edu.iastate.metnet.interfaces
Interface MyFacade

All Superinterfaces:

javax.ejb.EJBObject, java.rmi.Remote

public interface MyFacade
extends javax.ejb.EJBObject

Remote interface for MyFacade.

Version:

${version}

Author:

XDoclet

Method Summary

java.lang.Object[]	aaQuery(java.util.Collection ebidList, java.util.Collection pbidList, java.util.Collection eidList) run approximately amorphous graph query and visualize it
org._3pq.jgrapht.DirectedGraph	adjacentIbidList(java.lang.Integer ibid) things are complicated if we support multiple catalysis for one enzymatic reaction.
java.lang.Integer	checkInteraction(java.util.Vector leftPart, java.util.Vector rightPart) check if there is an interaction contains the same topolgy structure or super structure covers the provided adjacent nodes.
java.lang.Integer	checkTransInteraction(java.lang.Integer sourceBlockid, java.lang.Integer targetBlockid) create an transport, translation or transcription interaction and return the blockid of the interaction.
java.lang.Object[]	constructAlignmentMode(AlignmentObject alignment) (include all input graph element) we need construct the graph model for the alignment.
MultiPathwayGraph	constructMultiPathwayGraph(java.util.ArrayList pbidList) construct the multi-pathway graph model for TWO pathways
void	createUser(User userObject) create a new user and presume that the user does not exist
void	createUserRequest(java.lang.String username, java.lang.String organism) assign the species to the username, so this guy can only edit the data of the species.
java.util.Vector	detectAbnormalEntitywithcontext() detect abnormal record in the table entitywithcontext.
java.util.Map	detectDuplicationInteractions() get the group of same structure interactions by encoding the structure and compute the digest
java.util.Vector	detectOrphanInteraction() detect all orphan interaction in the database
java.util.Vector	detectOrphanInteraction2() detect all orphan interaction in the database
java.util.Vector	detectWrongInteraction() detect the wrong interaction which contains entitywithcontext
java.lang.Object[]	eaQuery(java.util.Collection ebidList, java.util.Collection pbidList, java.util.Collection eidList) run exactly amorphous graph query and visualize it
java.util.List	esQuery(java.util.Collection pbidList, org._3pq.jgrapht.DirectedGraph directedGraph) query the input graph from the selected pathways
java.util.List	esQuery(org._3pq.jgrapht.DirectedGraph directedGraph) esQuery.
java.util.Vector	filterCatalysis(java.util.Vector vector) given a set of interaction and remove all catalysis type interaction
java.util.Vector	findAmbiguousEntitywithlocation(java.lang.String name) find the blockunit containing the name, the name may contain double comma or tab delimer
java.util.Vector	findAmbiguousEntitywithlocationIDList(java.lang.String name) find the blockunit containing the name, the name may contain double comma or tab delimer
Blockunit	findAssociatedInteraction(java.lang.Integer leftid, java.lang.Integer rightid) find the associated interaction based on two nodes (do not consider catalysis and regulation
AtGeneSearchLocusObject	findAtGeneLocusObject(java.lang.String locusid) extract locus only information
java.util.ArrayList	findAtGeneLocusObjectList(java.lang.String searchString) extract the list of locus object
java.util.ArrayList	findAtGeneLocusObjectListByFulltext(java.lang.String searchString) extract the list of locus object by fulltext search
java.util.Map	findBlockunitInstance(java.util.Collection blockIdList) get the map id->blockunit
Blockunit	findBlockunitInstance(java.lang.Integer blockid) get the instance and join if necessary
java.util.Vector	findBrendaName(java.lang.String ecid) get the recommend name and synonym based on the ec number
java.util.Vector	findBrendaProduct(java.lang.String ecid) get the product based on the ec number
java.util.Vector	findBrendaSubstrate(java.lang.String ecid) get the substrate based on the ec number
java.util.Vector	findChebiCompoundsList() get the chebi compounds list
java.util.Vector	findChebiNamesList() get the chebi names list
ChebiOntologyName	findChebiOntologyName(java.lang.Integer chebiid) find the chebi id of the specified name from the chebi ontology
java.util.Vector	findChebiOntologyName(java.lang.String name) find the chebi id of the specified name from the chebi ontology
java.util.Vector	findCodelocationList() get the codelocation object list
java.util.Vector	findConfidenceList() get the confidence object list
java.util.Vector	findDatasourceList() get the data source object list
java.util.Vector	findDownstreamEntitywithlocation(java.lang.Integer blockid) find the substrates of the interaction
java.util.Vector	findDownstreamInteraction(Blockunit blockunit) special finder for enzymatic reaction and similar ones
java.util.Collection	findEbidListX(java.lang.String nameS, java.lang.String organism, java.lang.String entityType, java.lang.String location) find the live entity based on the name
java.util.Vector	findEntity(java.lang.String name) get all entity which contain "similar" name
java.util.Vector	findEntity(java.util.Vector nameList) get all entity which contain "similar" name in the prodvided list
Entity	findEntityInstance(java.lang.Integer entityid) get the instance and join if necessary
java.util.Map	findEntityInstance(java.util.Vector entityidvec) get the map id->entity
java.util.Vector	findEntityTypeList() get the entity type object list
java.util.Vector	findEntitywithlocation(boolean exactMatch, java.lang.String name, java.lang.String location, java.lang.String entityType, java.lang.String source) find the entitywithlocation according to the 4 criteria
java.util.Vector	findEntitywithlocation(java.lang.String name) get the entity with location contains the similar name
java.util.Vector	findEnzyme(java.lang.Integer blockid) find enzyme of the enzymatic interaction
java.util.Vector	findExactBlockunit(java.lang.String name) find the blockunit match the name exactly
java.util.Vector	findExactEntity(java.lang.String name) find the entityt match the name exactly
java.util.Vector	findExactEntity(java.lang.String name, java.lang.String entityType) find the entity based on the name and type
java.util.Vector	findExactEntitywithlocation(java.lang.String name) find the blockunit containing the name, the name may contain double comma or tab delimer
java.util.Vector	findExactEntitywithlocation(java.lang.String name, java.lang.String entityType, java.lang.String location) get the blockunit which contain the similar name and same entitytype and location
java.util.Vector	findExactInteractionInformation(java.lang.String name) search the interaction according to the entitywithlocation name
java.util.Vector	findGroupOfOwner(java.lang.String username) find the group of the owner
MyVersionGraph	findHistoryAsGraph(java.lang.Integer blockId, java.lang.String username) find all blockunit as a version graph
HistoryFlatInteraction	findHistoryFlatInteraction(java.lang.Integer blockId, java.lang.Integer recordId) get the instance of the history flat interaction
HistoryFlatLiveEntity	findHistoryFlatLiveEntity(java.lang.Integer blockId, java.lang.Integer recordId) get the instance of the history flat live entity
HistoryFlatPathway	findHistoryFlatPathway(java.lang.Integer blockId, java.lang.Integer recordId) get the instance of the history flat pathway
java.util.Collection	findIbidListX(java.lang.String nameS, java.lang.String organism, java.lang.String interactionType, java.lang.String location) find the interaction list based on the substrate and product name
java.util.Vector	findInteractionIDByEntitywithlocationID(java.lang.Integer blockid) find all associated interaction for the blockunit
java.util.Vector	findInteractionIDByName(java.lang.String name) find all associated interaction for the name
InteractionInformation	findInteractionInformation(java.lang.Integer blockid) find basic interaction informations
java.util.Vector	findInteractionInformation(java.lang.String name) search the interaction according to the entitywithlocation name
java.util.Vector	findInteractionInformationByEntitywithlocationID(java.lang.Integer entitywithlocationid) find all involved interaction except catalysis type
java.util.Vector	findInteractionTypeList() get the interaction type object list
java.util.Vector	findInvolvedPathway(Blockunit blockunit) find the involved pathway from the blockunit
