Package org.molgenis.vibe.core.formats

Class Entity

java.lang.Object

org.molgenis.vibe.core.formats.Entity

All Implemented Interfaces:

Comparable<Entity>, AllFieldsEquals, ResourceUri

Direct Known Subclasses:

BiologicalEntity, GeneSymbol, PubmedEvidence

public abstract class Entity
extends Object
implements ResourceUri, Comparable<Entity>, AllFieldsEquals

Describes an entity. Be sure to update toString() to include all new fields when subclassing! Please refer to org.molgenis.vibe.rdf_processing.GenesForPhenotypeRetrieverTester within the test code for more information.

Constructor Summary

Constructors

Constructor	Description
Entity(String id)
Entity(String id, String name)
Entity(URI uri)
Entity(URI uri, String name)

Method Summary

Modifier and Type	Method	Description
boolean	allFieldsEquals(Object o)
int	compareTo(Entity o)
boolean	equals(Object o)
String	getFormattedId()
String	getId()
protected abstract String	getIdPrefix()	The entity prefix.
protected abstract String	getIdRegex()	A regular expression an input String should adhere to when deriving the Entity from it.
String	getName()
protected abstract int	getRegexIdGroup()	The group within the regular expression the actual id is stored in.
URI	getUri()
protected abstract String	getUriPrefix()	The String describing the URI prefix it should match with.
int	hashCode()
protected String	retrieveIdFromString(String fullString)	Validates and retrieves the ID from a String describing an id (that also includes other information such as a prefix).
protected void	setName(String name)
String	toString()	While uniqueness is based on the id (as each id should only occur once and data belonging to it should be consistent), toString() can be used for testing whether data retrieval from external sources yielded the expected results.

Methods inherited from class java.lang.Object

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

Constructor Detail

Entity

public Entity(String id)

Entity

public Entity(URI uri)

Entity

public Entity(String id,
              String name)

Entity

public Entity(URI uri,
              String name)

Method Detail

getIdPrefix

protected abstract String getIdPrefix()

The entity prefix.

Returns:

a String containing the prefix.

getIdRegex

protected abstract String getIdRegex()

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

Returns:

getRegexIdGroup

protected abstract int getRegexIdGroup()

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

Returns:

getUriPrefix

protected abstract String getUriPrefix()

The String describing the URI prefix it should match with.

Returns:

getId

public String getId()

Returns:

the Entity ID without prefix.

getFormattedId

public String getFormattedId()

Returns:

the Entity ID with prefix.

getName

public String getName()

setName

protected void setName(String name)

getUri

public URI getUri()

Specified by:

getUri in interface ResourceUri

retrieveIdFromString

protected String retrieveIdFromString(String fullString)
                               throws InvalidStringFormatException

Validates and retrieves the ID from a String describing an id (that also includes other information such as a prefix).

Parameters:

fullString - the String to be digested

Returns:

a String containing the id only

Throws:

InvalidStringFormatException - if fullString did not adhere to the regular expression

toString

public String toString()

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

Overrides:

toString in class Object

Returns:

equals

public boolean equals(Object o)

Overrides:

equals in class Object

allFieldsEquals

public boolean allFieldsEquals(Object o)

Specified by:

allFieldsEquals in interface AllFieldsEquals

hashCode

public int hashCode()

Overrides:

hashCode in class Object

compareTo

public int compareTo(Entity o)

Specified by:

compareTo in interface Comparable<Entity>