uk.ac.ebi.intact.model
Class CvDagObject

java.lang.Object
  |
  +--uk.ac.ebi.intact.model.IntactObjectImpl
        |
        +--uk.ac.ebi.intact.model.BasicObjectImpl
              |
              +--uk.ac.ebi.intact.model.AnnotatedObjectImpl
                    |
                    +--uk.ac.ebi.intact.model.CvObject
                          |
                          +--uk.ac.ebi.intact.model.CvDagObject

All Implemented Interfaces:

AnnotatedObject, BasicObject, IntactObject, java.io.Serializable

Direct Known Subclasses:

CvGoNode, CvIdentification, CvInteraction, CvInteractionType

public abstract class CvDagObject

extends CvObject

Controlled vocabulary class for CVs which are organised in a Directed Acyclic Graph (DAG). Each node many have multiple parents and multiple children.

Version:

$Id: CvDagObject.java,v 1.11 2004/01/04 19:45:29 hhe Exp $

Author:

hhe

See Also:

Serialized Form

Field Summary

Fields inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

annotations, curator, curatorAc, fullName, references, shortLabel, xrefs

Fields inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

ac, NEW_LINE

Constructor Summary

protected	CvDagObject() no-arg constructor which will hopefully be removed later...
	CvDagObject(Institution owner, java.lang.String shortLabel) Creates a valid CvDagObject instance.

Method Summary

void	addChild(CvDagObject cvDagObject)
void	addParent(CvDagObject cvDagObject)
java.util.Collection	ancestors() TODO comments
java.util.Collection	getChildren()
java.util.Collection	getParents()
CvDagObject	getRoot() TODO coments
void	removeChild(CvDagObject cvDagObject)
void	removeParent(CvDagObject cvDagObject)
java.lang.String	toGoDag(int currentDepth, CvDagObject aParent, java.lang.String goidDatabase) TODO comments
java.lang.String	toGoDag(java.lang.String goidDatabase) Create the GO flat file representation of the current object and all its descendants.

Methods inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

addAlias, addAnnotation, addReference, addXref, equals, getAliases, getAnnotations, getCurator, getCuratorAc, getFullName, getReferences, getShortLabel, getXrefs, hashCode, removeAlias, removeAnnotation, removeReference, removeXref, setAliases, setAnnotation, setCurator, setCuratorAc, setFullName, setReferences, setShortLabel, setXrefs, toString, update, updateUniqueAnnotation

Methods inherited from class uk.ac.ebi.intact.model.BasicObjectImpl

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.intact.model.BasicObject

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from interface uk.ac.ebi.intact.model.IntactObject

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Constructor Detail

CvDagObject

protected CvDagObject()

no-arg constructor which will hopefully be removed later...

CvDagObject

public CvDagObject(Institution owner,
                   java.lang.String shortLabel)

Creates a valid CvDagObject instance. Requires at least a shortLabel and an owner to be specified.

Parameters:

shortLabel - The memorable label to identify this CvDagObject

owner - The Institution which owns this CvDagObject

Throws:

java.lang.NullPointerException - thrown if either parameters are not specified

Method Detail

getChildren

public java.util.Collection getChildren()

addChild

public void addChild(CvDagObject cvDagObject)

removeChild

public void removeChild(CvDagObject cvDagObject)

getParents

public java.util.Collection getParents()

addParent

public void addParent(CvDagObject cvDagObject)

removeParent

public void removeParent(CvDagObject cvDagObject)

ancestors

public java.util.Collection ancestors()

TODO comments

Returns:

All ancestors of the current object. Each node is listed only once.

getRoot

public CvDagObject getRoot()

TODO coments

Returns:

the root node of the current term

toGoDag

public java.lang.String toGoDag(int currentDepth,
                                CvDagObject aParent,
                                java.lang.String goidDatabase)

TODO comments

Parameters:

currentDepth - The current depth in the DAG. Translated into leading blanks.

aParent - The current parents. All parents exept aParent are listed in the DAG line as additional parents.

goidDatabase - The database xref from which to generate the goid

Returns:

a single string containing the GO DAG flatfile representation of the current object and all its decendents.

toGoDag

public java.lang.String toGoDag(java.lang.String goidDatabase)

Create the GO flat file representation of the current object and all its descendants.

Returns:

a single string containing the GO DAG flatfile representation of the current object and all its descendants.