java.util.List	findInvolvedPathways(java.util.Collection ebidList, java.util.Collection pbidList) collect all pathway objects related to the selected entitywithlocation
org.apache.commons.collections.keyvalue.MultiKey	findLatestControlLiveEntity(java.lang.Integer ibid, java.lang.Integer irid) find the latest control interaction
java.util.Map	findLatestInteractionPart(java.lang.Integer ibid, java.lang.Integer irid) find the latest record id list of the interaction part.
java.util.Map	findLatestPathwayPart(java.lang.Integer pbid, java.lang.Integer prid) find the latest record id list of the pathway part.
java.util.Vector	findLocationList() get the location object list
java.util.Collection	findNormalInteractionStructure(java.util.Collection leftList, java.util.Collection rightList) an optimized version of checkInteraction, should not containing interaction in the parameters.
java.util.Collection	findNormalInteractionStructureX(java.util.Map leftX, java.util.Map rightX) an extension version of finding interaction structure.
java.util.Vector	findOrganismList() get the organism object list
java.util.Collection	findPbidList(java.lang.String searchString, boolean includeEmpty) get all pathway blockid in the database for displaying in pathway selector
java.util.Collection	findPbidListX(java.lang.String nameS, java.lang.String organism) find the pathway blockid based on the name, this can be pathway name or entity name
java.util.Vector	findPubchemEntityID(java.util.Vector names) find the entity id list for the name
java.util.Vector	findPubchemID(java.util.Vector names) find the sid list according to the search name
java.util.Vector	findPubchemSynonym(java.util.Vector names) find the synonym for the given search name list
java.util.Vector	findReferenceTypeList() get the reference type object list
java.util.Vector	findRuleList() get the rule object list
java.util.Vector	findSimilarEntitywithlocationIDByName(java.lang.String name) find the name which appear in name/synonym/abbreviation EXACTLY.
java.util.Vector	findStrictPubchemEntityID(java.util.Vector names) find the entity id list for the name
java.util.Vector	findStrictPubchemID(java.util.Vector names) find the sid list according to the search name
java.util.Vector	findStrictPubchemSynonym(java.util.Vector names) find the synonym for the given search name list.
java.util.List	findTrivialMetabolite(java.lang.Integer degreeThreshold, java.lang.Integer limit) find the trivial metabolite that take part in one or more pathways
java.util.Vector	findUpstreamEntitywithlocation(java.lang.Integer blockid) find the product of the interaction
java.util.Vector	findUpstreamInteraction(Blockunit blockunit) special finder for enzymatic reaction and similar ones
User	findUserInstance(java.lang.String username) find the User instance based on the username
void	formalizeComposition() formalize the composition for those multi-enzyme reactions
java.util.Vector	getA() get the account name
java.util.Vector	getAbbreviationRules() get the abbreviation rule as "object list", mainly for SQL->Java Object
java.util.ArrayList	getAllElementNodeBlockIDList(java.lang.Integer pbid) get all member element node's blockid list for client to test the pathway membership
java.util.ArrayList	getAllPathwayObjectList2(java.lang.String searchString) get all pathway objects in the database for displaying in pathway selector
java.util.List	getAllUserList() get all users in the system
java.lang.String	getBiologicalType(java.lang.Integer blockId) get thebiological type like entitywithcontext, interaction or pathway
java.util.Map	getCandidate()
java.util.Map	getCandidate(int limit)
BidiMultiHashMap	getChebiidName() get the map of id and name
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.Vector	getCodeconfidenceList() get the codeconfidence
java.util.Vector	getCodedatasourceList() get the codeconfidence
java.util.Vector	getCodeentitytypeList() get the codeentitytype
java.util.Vector	getCodeinteractiontypeList() get the codeinteractiontype
java.util.Vector	getCodelocationList() get the codelocation
java.util.Vector	getCodeorganismList() get the codeorganism
java.util.Vector	getCodereferencetypeList() get the codereferencetype
java.util.Vector	getCoderuleList() get the coderule
java.util.List	getCoderules() get the coderule as "object list", mainly for SQL->Java Object
org.apache.commons.collections.map.MultiKeyMap	getCoefficientMap(java.util.ArrayList interactionIDList, java.util.ArrayList intermediumIDList) collect the coeffiecient given the interaction and entitywithlocation
int	getCounter() a test of state in stateless session bean
org.apache.commons.collections.map.MultiKeyMap	getEntityIdListOfPathway() collection version of getEntityIdListOfPathway()
java.util.Collection	getEntityIdListOfPathway(java.lang.Integer pbid) get the entity id list of specified pathway
java.lang.Integer	getEntityIdOfUniqueId(Blockunit blockunit) this function is used to test if the given AraCyc entry has a corresponding entity id in MetNetDB.
java.util.Collection	getEntityIdOfUniqueId(java.util.Collection blockunitList) collection version of getEntityIdOfUniqueId().
java.util.List	getGroupMemberList(java.lang.Integer groupid) get the member of the specified group
java.util.List	getHistoryReport(java.util.Date fromDate, java.util.Date toDate, java.lang.Integer numLimit) get the history report
java.lang.String	getInteractionChange(HistoryFlatInteraction history) get the summary report about the change of version
InteractionObject	getInteractionObject(java.lang.Integer blockid) get more interaction information
java.util.Set	getInvolvedPbidSet(java.lang.Integer ebid) get the involved pathway list
HistoryBlockunit	getLatestHistory(java.lang.Integer blockId) always get the latest history so we can determine if something is changed during the data load and update session.
java.lang.String	getLiveEntityChange(HistoryFlatLiveEntity history) get the summary report about the change of version
org.apache.commons.collections.map.MultiKeyMap	getMetaboliteMap() get the map from metabolite blockid to name
java.util.Vector	getP() get the password
java.lang.String	getPathwayChange(HistoryFlatPathway history) get the summary report about the change of version
java.util.Set	getPathwayComponentSet(java.util.Collection pbidList) get all element in the selected pathways
java.util.List	getPathwayCoverList(java.util.Collection ibidList) return the pathway that covers the selected interaction list
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.List	getPbidList() get the pbid list
java.util.Collection	getPbidList4Class(java.lang.Integer classId) get the collection of the pbid list for specified class id
boolean	isOrphanInteraction(java.lang.Integer blockid) detect if the blockunit is orphan
boolean	isVisibleBlockunit(Blockunit blockunit, java.lang.String username) determine the visibility of the blockunit based on the share capability
boolean	isVisibleBlockunit(java.lang.Integer blockid, java.lang.String username) determine the visibility of the blockunit based on the share capability
java.util.Vector	iterateCompositionInteraction(java.lang.Integer complexid) iterate the searching of the many-to-one interactions, be careful about loops.
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.
java.lang.Integer	recognizeControlInteraction() depends on the controlled interaction?
java.lang.Integer	recognizeNormalInteraction() recognize the interaction and create it if necesaary.
java.lang.Integer	recognizeNormalLiveEntity(java.lang.String name, java.lang.String entityType, java.lang.String location, java.lang.String organism, java.lang.String source, java.lang.String username, java.lang.String aracycId) recognize the live entity and create the live entity if necessary, since the data can be from expert data or aracyc, so source and username are parameters also.
java.lang.Object[]	remoteLayout(java.lang.String bitstream) run layout on the server
java.util.Vector	remoteSelect(java.lang.String hql) let hibernate run at remote side
java.util.List	sortAlignmentList(java.util.Collection alignList) sort the alignment list
boolean	testPathwayName(java.lang.String name, java.lang.String organism) test if the pathway name exists
void	updateUser(User userObject) create a new user and presume that the user does not exist

