uk.ac.ebi.intact.application.goDensity.business.dag
Class CvGoDag

java.lang.Object
  |
  +--uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag

public class CvGoDag

extends java.lang.Object

CvGoDag represents a GO graph within IntAct.
Furthermore, the method todb():void can be used, to store the GO-graph in an external table, which can be used for fast & direct access (FastGoDag.java). Before you can use this class, GO has to be imported (InsertGoFromFlatfile.java)

Version:

$Id: CvGoDag.java,v 1.4 2004/01/31 11:37:16 skerrien Exp $

Author:

Markus Brosch (markus @ brosch.cc)

Constructor Summary

CvGoDag()
Constructor retrieve the root element of GO hierarchy (of typ CvGoNode) from the database.

Method Summary

java.util.Collection	getAllChilds(java.lang.String goId)
java.util.Collection	getChilds(java.lang.String goId)
CvGoNode	getCvGoNode(java.lang.String goId) get a single CvGoNode by a GoId String
java.util.Collection	getInteractors(java.lang.String goId)
void	toDb() stores the GO dag to a external table, which only stores the go hierarchy, which is used by FastGoDag
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

CvGoDag

public CvGoDag()
        throws DatabaseEmptyException,
               IntactException,
               java.sql.SQLException,
               KeyNotFoundException

Constructor retrieve the root element of GO hierarchy (of typ CvGoNode) from the database.

Throws:

DatabaseEmptyException - if no go-dag-file is jet imported into db.

IntactException

java.sql.SQLException

KeyNotFoundException

Method Detail

toDb

public void toDb()

stores the GO dag to a external table, which only stores the go hierarchy, which is used by FastGoDag

getCvGoNode

public CvGoNode getCvGoNode(java.lang.String goId)
                     throws KeyNotFoundException

get a single CvGoNode by a GoId String

Parameters:

goId -

Returns:

a CvGoNode for the related GoId

Throws:

KeyNotFoundException - if no CvGoNode is present for this GoId request Could happen, if e.g. only a part of the go-dag.ontology is imported ...

getChilds

public java.util.Collection getChilds(java.lang.String goId)
                               throws KeyNotFoundException

Parameters:

goId - for which the children want to be known

Returns:

children of an specific GoId are returned as a Collection of CvGoNodes.

Throws:

KeyNotFoundException - if goId doesn't exist as an CvGoNode Object

getAllChilds

public java.util.Collection getAllChilds(java.lang.String goId)
                                  throws KeyNotFoundException

Parameters:

goId - for which all children and subchildren want to be known

Returns:

ALL children of the goId - but be aware: only the goId Strings of the children (primaryId) will be returned as a Collection

Throws:

KeyNotFoundException - if goId doesn't exist

getInteractors

public java.util.Collection getInteractors(java.lang.String goId)

Parameters:

goId - for which all associated Interactors want to be known

Returns:

a Collection of Interactors which are associated with this node

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

See Also:

Object.toString()