Package 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	Description
Xref(String id, DataSource ds)
Xref(String id, DataSource ds, boolean isPrimary)

Method Summary

Modifier and Type	Method	Description
int	compareTo(Xref idc)	Compares two Xrefs, asciibetically using string representation.
boolean	equals(Object o)
static Xref	fromBioregistryIdentifier(String compact)	This method will convert a Bioregistry.io identifier to an Xref.
static Xref	fromCompactIdentifier(String compact)	This method will convert a compact identifier to an Xref.
static Xref	fromMiriamUrn(String urn)	This method will convert a known Miriam Urn to an Xref
String	getBioregistryIdentifier()	Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.
String	getCompactidentifier()	Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.
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.
int	hashCode()	hashCode calculated from id and datasource combined.
boolean	isPrimary()
String	toString()	This string representation is not meant to be stored or parsed, it is there mostly for debugging purposes.

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.

Xref

public Xref(String id,
            DataSource ds,
            boolean isPrimary)

Parameters:

id - the Id part of this Xref

ds - the DataSource part of this Xref.

isPrimary - represents whether the id is primary or not

Method Detail

getDataSource

public DataSource getDataSource()

Returns:

the DataSource part of this Xref

getId

public String getId()

Returns:

the id part of this Xref

isPrimary

public boolean isPrimary()

Returns:

whether is id is primary or not

toString

public String toString()

This string representation is not meant to be stored or parsed, it is there mostly for debugging purposes.

Overrides:

toString in class Object

Returns:

short string representation for this Xref, for example En:ENSG000001:T or X:1004_at:F

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.

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

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

getBioregistryIdentifier

public String getBioregistryIdentifier()

Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.

Returns:

the compact identifier as string or null if no valid Bioregistry.io prefix is known

Since:

Version 3.0.0

getCompactidentifier

public String getCompactidentifier()

Uses DataSource.getCompactidentifier() to create a compact identifier, such as uniprot:P12345.

Returns:

the compact identifier as string or null if no valid Miriam namespace is known

Since:

Version 3.0.0

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

fromCompactIdentifier

public static Xref fromCompactIdentifier(String compact)

This method will convert a compact identifier to an Xref.

Parameters:

compact - a compact identifier

Returns:

A Xref or null if the urn is not in a compact identifier

Since:

Version 3.0.0

fromBioregistryIdentifier

public static Xref fromBioregistryIdentifier(String compact)

This method will convert a Bioregistry.io identifier to an Xref.

Parameters:

compact - a Bioregistry.io compact identifier

Returns:

A Xref or null if the urn is not in a compact identifier

Since:

Version 3.0.14