Methods inherited from interface javax.ejb.EJBObject

getEJBHome, getHandle, getPrimaryKey, isIdentical, remove

Method Detail

getAbbreviationRules

java.util.Vector getAbbreviationRules()
                                      throws java.rmi.RemoteException

get the abbreviation rule as "object list", mainly for SQL->Java Object

Returns:

the list of the class abbreviationrules

Throws:

java.rmi.RemoteException

getCoderules

java.util.List getCoderules()
                            throws java.rmi.RemoteException

get the coderule as "object list", mainly for SQL->Java Object

Returns:

the list of the class coderule

Throws:

java.rmi.RemoteException

getAllUserList

java.util.List getAllUserList()
                              throws java.rmi.RemoteException

get all users in the system

Returns:

the list of the users

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getGroupMemberList

java.util.List getGroupMemberList(java.lang.Integer groupid)
                                  throws java.rmi.RemoteException

get the member of the specified group

Parameters:

groupid -

Returns:

the user list of the group

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEntitywithlocation

java.util.Vector findEntitywithlocation(java.lang.String name)
                                        throws java.rmi.RemoteException

get the entity with location contains the similar name

Parameters:

name - the search string

Returns:

the entity list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findAmbiguousEntitywithlocation

java.util.Vector findAmbiguousEntitywithlocation(java.lang.String name)
                                                 throws java.rmi.RemoteException

find the blockunit containing the name, the name may contain double comma or tab delimer

Parameters:

name - the search string may containing double common or delimer

Returns:

the list of the entitywithlocation

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findExactEntitywithlocation

java.util.Vector findExactEntitywithlocation(java.lang.String name)
                                             throws java.rmi.RemoteException

find the blockunit containing the name, the name may contain double comma or tab delimer

Parameters:

name - the search string may containing double common or delimer

Returns:

the list of the entitywithlocation

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findAmbiguousEntitywithlocationIDList

java.util.Vector findAmbiguousEntitywithlocationIDList(java.lang.String name)
                                                       throws java.rmi.RemoteException

find the blockunit containing the name, the name may contain double comma or tab delimer

Parameters:

name - the search string may containing double common or delimer

Returns:

the list of id of the entitywithlocation

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findBlockunitInstance

java.util.Map findBlockunitInstance(java.util.Collection blockIdList)
                                    throws java.rmi.RemoteException

get the map id->blockunit

Parameters:

blockIdList - the list of blockid

Returns:

the map of id->blockunit

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEntityInstance

java.util.Map findEntityInstance(java.util.Vector entityidvec)
                                 throws java.rmi.RemoteException

get the map id->entity

Parameters:

blockidvec - the list of entityid

Returns:

the map of id->entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findBrendaProduct

java.util.Vector findBrendaProduct(java.lang.String ecid)
                                   throws java.rmi.RemoteException

get the product based on the ec number

Parameters:

ecid - ec number

Returns:

list of product

Throws:

EJBException

java.rmi.RemoteException

findBrendaSubstrate

java.util.Vector findBrendaSubstrate(java.lang.String ecid)
                                     throws java.rmi.RemoteException

get the substrate based on the ec number

Parameters:

ecid - ec number

Returns:

list of substrate

Throws:

EJBException

java.rmi.RemoteException

findBrendaName

java.util.Vector findBrendaName(java.lang.String ecid)
                                throws java.rmi.RemoteException

get the recommend name and synonym based on the ec number

Parameters:

ecid - the ec number

Returns:

name/synonym list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findBlockunitInstance

Blockunit findBlockunitInstance(java.lang.Integer blockid)
                                throws java.rmi.RemoteException

