cytoscape.data.annotation
Class Annotation

java.lang.Object
  cytoscape.data.annotation.Annotation

All Implemented Interfaces:

Serializable

public class Annotation
extends Object
implements Serializable

Store any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from an ontology (a controlled vocabulary for some subject domain, expressed as a directed acyclic graph). For example:

• for the species Halobacterium
• with respect to the KEGG metabolic pathways ontology
• gene VNG0623G has been assigned into the following categories
  1. Valine, leucine and isoleucine degradation
  2. Propanoate metabolism

This simple assignment of two classifications to one gene becomes richer when we refer to the ontology: in the KEGG ontology, these two terms belong to a tree, expressed linearly, and from the top (most general term) down as

• metablolism -> amino acid metabolism -> valine, leucine and isoleucine degradation
• metabolism -> carbohydrate metabolism -> propanoate metabolism
  Thus the combination of an annotation (the present class) with an ontology provides a means to richly and flexibly describe an object.

  See Also:

  Serialized Form

  Constructor Summary

  Annotation(String species, String type, Ontology ontology)
  Creates a new Annotation object.

  Annotation(String species, String type, String curator)
  Creates a new Annotation object.

  Method Summary

  void	add(String name, int classificationID) create a new annotation for an entity (typically a gene) of the current species and with respect to the current ontology. an entity may have more than one classification.
  int	count() total number of entities, usually ORFs.
  String[][]	getAllHierarchyPathsAsNames(String name) DOCUMENT ME!
  int[]	getClassifications() returns an array of all the classifications in the current annotation
  int[]	getClassifications(String name) all of the ontology identifiers registered for the specified entity
  Vector	getClassificationsVector(String name) all of the ontology identifiers registered for the specified entity, as a Vector of Integers
  String	getCurator() DOCUMENT ME!
  HashMap	getMap() DOCUMENT ME!
  String[]	getNames() returns an array of all the names (usually ORFs) currently annotated
  Ontology	getOntology() DOCUMENT ME!
  String	getOntologyType() DOCUMENT ME!
  String	getSpecies() DOCUMENT ME!
  String	getType() DOCUMENT ME!
  int	maxDepth() get all of the full paths (as ints) from the ontology for all of the currently annotated entities. then traverse this (possibly large) list and return the longest path.
  void	setOntology(Ontology newValue) DOCUMENT ME!
  int	size() total number of classifications. this will usually be larget than count (), since entities are frequently given two or more classifications, reflecting the multiple roles of many biological entities.
  String	toString() DOCUMENT ME!

  Methods inherited from class java.lang.Object

  equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

  Constructor Detail

  Annotation

  public Annotation(String species,
                    String type,
                    Ontology ontology)

  Creates a new Annotation object.

  Parameters:

  species - DOCUMENT ME!

  type - DOCUMENT ME!

  ontology - DOCUMENT ME!

  Annotation

  public Annotation(String species,
                    String type,
                    String curator)

  Creates a new Annotation object.

  Parameters:

  species - DOCUMENT ME!

  type - DOCUMENT ME!

  curator - DOCUMENT ME!

  Method Detail

  getMap

  public HashMap getMap()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  setOntology

  public void setOntology(Ontology newValue)

  DOCUMENT ME!

  Parameters:

  newValue - DOCUMENT ME!

  getOntology

  public Ontology getOntology()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  getCurator

  public String getCurator()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  getType

  public String getType()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  getOntologyType

  public String getOntologyType()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  getSpecies

  public String getSpecies()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  add

  public void add(String name,
                  int classificationID)

  create a new annotation for an entity (typically a gene) of the current species and with respect to the current ontology. an entity may have more than one classification.

  Parameters:

  name - usually an ORF name, a unique identifier for this species

  classificationID - a pointer into the ontology hierarchy

  getNames

  public String[] getNames()

  returns an array of all the names (usually ORFs) currently annotated

  getClassifications

  public int[] getClassifications()

  returns an array of all the classifications in the current annotation

  getClassifications

  public int[] getClassifications(String name)

  all of the ontology identifiers registered for the specified entity

  getClassificationsVector

  public Vector getClassificationsVector(String name)

  all of the ontology identifiers registered for the specified entity, as a Vector of Integers

  getAllHierarchyPathsAsNames

  public String[][] getAllHierarchyPathsAsNames(String name)

  DOCUMENT ME!

  Parameters:

  name - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

  count

  public int count()

  total number of entities, usually ORFs.

  size

  public int size()

  total number of classifications. this will usually be larget than count (), since entities are frequently given two or more classifications, reflecting the multiple roles of many biological entities.

  maxDepth

  public int maxDepth()

  get all of the full paths (as ints) from the ontology for all of the currently annotated entities. then traverse this (possibly large) list and return the longest path.

  toString

  public String toString()

  DOCUMENT ME!

  Overrides:

  toString in class Object

  Returns:

  DOCUMENT ME!