Package org.molgenis.vibe.core.formats

Class Gene

java.lang.Object

org.molgenis.vibe.core.formats.Entity

org.molgenis.vibe.core.formats.BiologicalEntity

org.molgenis.vibe.core.formats.Gene

All Implemented Interfaces:

Comparable<Entity>, AllFieldsEquals, EntityWithIntId, ResourceUri

public class Gene
extends BiologicalEntity
implements EntityWithIntId

A gene. Note that equality is determined through URIs from the domain http://identifiers.org describing NCBI Entrez gene identifiers. This was done as DisGeNET converted other gene-identifiers (such as HGNC symbols) into NCBI Entrez gene identifiers (source) within the database.

Field Summary

Fields

Modifier and Type	Field	Description
static String	ID_PREFIX

Constructor Summary

Constructors

Constructor	Description
Gene(String id, GeneSymbol symbol)
Gene(URI uri, GeneSymbol symbol)

Method Summary

Modifier and Type	Method	Description
boolean	allFieldsEquals(Object o)
int	compareTo(Entity o)
int	getIdInt()
protected String	getIdPrefix()	The entity prefix.
protected String	getIdRegex()	A regular expression an input String should adhere to when deriving the Entity from it.
protected int	getRegexIdGroup()	The group within the regular expression the actual Entity.id is stored in.
GeneSymbol	getSymbol()
protected String	getUriPrefix()	The String describing the URI prefix it should match with.
String	toString()	While uniqueness is based on the Entity.id (as each Entity.id should only occur once and data belonging to it should be consistent), Entity.toString() can be used for testing whether data retrieval from external sources yielded the expected results.

Methods inherited from class org.molgenis.vibe.core.formats.Entity

equals, getFormattedId, getId, getName, getUri, hashCode, retrieveIdFromString, setName

Methods inherited from class java.lang.Object

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

Field Detail

ID_PREFIX

public static final String ID_PREFIX

See Also:

Constant Field Values

Constructor Detail

Gene

public Gene(String id,
            GeneSymbol symbol)

Gene

public Gene(URI uri,
            GeneSymbol symbol)

Method Detail

getSymbol

public GeneSymbol getSymbol()

getIdInt

public int getIdInt()

Specified by:

getIdInt in interface EntityWithIntId

getIdPrefix

protected String getIdPrefix()

Description copied from class: Entity

The entity prefix.

Specified by:

getIdPrefix in class Entity

Returns:

a String containing the prefix.

getIdRegex

protected String getIdRegex()

Description copied from class: Entity

A regular expression an input String should adhere to when deriving the Entity from it.

Specified by:

getIdRegex in class Entity

Returns:

getRegexIdGroup

protected int getRegexIdGroup()

Description copied from class: Entity

The group within the regular expression the actual Entity.id is stored in.

Specified by:

getRegexIdGroup in class Entity

Returns:

getUriPrefix

protected String getUriPrefix()

Description copied from class: Entity

The String describing the URI prefix it should match with.

Specified by:

getUriPrefix in class Entity

Returns:

toString

public String toString()

While uniqueness is based on the Entity.id (as each Entity.id should only occur once and data belonging to it should be consistent), Entity.toString() can be used for testing whether data retrieval from external sources yielded the expected results.

Overrides:

toString in class Entity

compareTo

public int compareTo(Entity o)

Specified by:

compareTo in interface Comparable<Entity>

Overrides:

compareTo in class Entity

allFieldsEquals

public boolean allFieldsEquals(Object o)

Specified by:

allFieldsEquals in interface AllFieldsEquals

Overrides:

allFieldsEquals in class Entity