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

java.rmi.RemoteException

findEntityInstance

Entity findEntityInstance(java.lang.Integer entityid)
                          throws java.rmi.RemoteException

get the instance and join if necessary

Parameters:

entityid - the id of the entity

Returns:

the instance with the synonyms

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findUserInstance

User findUserInstance(java.lang.String username)
                      throws java.rmi.RemoteException

find the User instance based on the username

Parameters:

username - the account of the user

Returns:

the User instance

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createUser

void createUser(User userObject)
                throws java.rmi.RemoteException

create a new user and presume that the user does not exist

Parameters:

userObject - new user

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

updateUser

void updateUser(User userObject)
                throws java.rmi.RemoteException

create a new user and presume that the user does not exist

Parameters:

userObject - new user

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getCodelocationList

java.util.Vector getCodelocationList()
                                     throws java.rmi.RemoteException

get the codelocation

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodeconfidenceList

java.util.Vector getCodeconfidenceList()
                                       throws java.rmi.RemoteException

get the codeconfidence

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodedatasourceList

java.util.Vector getCodedatasourceList()
                                       throws java.rmi.RemoteException

get the codeconfidence

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodeentitytypeList

java.util.Vector getCodeentitytypeList()
                                       throws java.rmi.RemoteException

get the codeentitytype

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodeinteractiontypeList

java.util.Vector getCodeinteractiontypeList()
                                            throws java.rmi.RemoteException

get the codeinteractiontype

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodeorganismList

java.util.Vector getCodeorganismList()
                                     throws java.rmi.RemoteException

get the codeorganism

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCodereferencetypeList

java.util.Vector getCodereferencetypeList()
                                          throws java.rmi.RemoteException

get the codereferencetype

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

getCoderuleList

java.util.Vector getCoderuleList()
                                 throws java.rmi.RemoteException

get the coderule

Returns:

the list of codelocation

Throws:

any - remote call exception

java.rmi.RemoteException

findDownstreamInteraction

java.util.Vector findDownstreamInteraction(Blockunit blockunit)
                                           throws java.rmi.RemoteException

special finder for enzymatic reaction and similar ones

Parameters:

blockunit - the catalysis interaction

Returns:

the list of enzymatic interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

filterCatalysis

java.util.Vector filterCatalysis(java.util.Vector vector)
                                 throws java.rmi.RemoteException

given a set of interaction and remove all catalysis type interaction

Parameters:

vector - the list of the interactions

Returns:

interaction list without catalysis type interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findUpstreamInteraction

java.util.Vector findUpstreamInteraction(Blockunit blockunit)
                                         throws java.rmi.RemoteException

special finder for enzymatic reaction and similar ones

Parameters:

blockunit - the enzymatic reactions

Returns:

the list of catalysis reactions

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteSelect

java.util.Vector remoteSelect(java.lang.String hql)
                              throws java.rmi.RemoteException

let hibernate run at remote side

Parameters:

hql - the HQL to do the select

Returns:

the object lists

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findConfidenceList

java.util.Vector findConfidenceList()
                                    throws java.rmi.RemoteException

get the confidence object list

Returns:

the confidence object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findChebiCompoundsList

java.util.Vector findChebiCompoundsList()
                                        throws java.rmi.RemoteException

get the chebi compounds list

Returns:

the object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findChebiNamesList

java.util.Vector findChebiNamesList()
                                    throws java.rmi.RemoteException

get the chebi names list

Returns:

the object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findSimilarEntitywithlocationIDByName

java.util.Vector findSimilarEntitywithlocationIDByName(java.lang.String name)
                                                       throws java.rmi.RemoteException

find the name which appear in name/synonym/abbreviation EXACTLY.

Parameters:

name - the search name

Returns:

the list of blockid

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findDatasourceList

java.util.Vector findDatasourceList()
                                    throws java.rmi.RemoteException

get the data source object list

Returns:

the data source object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findOrganismList

java.util.Vector findOrganismList()
                                  throws java.rmi.RemoteException

get the organism object list

Returns:

the organism object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEntityTypeList

java.util.Vector findEntityTypeList()
                                    throws java.rmi.RemoteException

get the entity type object list

Returns:

the entity type object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionTypeList

java.util.Vector findInteractionTypeList()
                                         throws java.rmi.RemoteException

get the interaction type object list

Returns:

the interaction type object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findLocationList

java.util.Vector findLocationList()
                                  throws java.rmi.RemoteException

get the location object list

Returns:

the location object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findCodelocationList

java.util.Vector findCodelocationList()
                                      throws java.rmi.RemoteException

get the codelocation object list

Returns:

the codelocation object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findReferenceTypeList

java.util.Vector findReferenceTypeList()
                                       throws java.rmi.RemoteException

get the reference type object list

Returns:

the reference type object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findRuleList

java.util.Vector findRuleList()
                              throws java.rmi.RemoteException

get the rule object list

Returns:

the rule object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findExactBlockunit

java.util.Vector findExactBlockunit(java.lang.String name)
                                    throws java.rmi.RemoteException

find the blockunit match the name exactly

Parameters:

name - the name

Returns:

the list of the blockunit

Throws:

EJBException - any remote cal exception

java.rmi.RemoteException

findExactEntity

java.util.Vector findExactEntity(java.lang.String name)
                                 throws java.rmi.RemoteException

find the entityt match the name exactly

Parameters:

name - the name

Returns:

the list of the entity

Throws:

EJBException - any remote cal exception

java.rmi.RemoteException

getCandidate

java.util.Map getCandidate()
                           throws java.rmi.RemoteException

Throws:

java.rmi.RemoteException

getCandidate

java.util.Map getCandidate(int limit)
                           throws java.rmi.RemoteException

Throws:

java.rmi.RemoteException

findExactEntity

java.util.Vector findExactEntity(java.lang.String name,
                                 java.lang.String entityType)
                                 throws java.rmi.RemoteException

find the entity based on the name and type

Parameters:

name - the name of the entity

entityType - the type of the entity

Returns:

the list of the entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEnzyme

java.util.Vector findEnzyme(java.lang.Integer blockid)
                            throws java.rmi.RemoteException

find enzyme of the enzymatic interaction

Parameters:

blockid - the id of enzymatic interaction

Returns:

the blockid list of the enzyme

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEntity

java.util.Vector findEntity(java.lang.String name)
                            throws java.rmi.RemoteException

get all entity which contain "similar" name

Parameters:

name - the search string

Returns:

the vector of the entity

Throws:

