cytoscape.data.annotation
Class AnnotationDescription

java.lang.Object
  cytoscape.data.annotation.AnnotationDescription

All Implemented Interfaces:

Serializable

Deprecated. Use regular CyAttributes for annotation.

@Deprecated
public class AnnotationDescription
extends Object
implements Serializable

Distinguish among different ontologies, by curator and type. For example, KEGG maintains two ontologies: metabolic pathways, and regulatory pathways. GO has three: biological process, molecular function, cellular component. This simple class captures these distinctions It will perhaps prove most useful when some data source (a biodata server, for example) contains a number of ontologies, and needs to communicate a summary of these to a client.

See Also:

Serialized Form

Field Summary

protected String	annotationType Deprecated.
protected String	curator Deprecated.
protected String	species Deprecated.

Constructor Summary

AnnotationDescription(String species, String curator, String annotationType)
Deprecated.

Method Summary

boolean	equals(Object obj) Deprecated. redefine equals so that instances with the same contents are equal.
String	getCurator() Deprecated. DOCUMENT ME!
String	getSpecies() Deprecated. DOCUMENT ME!
String	getType() Deprecated. DOCUMENT ME!
int	hashCode() Deprecated. redefine hashCode so that instances with the same contents have the same hashCode.
String	toString() Deprecated. DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Field Detail

species

protected String species

Deprecated.

curator

protected String curator

Deprecated.

annotationType

protected String annotationType

Deprecated.

Constructor Detail

AnnotationDescription

public AnnotationDescription(String species,
                             String curator,
                             String annotationType)

Deprecated.

Parameters:

species - The formal Linnaean name (genus and species) is preferred

curator - The institute or group which maintains this annotation

annotationType - The nature of this annotation, eg, "metabolic pathway", "molecular function", or "cellular component"

Method Detail

getSpecies

public String getSpecies()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

getCurator

public String getCurator()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

getType

public String getType()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

equals

public boolean equals(Object obj)

Deprecated.

redefine equals so that instances with the same contents are equal. this emulates the way that String equality is judged.

Overrides:

equals in class Object

Parameters:

obj - DOCUMENT ME!

Returns:

DOCUMENT ME!

hashCode

public int hashCode()

Deprecated.

redefine hashCode so that instances with the same contents have the same hashCode. this will make them identical when used as the keys in HashMaps, the purpose for which they were invented.

Overrides:

hashCode in class Object

Returns:

DOCUMENT ME!

toString

public String toString()

Deprecated.

DOCUMENT ME!

Overrides:

toString in class Object

Returns:

DOCUMENT ME!