeScienceIdentifier)?

From the spec:
For various purposes such as caching and replication, it's often desirable to determine if two LSIDs are the same without resolving them. The general purpose means of doing so is by testing for "lexical equivalence" as defined: LSIDs are lexically equivalent if the AuthorityID, NamespaceID, ObjectID, and RevisionID are all identical (case-insensitive comparison).

Author:

Michael Heuer

See Also:

Serialized Form

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object value)
String	getAuthorityId()	Return the authority id for this identifier.
String	getNamespaceId()	Return the namespace id for this identifier within the authority.
String	getObjectId()	Return the object id of this identifier.
String	getRevisionId()	Return the revision id of this identifier.
int	hashCode()
String	toString()
static LifeScienceIdentifier	valueOf(String lsid)	Create a new LifeScienceIdentifier parsed from the properly formatted string lsid.
static LifeScienceIdentifier	valueOf(String authorityId, String namespaceId, String objectId)	Create a new LifeScienceIdentifier from the specified parameters.
static LifeScienceIdentifier	valueOf(String authorityId, String namespaceId, String objectId, String revisionId)	Create a new LifeScienceIdentifier from the specified parameters.

Methods inherited from class java.lang.Object

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

Method Detail

getAuthorityId

public String getAuthorityId()

Return the authority id for this identifier.

getNamespaceId

public String getNamespaceId()

Return the namespace id for this identifier within the authority.

getObjectId

public String getObjectId()

Return the object id of this identifier.

getRevisionId

public String getRevisionId()

Return the revision id of this identifier. May return null.

equals

public boolean equals(Object value)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

valueOf

public static LifeScienceIdentifier valueOf(String lsid)
                                     throws LifeScienceIdentifierParseException

Create a new LifeScienceIdentifier parsed from the properly formatted string lsid.

Parameters:

lsid - formatted LifeScienceIdentifier string

Throws:

LifeScienceIdentifierParseException - if lsid is not properly formatted

valueOf

public static LifeScienceIdentifier valueOf(String authorityId,
                                            String namespaceId,
                                            String objectId,
                                            String revisionId)

Create a new LifeScienceIdentifier from the specified parameters.

Parameters:

authorityId - identifies the organization

namespaceId - namespace to scope the identifier value

objectId - identifer of the object within namespace

revisionId - optional version information

Throws:

NullPointerException - if any of authorityId, namespaceId, or objectId are null

valueOf

public static LifeScienceIdentifier valueOf(String authorityId,
                                            String namespaceId,
                                            String objectId)

Create a new LifeScienceIdentifier from the specified parameters.

Parameters:

authorityId - identifies the organization

namespaceId - namespace to scope the identifier value

objectId - identifer of the object within namespace

Throws:

NullPointerException - if any of authorityId, namespaceId, or objectId are null