EJBException - any remote exception

java.rmi.RemoteException

findEntity

java.util.Vector findEntity(java.util.Vector nameList)
                            throws java.rmi.RemoteException

get all entity which contain "similar" name in the prodvided list

Parameters:

nameList - the search string list

Returns:

the vector of the entity

Throws:

EJBException - any remote exception

java.rmi.RemoteException

findExactEntitywithlocation

java.util.Vector findExactEntitywithlocation(java.lang.String name,
                                             java.lang.String entityType,
                                             java.lang.String location)
                                             throws java.rmi.RemoteException

get the blockunit which contain the similar name and same entitytype and location

Parameters:

name - entity name

entityType - entity type

location - location of the entity

Returns:

vector of the entities

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findDownstreamEntitywithlocation

java.util.Vector findDownstreamEntitywithlocation(java.lang.Integer blockid)
                                                  throws java.rmi.RemoteException

find the substrates of the interaction

Parameters:

blockid - the blockid of the interaction

Returns:

the list of the substrates

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findUpstreamEntitywithlocation

java.util.Vector findUpstreamEntitywithlocation(java.lang.Integer blockid)
                                                throws java.rmi.RemoteException

find the product of the interaction

Parameters:

blockid - the blockid of the interaction

Returns:

the list of the product

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

detectWrongInteraction

java.util.Vector detectWrongInteraction()
                                        throws java.rmi.RemoteException

detect the wrong interaction which contains entitywithcontext

Returns:

the blockid list of the wrong interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionIDByEntitywithlocationID

java.util.Vector findInteractionIDByEntitywithlocationID(java.lang.Integer blockid)
                                                         throws java.rmi.RemoteException

find all associated interaction for the blockunit

Parameters:

blockid - the id of the entitywithlocation

Returns:

the interaction id list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionIDByName

java.util.Vector findInteractionIDByName(java.lang.String name)
                                         throws java.rmi.RemoteException

find all associated interaction for the name

Parameters:

name - the search string

Returns:

the interaction id list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionInformation

InteractionInformation findInteractionInformation(java.lang.Integer blockid)
                                                  throws java.rmi.RemoteException

find basic interaction informations

Parameters:

blockid - the id of the interaction

Returns:

the basic informatiof the interaction, which includes pathways, name, type, substrates, products and enzymes

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionInformation

java.util.Vector findInteractionInformation(java.lang.String name)
                                            throws java.rmi.RemoteException

search the interaction according to the entitywithlocation name

Parameters:

name - entitywithlocation name

Returns:

the involved interaction list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findExactInteractionInformation

java.util.Vector findExactInteractionInformation(java.lang.String name)
                                                 throws java.rmi.RemoteException

search the interaction according to the entitywithlocation name

Parameters:

name - entitywithlocation name

Returns:

the involved interaction list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInteractionInformationByEntitywithlocationID

java.util.Vector findInteractionInformationByEntitywithlocationID(java.lang.Integer entitywithlocationid)
                                                                  throws java.rmi.RemoteException

find all involved interaction except catalysis type

Parameters:

blockid - the entitywithlocation's blockid

Returns:

the involved interactions

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

iterateCompositionInteraction

java.util.Vector iterateCompositionInteraction(java.lang.Integer complexid)
                                               throws java.rmi.RemoteException

iterate the searching of the many-to-one interactions, be careful about loops. notice that these interaction compose of an arbitrary pathway model

Parameters:

blockid - the start point of the whole arbitrary pathway

Returns:

all of the interactions, which has been joined

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findChebiOntologyName

java.util.Vector findChebiOntologyName(java.lang.String name)
                                       throws java.rmi.RemoteException

find the chebi id of the specified name from the chebi ontology

Parameters:

name - search name

Returns:

the list of chebiid

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getAllPathwayObjectList2

java.util.ArrayList getAllPathwayObjectList2(java.lang.String searchString)
                                             throws java.rmi.RemoteException

get all pathway objects in the database for displaying in pathway selector

Returns:

the list of all pathway objects

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPathwayObjectList

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

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

java.rmi.RemoteException

findInvolvedPathways

java.util.List findInvolvedPathways(java.util.Collection ebidList,
                                    java.util.Collection pbidList)
                                    throws java.rmi.RemoteException

collect all pathway objects related to the selected entitywithlocation

Parameters:

ebidList - the blockid list of the selected entitywithlocation

pbidList - the blockid list of pathway NOT to be returned

Returns:

the pathway object list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findChebiOntologyName

ChebiOntologyName findChebiOntologyName(java.lang.Integer chebiid)
                                        throws java.rmi.RemoteException

find the chebi id of the specified name from the chebi ontology

Parameters:

chebiid - the id of chebi

Returns:

the chebiontologyname object contains all descendant name source

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getChebiidName

BidiMultiHashMap getChebiidName()
                                throws java.rmi.RemoteException

get the map of id and name

Returns:

the mapping

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findPubchemID

java.util.Vector findPubchemID(java.util.Vector names)
                               throws java.rmi.RemoteException

find the sid list according to the search name

Parameters:

names - the search name list

Returns:

the sid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findPubchemSynonym

java.util.Vector findPubchemSynonym(java.util.Vector names)
                                    throws java.rmi.RemoteException

find the synonym for the given search name list

Parameters:

names - the search name list

Returns:

the list of the synonym

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findPubchemEntityID

java.util.Vector findPubchemEntityID(java.util.Vector names)
                                     throws java.rmi.RemoteException

find the entity id list for the name

Parameters:

names - the search name

Returns:

the entityid list

Throws:

EJBException

java.rmi.RemoteException

findStrictPubchemEntityID

java.util.Vector findStrictPubchemEntityID(java.util.Vector names)
                                           throws java.rmi.RemoteException

find the entity id list for the name

Parameters:

names - the search name

Returns:

the entityid list

Throws:

EJBException

java.rmi.RemoteException

findStrictPubchemID

java.util.Vector findStrictPubchemID(java.util.Vector names)
                                     throws java.rmi.RemoteException

find the sid list according to the search name

Parameters:

names - the search name list

Returns:

the sid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findStrictPubchemSynonym

java.util.Vector findStrictPubchemSynonym(java.util.Vector names)
                                          throws java.rmi.RemoteException

find the synonym for the given search name list.

