edu.iastate.metnet.hivemindService
Class AnnotationService

java.lang.Object
  edu.iastate.metnet.hivemindService.AnnotationService

public class AnnotationService
extends java.lang.Object

HiveMind service provides annotation and ontology data (mostly used by BirdsEyeView)

Author:

Mohammed Alabsi

Constructor Summary

AnnotationService()

Method Summary

java.util.HashMap	getAllLocationInfo() returns all locations in MetNetDB
static java.util.HashMap	getAllLocationMap()
static java.util.Hashtable	getAnnotationTable()
static Gene	getGeneObj(java.lang.String id) The Gene object returned by this method is not fully populated.
java.util.ArrayList	getGoBioProcesses(java.lang.Integer goID)
java.util.ArrayList	getGoChildren(java.lang.Integer goNodeID)
java.util.ArrayList	getGoFunctions(java.lang.Integer goID)
java.lang.Integer	getGoGeneProductID(java.lang.String locusID)
java.lang.String	getGoNodeName(java.lang.Integer goNodeID)
java.util.ArrayList	getGoNodesWithinDistance(java.lang.Integer rootNodeID, int distance)
java.util.ArrayList	getGoTermAncestors(java.lang.Integer goTermID)
java.util.ArrayList	getLocations(java.lang.Integer entityID)
java.util.ArrayList	getLocusIDs(java.lang.String affyID)
java.lang.Integer	getMetnetEntityID(java.lang.String locusID)
java.util.ArrayList	getPathways(java.lang.Integer entityID)
java.util.Map	getPolypeptides(java.lang.Integer entityID)
java.util.Map	getProteinComplexes(java.lang.Integer entityID)
static void	setAllLocationMap(java.util.HashMap allLocationMap)
static void	setAnnotationTable(java.util.Hashtable annotationTable)

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotationService

public AnnotationService()

Method Detail

getAllLocationInfo

public java.util.HashMap getAllLocationInfo()

returns all locations in MetNetDB

Returns:

HashMap

getGoBioProcesses

public java.util.ArrayList getGoBioProcesses(java.lang.Integer goID)

Parameters:

goID -

Returns:

ArrayList

getGoChildren

public java.util.ArrayList getGoChildren(java.lang.Integer goNodeID)

Parameters:

goNodeID -

Returns:

getGoFunctions

public java.util.ArrayList getGoFunctions(java.lang.Integer goID)

Parameters:

goID -

Returns:

getGoGeneProductID

public java.lang.Integer getGoGeneProductID(java.lang.String locusID)

Parameters:

locusID -

Returns:

getGoNodeName

public java.lang.String getGoNodeName(java.lang.Integer goNodeID)

Parameters:

goNodeID -

Returns:

getGoNodesWithinDistance

public java.util.ArrayList getGoNodesWithinDistance(java.lang.Integer rootNodeID,
                                                    int distance)

Parameters:

rootNodeID -

distance -

Returns:

getGoTermAncestors

public java.util.ArrayList getGoTermAncestors(java.lang.Integer goTermID)

Parameters:

goTermID -

Returns:

getLocations

public java.util.ArrayList getLocations(java.lang.Integer entityID)

Parameters:

entityID -

Returns:

getLocusIDs

public java.util.ArrayList getLocusIDs(java.lang.String affyID)

Parameters:

affyID -

Returns:

getMetnetEntityID

public java.lang.Integer getMetnetEntityID(java.lang.String locusID)

Parameters:

locusID -

Returns:

getPathways

public java.util.ArrayList getPathways(java.lang.Integer entityID)

Parameters:

entityID -

Returns:

getPolypeptides

public java.util.Map getPolypeptides(java.lang.Integer entityID)

Parameters:

entityID -

Returns:

getProteinComplexes

public java.util.Map getProteinComplexes(java.lang.Integer entityID)

Parameters:

entityID -

Returns:

getAllLocationMap

public static java.util.HashMap getAllLocationMap()

Returns:

setAllLocationMap

public static void setAllLocationMap(java.util.HashMap allLocationMap)

Parameters:

allLocationMap -

setAnnotationTable

public static void setAnnotationTable(java.util.Hashtable annotationTable)

Parameters:

annotationTable -

getAnnotationTable

public static java.util.Hashtable getAnnotationTable()

Returns:

getGeneObj

public static Gene getGeneObj(java.lang.String id)

The Gene object returned by this method is not fully populated. It contains the following data: 1) locusId 2) affy ids 3) location 4) pathways name 5) gene name

Parameters:

id -

Returns: