procope.evaluation.complexquality.go
Class GONetwork

java.lang.Object
  procope.evaluation.complexquality.go.GONetwork

public class GONetwork
extends Object

Represents the ontology network of one GO namespace.

Author:

Jan Krumsiek

Nested Class Summary

static class	GONetwork.Namespace The GO namespaces.
static class	GONetwork.Relationships GO ontology relationships which can be followed while constructing the ontology network.

Constructor Summary

GONetwork(File fileOntologies, GONetwork.Namespace namespace, GONetwork.Relationships relationships)
Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

GONetwork(String fileOntologies, GONetwork.Namespace namespace, GONetwork.Relationships relationships)
Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

Method Summary

Collection<GOTerm>	getAllTerms() Get set of all term objects in the current network.
GONetwork.Namespace	getNamespace() Returns the namespace used in this network.
GOTerm	getRoot() Returns the root term of this ontology network (actually of the namespace which is used in this network).
GOTerm	getTerm(String ID) Returns the term object with a given GO identifier.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GONetwork

public GONetwork(String fileOntologies,
                 GONetwork.Namespace namespace,
                 GONetwork.Relationships relationships)
          throws IOException

Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

Parameters:

fileOntologies - file with ontologies in OBO format

namespace - the namespace to be used

relationships - the relationships which are followed to contruct the network

Throws:

IOException - if something went wrong reading the ontology file

GONetwork

public GONetwork(File fileOntologies,
                 GONetwork.Namespace namespace,
                 GONetwork.Relationships relationships)
          throws IOException

Creates a GO network from a given file in OBO format, using a given namespaces and the specified relationships

Parameters:

fileOntologies - file with ontologies in OBO format

namespace - the namespace to be used

relationships - the relationships which are followed to contruct the network

Throws:

IOException - if something went wrong reading the ontology file

Method Detail

getRoot

public GOTerm getRoot()

Returns the root term of this ontology network (actually of the namespace which is used in this network).

Returns:

root term of the network

getTerm

public GOTerm getTerm(String ID)

Returns the term object with a given GO identifier.

Parameters:

ID - identfier of term to look up

Returns:

the term object or null if this term is not present in the network

getAllTerms

public Collection<GOTerm> getAllTerms()

Get set of all term objects in the current network.

Returns:

Set of all terms in the network.

getNamespace

public GONetwork.Namespace getNamespace()

Returns the namespace used in this network.

Returns:

namespace used in this network