Parameters:

names - the search name list

Returns:

the list of the synonym

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findAssociatedInteraction

Blockunit findAssociatedInteraction(java.lang.Integer leftid,
                                    java.lang.Integer rightid)
                                    throws java.rmi.RemoteException

find the associated interaction based on two nodes (do not consider catalysis and regulation

Parameters:

leftid - the blockid of the left node

rightid - the blockid of the right node

Returns:

the interaction object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getA

java.util.Vector getA()
                      throws java.rmi.RemoteException

get the account name

Returns:

the account name

Throws:

EJBException

java.rmi.RemoteException

getP

java.util.Vector getP()
                      throws java.rmi.RemoteException

get the password

Returns:

the password

Throws:

EJBException

java.rmi.RemoteException

findGroupOfOwner

java.util.Vector findGroupOfOwner(java.lang.String username)
                                  throws java.rmi.RemoteException

find the group of the owner

Parameters:

username - the owner

Returns:

the list of the group object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

isVisibleBlockunit

boolean isVisibleBlockunit(java.lang.Integer blockid,
                           java.lang.String username)
                           throws java.rmi.RemoteException

determine the visibility of the blockunit based on the share capability

Parameters:

blockid - the id of the blockunit

username - the id of the user

Returns:

true if visible, false if not

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

isVisibleBlockunit

boolean isVisibleBlockunit(Blockunit blockunit,
                           java.lang.String username)
                           throws java.rmi.RemoteException

determine the visibility of the blockunit based on the share capability

Parameters:

blockunit - the blockunit

username - the id of the user

Returns:

true if visible, false if not

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEntitywithlocation

java.util.Vector findEntitywithlocation(boolean exactMatch,
                                        java.lang.String name,
                                        java.lang.String location,
                                        java.lang.String entityType,
                                        java.lang.String source)
                                        throws java.rmi.RemoteException

find the entitywithlocation according to the 4 criteria

Parameters:

exactMatch - if search by exact match

name - search nme

location - entity's location

entityType - entity type

source - data source

Returns:

vector of entitywithlocation instance

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

isOrphanInteraction

boolean isOrphanInteraction(java.lang.Integer blockid)
                            throws java.rmi.RemoteException

detect if the blockunit is orphan

Parameters:

blockid - the id of the blockunit

Returns:

true if orphan and false if not

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

detectOrphanInteraction

java.util.Vector detectOrphanInteraction()
                                         throws java.rmi.RemoteException

detect all orphan interaction in the database

Returns:

the vector of the blockid of the orphan interaction in the database

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

detectOrphanInteraction2

java.util.Vector detectOrphanInteraction2()
                                          throws java.rmi.RemoteException

detect all orphan interaction in the database

Returns:

the pathway name where orphan exists

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getCounter

int getCounter()
               throws java.rmi.RemoteException

a test of state in stateless session bean

Throws:

java.rmi.RemoteException

detectDuplicationInteractions

java.util.Map detectDuplicationInteractions()
                                            throws java.rmi.RemoteException

get the group of same structure interactions by encoding the structure and compute the digest

Returns:

the map (digest->list of interaction id(s))

Throws:

java.rmi.RemoteException

detectAbnormalEntitywithcontext

java.util.Vector detectAbnormalEntitywithcontext()
                                                 throws java.rmi.RemoteException

detect abnormal record in the table entitywithcontext.

Returns:

list of distinct blockname, this is for manually caration, so blockid is not useful

Throws:

EJBException

java.rmi.RemoteException

checkInteraction

java.lang.Integer checkInteraction(java.util.Vector leftPart,
                                   java.util.Vector rightPart)
                                   throws java.rmi.RemoteException

check if there is an interaction contains the same topolgy structure or super structure covers the provided adjacent nodes.

Parameters:

leftPart - blockid of left part of the proposed interaction

rightPart - blockid of right part of the proposed interaction

Returns:

the blockid with same topology structure or null is not found

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getCoefficientMap

org.apache.commons.collections.map.MultiKeyMap getCoefficientMap(java.util.ArrayList interactionIDList,
                                                                 java.util.ArrayList intermediumIDList)
                                                                 throws java.rmi.RemoteException

collect the coeffiecient given the interaction and entitywithlocation

Parameters:

interactionIDList - the blockid list of the interactions

intermediumIDList - the blockid list o f the entitywithlocations

Returns:

thw multikeymap like (interaction_id, entity_id)=>coefficient

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

formalizeComposition

void formalizeComposition()
                          throws java.rmi.RemoteException

formalize the composition for those multi-enzyme reactions

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findAtGeneLocusObject

AtGeneSearchLocusObject findAtGeneLocusObject(java.lang.String locusid)
                                              throws java.rmi.RemoteException

extract locus only information

Parameters:

locusid - the locus id from the input

Returns:

the locus information object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findInvolvedPathway

java.util.Vector findInvolvedPathway(Blockunit blockunit)
                                     throws java.rmi.RemoteException

find the involved pathway from the blockunit

Parameters:

blockunit - interaction or entityeithlocation

Returns:

the list of pathway object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findAtGeneLocusObjectList

java.util.ArrayList findAtGeneLocusObjectList(java.lang.String searchString)
                                              throws java.rmi.RemoteException

extract the list of locus object

Parameters:

searchString - any input string separated by non-alphanum characters

Returns:

the list of locus object

Throws:

EJBException - any remote exception

java.rmi.RemoteException

findAtGeneLocusObjectListByFulltext

java.util.ArrayList findAtGeneLocusObjectListByFulltext(java.lang.String searchString)
                                                        throws java.rmi.RemoteException

extract the list of locus object by fulltext search

Parameters:

searchString - any input string for fulltext search

Returns:

the list of locus object

Throws:

EJBException - any remote exception

java.rmi.RemoteException

getChebiObjectByBlockID

ChebiObject getChebiObjectByBlockID(java.lang.Integer blockid)
                                    throws java.rmi.RemoteException

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

java.rmi.RemoteException

getInteractionObject

InteractionObject getInteractionObject(java.lang.Integer blockid)
                                       throws java.rmi.RemoteException

get more interaction information

Parameters:

blockid - the blockid of the interaction

Returns:

the interaction infomation data object

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getAllElementNodeBlockIDList

java.util.ArrayList getAllElementNodeBlockIDList(java.lang.Integer pbid)
                                                 throws java.rmi.RemoteException

get all member element node's blockid list for client to test the pathway membership

Parameters:

pbid - the blockid of the pathway

Returns:

the member's blockid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

constructMultiPathwayGraph

MultiPathwayGraph constructMultiPathwayGraph(java.util.ArrayList pbidList)
                                             throws java.rmi.RemoteException

construct the multi-pathway graph model for TWO pathways

Parameters:

pbidList - the pathway id list, we only use the first two

Returns:

the multi-pathway graph model

Throws:

EJBException - any remote exception

java.rmi.RemoteException

findTrivialMetabolite

java.util.List findTrivialMetabolite(java.lang.Integer degreeThreshold,
                                     java.lang.Integer limit)
                                     throws java.rmi.RemoteException

find the trivial metabolite that take part in one or more pathways

Parameters:

degreeThreshold - the threshold of the degree

limit - the return list upper size

Returns:

the list of trivial nodes

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

remoteLayout

java.lang.Object[] remoteLayout(java.lang.String bitstream)
                                throws java.rmi.RemoteException

run layout on the server

Parameters:

bitstream - the bitstream of GraphViz

Returns:

the tuple containing zvertex list and zedge list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

eaQuery

java.lang.Object[] eaQuery(java.util.Collection ebidList,
                           java.util.Collection pbidList,
                           java.util.Collection eidList)
                           throws java.rmi.RemoteException

run exactly amorphous graph query and visualize it

Parameters:

ebidList - the entity blockid list

pbidList - the pathway blockid list

eidList - the trivial node entity id list *

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

aaQuery

java.lang.Object[] aaQuery(java.util.Collection ebidList,
                           java.util.Collection pbidList,
                           java.util.Collection eidList)
                           throws java.rmi.RemoteException

run approximately amorphous graph query and visualize it

Parameters:

ebidList - the entity blockid list

pbidList - the pathway blockid list

eidList - the trivial node entity id list

Returns:

the system subgraph, type map and derived system node list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

esQuery

java.util.List esQuery(org._3pq.jgrapht.DirectedGraph directedGraph)
                       throws java.rmi.RemoteException

esQuery.

Parameters:

directedGraph - directed graph model, vertex is the blockid

Returns:

sorted shrinked alignment list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

esQuery

java.util.List esQuery(java.util.Collection pbidList,
                       org._3pq.jgrapht.DirectedGraph directedGraph)
                       throws java.rmi.RemoteException

query the input graph from the selected pathways

Parameters:

pbidList - the blockid list of selected pathways

inputGraph - the input graph

Returns:

sorted shrinked alignment list

Throws:

java.rmi.RemoteException

sortAlignmentList

java.util.List sortAlignmentList(java.util.Collection alignList)
                                 throws java.rmi.RemoteException

sort the alignment list

Parameters:

alignList - the alignment list

Returns:

sorted list

Throws:

java.rmi.RemoteException

findHistoryAsGraph

MyVersionGraph findHistoryAsGraph(java.lang.Integer blockId,
                                  java.lang.String username)
                                  throws java.rmi.RemoteException

find all blockunit as a version graph

Parameters:

blockid - the blockid of the blockunit(s)

username - session username

Returns:

the version graph

Throws:

EJBException - any remote exception

java.rmi.RemoteException

findLatestPathwayPart

java.util.Map findLatestPathwayPart(java.lang.Integer pbid,
                                    java.lang.Integer prid)
                                    throws java.rmi.RemoteException

find the latest record id list of the pathway part.

Parameters:

pbid - the blockid of the interaction

prid - the record id of the interaction

Throws:

java.rmi.RemoteException

findLatestInteractionPart

java.util.Map findLatestInteractionPart(java.lang.Integer ibid,
                                        java.lang.Integer irid)
                                        throws java.rmi.RemoteException

find the latest record id list of the interaction part.

Parameters:

ibid - the blockid of the interaction

irid - the record id of the interaction

return - the mapping of ebid and erid of live entity

Throws:

java.rmi.RemoteException

findHistoryFlatInteraction

HistoryFlatInteraction findHistoryFlatInteraction(java.lang.Integer blockId,
                                                  java.lang.Integer recordId)
                                                  throws java.rmi.RemoteException

get the instance of the history flat interaction

Parameters:

blockId - the blockid of the interaction

recordId - the record id of the interaction

Returns:

the instance of the interaction

Throws:

java.rmi.RemoteException

findHistoryFlatLiveEntity

HistoryFlatLiveEntity findHistoryFlatLiveEntity(java.lang.Integer blockId,
                                                java.lang.Integer recordId)
                                                throws java.rmi.RemoteException

get the instance of the history flat live entity

Parameters:

blockId - the blockid of the live entity

recordId - the record id of the live entity

Returns:

the instance of the live entity

Throws:

java.rmi.RemoteException

findHistoryFlatPathway

HistoryFlatPathway findHistoryFlatPathway(java.lang.Integer blockId,
                                          java.lang.Integer recordId)
                                          throws java.rmi.RemoteException

get the instance of the history flat pathway

Parameters:

blockId - the blockid of the pathway

recordId - the record id of the pathway

Returns:

the instance of the pathway

Throws:

java.rmi.RemoteException

findLatestControlLiveEntity

org.apache.commons.collections.keyvalue.MultiKey findLatestControlLiveEntity(java.lang.Integer ibid,
                                                                             java.lang.Integer irid)
                                                                             throws java.rmi.RemoteException

find the latest control interaction

Parameters:

ibid - the blockid of the interaction

irid - the recordid of the interaction

Returns:

the control live entity's blockid and record id, or null if no control live entity found

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getLiveEntityChange

java.lang.String getLiveEntityChange(HistoryFlatLiveEntity history)
                                     throws java.rmi.RemoteException

get the summary report about the change of version

Parameters:

history - the current version

Returns:

the difference between this version and last version

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getInteractionChange

java.lang.String getInteractionChange(HistoryFlatInteraction history)
                                      throws java.rmi.RemoteException

get the summary report about the change of version

Parameters:

history - the current version

Returns:

the difference between this version and last version

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPathwayChange

java.lang.String getPathwayChange(HistoryFlatPathway history)
                                  throws java.rmi.RemoteException

get the summary report about the change of version

Parameters:

history - the current version

Returns:

the difference between this version and last version

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getHistoryReport

java.util.List getHistoryReport(java.util.Date fromDate,
                                java.util.Date toDate,
                                java.lang.Integer numLimit)
                                throws java.rmi.RemoteException

get the history report

Parameters:

fromDate - the start date

toDate - the end date

numLimit - the number up to what to be returned

Returns:

the returned report

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getInvolvedPbidSet

java.util.Set getInvolvedPbidSet(java.lang.Integer ebid)
                                 throws java.rmi.RemoteException

get the involved pathway list

Parameters:

ebid - the blockid of the live entity

Returns:

the pbid set

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

testPathwayName

boolean testPathwayName(java.lang.String name,
                        java.lang.String organism)
                        throws java.rmi.RemoteException

test if the pathway name exists

Parameters:

name - the name to be test

organism - the organism to be test

Returns:

true if exists, false if not

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getLatestHistory

HistoryBlockunit getLatestHistory(java.lang.Integer blockId)
                                  throws java.rmi.RemoteException

always get the latest history so we can determine if something is changed during the data load and update session.

