org.bridgedb

Class Xref

java.lang.Object

org.bridgedb.Xref

All Implemented Interfaces:

Comparable<Xref>

public class Xref
extends Object
implements Comparable<Xref>

Stores an id + DataSource combination, which represents an unique gene product.

Immutable class, thread safe

Constructor Summary

Constructors

Constructor and Description
Xref(String id, DataSource ds)

Method Summary

Modifier and Type	Method and Description
int	compareTo(Xref idc) Compares two Xrefs, asciibetically using string representation.
boolean	equals(Object o)
static Xref	fromMiriamUrn(String urn) This method will convert a known Miriam Urn to an Xref
static Xref	fromUrn(String urn) Deprecated.
DataSource	getDataSource()
String	getId()
String	getKnownUrl() Uses DataSource.getKnownUrl to create a valid URL for an online webpage describing this entity.
String	getMiriamURN() Uses DataSource.getMiriamURN() to create a global identifier, such as urn:miriam:uniprot:P12345.
String	getUrl() Deprecated. As it will return just the id if no UriPattern is known
String	getURN() Deprecated.
int	hashCode() hashCode calculated from id and datasource combined.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Xref

public Xref(String id,
            DataSource ds)

Parameters:

id - the Id part of this Xref

ds - the DataSource part of this Xref.

Method Detail

getDataSource

public DataSource getDataSource()

Returns:

the DataSource part of this Xref

getId

public String getId()

Returns:

the id part of this Xref

toString

public String toString()

Overrides:

toString in class Object

Returns:

short string representation for this Xref, for example En:ENSG000001 or X:1004_at This string representation is not meant to be stored or parsed, it is there mostly for debugging purposes.

hashCode

public int hashCode()

hashCode calculated from id and datasource combined.

Overrides:

hashCode in class Object

Returns:

the hashCode

equals

public boolean equals(Object o)

Overrides:

equals in class Object

Parameters:

o - Object to compare to

Returns:

true if both the id and the datasource are equal.

compareTo

public int compareTo(Xref idc)

Compares two Xrefs, asciibetically using string representation.

Specified by:

compareTo in interface Comparable<Xref>

Parameters:

idc - Xref to compare to

Returns:

0 if equal, positive number if higher, negative number if lower.

getUrl

public String getUrl()

Deprecated. As it will return just the id if no UriPattern is known

Uses DataSource.getUrl() to create a valid URL for an online webpage describing this entity.

Returns:

url as a String.

getKnownUrl

public String getKnownUrl()

Uses DataSource.getKnownUrl to create a valid URL for an online webpage describing this entity.

Returns:

url as a String, or null if no UriPattern is known.

Since:

Version 2.0.0

getURN

public String getURN()

Deprecated.

Uses DataSource.getURN() to create a global identifier, such as urn:miriam:uniprot:P12345. Deprecated as this method is inconsistent as to the type of urn returned

Returns:

the URN as string

getMiriamURN

public String getMiriamURN()

Uses DataSource.getMiriamURN() to create a global identifier, such as urn:miriam:uniprot:P12345.

Returns:

the URN as string or null if no valid Miriam urn is known

Since:

Version 2.0.0

fromMiriamUrn

public static Xref fromMiriamUrn(String urn)

This method will convert a known Miriam Urn to an Xref

Parameters:

urn -

Returns:

A Xref or null if the urn is not in Miriam Format or

Since:

Version 2.0.0

fromUrn

public static Xref fromUrn(String urn)

Deprecated.

Returns an xref based on this urn, even if it has to create a new DataSource to do so This method could end up creating an previously none existing DataSource so is not recommended.

Parameters:

urn -

Returns: