edu.iastate.metnet.interfaces
Interface MyMetnetServiceLocal

All Superinterfaces:

javax.ejb.EJBLocalObject

public interface MyMetnetServiceLocal
extends javax.ejb.EJBLocalObject

Local interface for MyMetnetService.

Version:

${version}

Author:

XDoclet

Method Summary

java.util.HashMap	bevGetAllLocationInfo() BirdsEyeView code
java.util.ArrayList	bevGetGoBioProcesses(java.lang.Integer goID) BirdsEyeView code
java.util.ArrayList	bevGetGoChildren(java.lang.Integer goNodeID) BirdsEyeView code
java.util.ArrayList	bevGetGoFunctions(java.lang.Integer goID) BirdsEyeView code
java.lang.Integer	bevGetGoGeneProductID(java.lang.String locusID) BirdsEyeView code
java.lang.String	bevGetGoNodeName(java.lang.Integer goNodeID) BirdsEyeView code
java.util.ArrayList	bevGetGoNodesWithinDistance(java.lang.Integer rootNodeID, int distance) BirdsEyeView code
java.util.ArrayList	bevGetGoTermAncestors(java.lang.Integer goTermID) BirdsEyeView code
java.util.ArrayList	bevGetLocations(java.lang.Integer entityID) BirdsEyeView code
java.util.ArrayList	bevGetLocusIDs(java.lang.String affyID) BirdsEyeView code
java.lang.Integer	bevGetMetnetEntityID(java.lang.String locusID) BirdsEyeView code
java.util.ArrayList	bevGetPathways(java.lang.Integer entityID) BirdsEyeView code
java.util.Map	bevGetPolypeptides(java.lang.Integer entityID) BirdsEyeView code
java.util.Map	bevGetProteinComplexes(java.lang.Integer entityID) BirdsEyeView code
java.lang.Object[]	eaQuery(java.util.Collection ebidList) we use some default values and do NOT generate JUNG graph model since it is not serializable.
AtGeneSearchLocusObject	findAtGeneLocusObject(java.lang.String locusid) test the prepared statement to handle the escape sequence in SQL language and enhance the query performance if it is used more than 60-200 times.
java.util.List	findAtGeneLocusObjectList(java.lang.String searchString) extract the list of locus object, test PHYA-3'
java.util.Map	findBlockunitInstance(java.util.Collection blockIdList) get the instance and join if necessary
Blockunit	findBlockunitInstance(java.lang.Integer blockid) get the instance and join if necessary
java.util.Collection	findCodelocationList() get the codelocation object list
java.util.Collection	findCommunityInteractionList(java.util.Collection blockIdList, int step) get the community interaction in p-step
java.util.Collection	findLiveEntityList(boolean exactMatch, java.lang.String name, java.lang.String location, java.lang.String entityType) find the live entities according to the specified query condition
java.util.List	getAllUserList() get all users in the system
java.util.Map	getBasicInformation(java.util.Map typeMap) get the basic information, name, location nad biological type for collection of blockid
java.util.List	getBlockIdList(java.util.Collection entityIdList) get the blockid based on the entityid
ChebiObject	getChebiObjectByBlockID(java.lang.Integer blockId) get the chebi information based on the compound id.
org._3pq.jgrapht.DirectedGraph	getClassNet(boolean containPathway) get current class network
java.util.ArrayList	getEidByName(java.lang.String searchString) search the entity exact match the search string.
java.util.ArrayList	getEidByName(java.lang.String searchString, java.lang.String entityType) search the entity exact match the search string.
org.apache.commons.collections.map.MultiKeyMap	getFullGeneAnnotationList() batch model query, not an object
org.apache.commons.collections.map.MultiKeyMap	getMetaboliteMap() get the map from metabolite blockid to name
java.util.Map	getNodeType(java.util.Collection blockIdList) get the node type of the collected blockid
org.apache.commons.collections.map.MultiKeyMap	getPathwayElementMap() get the full mapping between the pathways and their elements
org.apache.commons.collections.map.MultiKeyMap	getPathwayLocusMap() get the full map to pathway, locus and affy probe sets
org.apache.commons.collections.map.MultiKeyMap	getPathwayMetaboliteMap() get the map from pathway blockid to metabolite blockid
java.util.List	getPathwayObjectList(java.util.Collection pbidList, boolean includeEmpty) get the pathway object list
java.util.Collection	pubchemCasFilter(java.util.Collection nameList) filter out the cas number from synonyms
java.util.Collection	pubchemCid2Name(java.util.Collection cidList) get the pubchem synonym from pubchem cid
java.util.Collection	pubchemName2Cid(java.util.Collection nameList) this function search the table pubchem_cid_synonym to get the cid based on the name.

Methods inherited from interface javax.ejb.EJBLocalObject

getEJBLocalHome, getPrimaryKey, isIdentical, remove

Method Detail

getAllUserList

java.util.List getAllUserList()
                              throws javax.ejb.EJBException

get all users in the system

Returns:

the list of the users

Throws:

EJBException - any remote call exception

eaQuery

java.lang.Object[] eaQuery(java.util.Collection ebidList)
                           throws javax.ejb.EJBException

we use some default values and do NOT generate JUNG graph model since it is not serializable.

Parameters:

ebidList - the system nodes list

Returns:

the graph and type model

Throws:

EJBException - any remote call exception

getBlockIdList

java.util.List getBlockIdList(java.util.Collection entityIdList)
                              throws javax.ejb.EJBException

get the blockid based on the entityid

Parameters:

entityIdList - list of entity id

Returns:

the blockid list

Throws:

EJBException - any remote call exception

getBasicInformation

java.util.Map getBasicInformation(java.util.Map typeMap)
                                  throws javax.ejb.EJBException

get the basic information, name, location nad biological type for collection of blockid

Parameters:

typeMap - the type map

Returns:

the map of blockid and pathway element node

Throws:

EJBException - any remote call exception

getNodeType

java.util.Map getNodeType(java.util.Collection blockIdList)

get the node type of the collected blockid

Parameters:

collection - the blockid list

Returns:

the map from id to type

Throws:

EJBException - any remote call exception

findBlockunitInstance

java.util.Map findBlockunitInstance(java.util.Collection blockIdList)
                                    throws javax.ejb.EJBException

get the instance and join if necessary

Parameters:

blockid - the id of the blockunit

Returns:

the map of id->blockunit

Throws:

EJBException - any remote call exception

findBlockunitInstance

Blockunit findBlockunitInstance(java.lang.Integer blockid)
                                throws javax.ejb.EJBException

get the instance and join if necessary

Parameters:

blockid - the id of the blockunit

Returns:

the instance with the synonyms

Throws:

EJBException - any remote call exception

findCommunityInteractionList

java.util.Collection findCommunityInteractionList(java.util.Collection blockIdList,
                                                  int step)

get the community interaction in p-step

Parameters:

blockIdList - the starting point

step - the p-step

Returns:

the local community

Throws:

EJBException - any remote call exception

findCodelocationList

java.util.Collection findCodelocationList()
                                          throws javax.ejb.EJBException

get the codelocation object list

Returns:

the codelocation object list

Throws:

EJBException - any remote call exception

findLiveEntityList

java.util.Collection findLiveEntityList(boolean exactMatch,
                                        java.lang.String name,
                                        java.lang.String location,
                                        java.lang.String entityType)
                                        throws javax.ejb.EJBException

find the live entities according to the specified query condition

Parameters:

exactMatch - true if the name or synonym is exactly matched. false, if the name parameter can be a substring of the entity name or synonym

name - the search string, can be the full name or substring of the name.

location - subcellular compartment, can be null if not known

entityType - entity type like gene, metabolite, can be null if not known

Returns:

the blockunit information

Throws:

EJBException - any remote call exception

getClassNet

org._3pq.jgrapht.DirectedGraph getClassNet(boolean containPathway)
                                           throws javax.ejb.EJBException

get current class network

Parameters:

containPathway - if contains pathway nodes

Returns:

the class network

Throws:

EJBException - any remote call exception

findAtGeneLocusObjectList

java.util.List findAtGeneLocusObjectList(java.lang.String searchString)
                                         throws javax.ejb.EJBException

extract the list of locus object, test PHYA-3'

Parameters:

searchString - any input string separated by non-alphanum characters

Returns:

the list of locus object

Throws:

EJBException - any remote exception

getChebiObjectByBlockID

ChebiObject getChebiObjectByBlockID(java.lang.Integer blockId)
                                    throws javax.ejb.EJBException

get the chebi information based on the compound id. Notice that the ID should be parent id which is from the entity_ontology table

Parameters:

chebiCompoundID - the chebi compound id

Returns:

the chebi information data object

Throws:

EJBException - any remote call exception

pubchemCasFilter

java.util.Collection pubchemCasFilter(java.util.Collection nameList)
                                      throws javax.ejb.EJBException

filter out the cas number from synonyms

Parameters:

nameList - the synonym list

Returns:

the cas list

Throws:

EJBException - any remote call exception

pubchemName2Cid

java.util.Collection pubchemName2Cid(java.util.Collection nameList)
                                     throws javax.ejb.EJBException

this function search the table pubchem_cid_synonym to get the cid based on the name. It is not same as the query from name > sid > cid. This function, based on the description of pubchem, only consider the sid such that the cid is the standardized form of it, while the other query consider all 3 types of compound of one substance. The data set used in this function is also dowloaded from pubchem. We may use it to simplify maintainance.

Parameters:

nameList - the compound name list

Returns:

the cid list

Throws:

EJBException - any remote call exception

pubchemCid2Name

java.util.Collection pubchemCid2Name(java.util.Collection cidList)
                                     throws javax.ejb.EJBException

get the pubchem synonym from pubchem cid

Parameters:

cidList - cid list

Returns:

name list pubchem synonym list

Throws:

EJBException - any remote call exception

findAtGeneLocusObject

AtGeneSearchLocusObject findAtGeneLocusObject(java.lang.String locusid)
                                              throws javax.ejb.EJBException

test the prepared statement to handle the escape sequence in SQL language and enhance the query performance if it is used more than 60-200 times. It is said the preparedstatement is not necessary faster than the normal statement. extract locus only information

Parameters:

locusid - the locus id from the input, should be uppercase

Returns:

the locus information object

Throws:

EJBException - any remote call exception

getEidByName

java.util.ArrayList getEidByName(java.lang.String searchString)
                                 throws javax.ejb.EJBException

search the entity exact match the search string. This function copies from edu.iastate.metnet.ejb.MyName

Parameters:

searchString - search string

Returns:

the exact matched entities

Throws:

EJBException - any remote call exception

getEidByName

java.util.ArrayList getEidByName(java.lang.String searchString,
                                 java.lang.String entityType)
                                 throws javax.ejb.EJBException

search the entity exact match the search string. This function copies from edu.iastate.metnet.ejb.MyName

Parameters:

searchString - search string

Returns:

the exact matched entities

Throws:

EJBException - any remote call exception

getPathwayObjectList

java.util.List getPathwayObjectList(java.util.Collection pbidList,
                                    boolean includeEmpty)

get the pathway object list

Parameters:

pbidList - the pathway blockid list

includeEmpty - include emtpy structure?

Returns:

the pathway object list

Throws:

EJBException - any remote call exception

getPathwayElementMap

org.apache.commons.collections.map.MultiKeyMap getPathwayElementMap()
                                                                    throws javax.ejb.EJBException

get the full mapping between the pathways and their elements

Returns:

the collection of [pathway blockid, pathway name, pathway organism, entity blockid, entity name, entity location, entity organism, entityid, entity type, 1].

Throws:

EJBException - any remote call exception

getPathwayLocusMap

org.apache.commons.collections.map.MultiKeyMap getPathwayLocusMap()
                                                                  throws javax.ejb.EJBException

get the full map to pathway, locus and affy probe sets

Returns:

the collection of [pathway blockid, pathway name, pathway organism, gene blockid, gene name/locus name, gene location, gene organism, gene entity id, 'gene', affy25k id, affy8k id, 1].

Throws:

EJBException - any remote call exception

getPathwayMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getPathwayMetaboliteMap()
                                                                       throws javax.ejb.EJBException

get the map from pathway blockid to metabolite blockid

Returns:

the collection of [pathway blockid, pathway name, pathway organism, metabolite blockid, metabolite name, metabolite location, metabolite organism, metabolite entity id, 'metabolite', 1].

Throws:

EJBException - any remote call exception

getMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getMetaboliteMap()
                                                                throws javax.ejb.EJBException

get the map from metabolite blockid to name

Returns:

the collection of [blockId, name, 1].

Throws:

EJBException - any remote call exception

bevGetMetnetEntityID

java.lang.Integer bevGetMetnetEntityID(java.lang.String locusID)
                                       throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

locusID - na

Returns:

na

Throws:

EJBException - na

bevGetLocusIDs

java.util.ArrayList bevGetLocusIDs(java.lang.String affyID)
                                   throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

affyID - na

Returns:

na

Throws:

EJBException - na

bevGetPolypeptides

java.util.Map bevGetPolypeptides(java.lang.Integer entityID)
                                 throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

Throws:

EJBException - na

bevGetProteinComplexes

java.util.Map bevGetProteinComplexes(java.lang.Integer entityID)
                                     throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

Throws:

EJBException - na

bevGetLocations

java.util.ArrayList bevGetLocations(java.lang.Integer entityID)
                                    throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

Throws:

EJBException - na

bevGetPathways

java.util.ArrayList bevGetPathways(java.lang.Integer entityID)
                                   throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

Throws:

EJBException - na

bevGetGoGeneProductID

java.lang.Integer bevGetGoGeneProductID(java.lang.String locusID)
                                        throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

locusID - na

Returns:

na

Throws:

EJBException - na

bevGetGoBioProcesses

java.util.ArrayList bevGetGoBioProcesses(java.lang.Integer goID)
                                         throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

goID - na

Returns:

na

Throws:

EJBException - na

bevGetGoFunctions

java.util.ArrayList bevGetGoFunctions(java.lang.Integer goID)
                                      throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

goID - na

Returns:

na

Throws:

EJBException - na

bevGetGoChildren

java.util.ArrayList bevGetGoChildren(java.lang.Integer goNodeID)
                                     throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

goNodeID - na

Returns:

na

Throws:

EJBException - na

bevGetGoTermAncestors

java.util.ArrayList bevGetGoTermAncestors(java.lang.Integer goTermID)
                                          throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

goTermID - na

Returns:

na

Throws:

EJBException - na

bevGetGoNodesWithinDistance

java.util.ArrayList bevGetGoNodesWithinDistance(java.lang.Integer rootNodeID,
                                                int distance)
                                                throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

rootNodeID - na

distance - na

Returns:

na

Throws:

EJBException - na

bevGetGoNodeName

java.lang.String bevGetGoNodeName(java.lang.Integer goNodeID)
                                  throws javax.ejb.EJBException

BirdsEyeView code

Parameters:

goNodeID - na

Returns:

na

Throws:

EJBException - na

bevGetAllLocationInfo

java.util.HashMap bevGetAllLocationInfo()
                                        throws javax.ejb.EJBException

BirdsEyeView code

Returns:

na

Throws:

EJBException - na

getFullGeneAnnotationList

org.apache.commons.collections.map.MultiKeyMap getFullGeneAnnotationList()
                                                                         throws javax.ejb.EJBException

batch model query, not an object

Returns:

maps

Throws:

EJBException - any remote call exception