Parameters:

blockId - the blockid of the blockunit

Returns:

the current latest version of the blockunit, if no, return null

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

constructAlignmentMode

java.lang.Object[] constructAlignmentMode(AlignmentObject alignment)
                                          throws java.rmi.RemoteException

(include all input graph element) we need construct the graph model for the alignment.

Parameters:

alignment - the alignment object

Returns:

the network, type map, alignment object again

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPbidList

java.util.List getPbidList()
                           throws java.rmi.RemoteException

get the pbid list

Returns:

the pbid list

Throws:

java.rmi.RemoteException

getClassNet

org._3pq.jgrapht.DirectedGraph getClassNet(boolean containPathway)
                                           throws java.rmi.RemoteException

get current class network

Parameters:

containPathway - if contains pathway nodes

Returns:

the class network

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPbidList4Class

java.util.Collection getPbidList4Class(java.lang.Integer classId)
                                       throws java.rmi.RemoteException

get the collection of the pbid list for specified class id

Parameters:

classId - the class id

Returns:

the pathway blockid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

createUserRequest

void createUserRequest(java.lang.String username,
                       java.lang.String organism)
                       throws java.rmi.RemoteException

assign the species to the username, so this guy can only edit the data of the species.

Parameters:

username - the account name

organism - the organism

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findNormalInteractionStructure

java.util.Collection findNormalInteractionStructure(java.util.Collection leftList,
                                                    java.util.Collection rightList)
                                                    throws java.rmi.RemoteException

an optimized version of checkInteraction, should not containing interaction in the parameters.

Parameters:

leftList - the left substrates

rightList - the right substrates

considerInteraction - if consider the connected interaction or only compare the live entity structure

validIbidSet - if consider the interaction, this contains all available interaction set

Returns:

the blockid list of interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findPbidList

java.util.Collection findPbidList(java.lang.String searchString,
                                  boolean includeEmpty)
                                  throws java.rmi.RemoteException

get all pathway blockid in the database for displaying in pathway selector

Returns:

the list of all pathway objects

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPathwayCoverList

java.util.List getPathwayCoverList(java.util.Collection ibidList)
                                   throws java.rmi.RemoteException

return the pathway that covers the selected interaction list

Parameters:

ibidList - the interaction list

Returns:

the pathway list and how many interaction they covers. The map is from pbid to the ibid count.

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPathwayComponentSet

java.util.Set getPathwayComponentSet(java.util.Collection pbidList)
                                     throws java.rmi.RemoteException

get all element in the selected pathways

Parameters:

pbidList - the pathway blockid list

Returns:

the elements in these pathways

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

recognizeNormalLiveEntity

java.lang.Integer recognizeNormalLiveEntity(java.lang.String name,
                                            java.lang.String entityType,
                                            java.lang.String location,
                                            java.lang.String organism,
                                            java.lang.String source,
                                            java.lang.String username,
                                            java.lang.String aracycId)
                                            throws java.rmi.RemoteException

recognize the live entity and create the live entity if necessary, since the data can be from expert data or aracyc, so source and username are parameters also. Notice that the recognization of live entity is totally depending on the name, entity type, organism and subcellular location. This should be only used for metabolite, gene, RNA and polypeptide.

Parameters:

name - name of the live entity

entityType - entity type of the live entity

location - location of the live entity

organism - organism of the live entity

source - source of the data

username - username of the data source

Returns:

blockid of the live entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

recognizeNormalInteraction

java.lang.Integer recognizeNormalInteraction()
                                             throws java.rmi.RemoteException

recognize the interaction and create it if necesaary. Notice that the recognization of interaction is totally depending on the blockid of the left part and right part. Any other addition information is not used including the interaction type. This may cause some problems when we want to recognize the protein complex, which totally determined by the component only.

Returns:

blockid of the live interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

recognizeControlInteraction

java.lang.Integer recognizeControlInteraction()
                                              throws java.rmi.RemoteException

depends on the controlled interaction?

Returns:

the blockid of the control interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findPbidListX

java.util.Collection findPbidListX(java.lang.String nameS,
                                   java.lang.String organism)
                                   throws java.rmi.RemoteException

find the pathway blockid based on the name, this can be pathway name or entity name

Parameters:

nameS - the name, may containing AND and OR

organism - organism

Returns:

the blockid of the pathway list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findEbidListX

java.util.Collection findEbidListX(java.lang.String nameS,
                                   java.lang.String organism,
                                   java.lang.String entityType,
                                   java.lang.String location)
                                   throws java.rmi.RemoteException

find the live entity based on the name

Parameters:

nameS - the name, may containing AND and OR

organism - organism

entityType - entity type

location - location

Returns:

the blockid of the live entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

findIbidListX

java.util.Collection findIbidListX(java.lang.String nameS,
                                   java.lang.String organism,
                                   java.lang.String interactionType,
                                   java.lang.String location)
                                   throws java.rmi.RemoteException

find the interaction list based on the substrate and product name

Parameters:

nameS - the name, may containing AND and OR

organism - organism

interactionType - interaction type

location - location

Returns:

the blockid of the interaction list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

checkTransInteraction

java.lang.Integer checkTransInteraction(java.lang.Integer sourceBlockid,
                                        java.lang.Integer targetBlockid)
                                        throws java.rmi.RemoteException

create an transport, translation or transcription interaction and return the blockid of the interaction.

Parameters:

sourceBlockid - the blockid of the blockunit in the source location

targetBlockid - the blockid of the blockunit in the target location

Returns:

the trans-interaction interaction's blockid

Throws:

java.rmi.RemoteException

adjacentIbidList

org._3pq.jgrapht.DirectedGraph adjacentIbidList(java.lang.Integer ibid)
                                                throws java.rmi.RemoteException

things are complicated if we support multiple catalysis for one enzymatic reaction. so we need to do it twice.

Parameters:

ibid - one interaction in an interaction cluster

Returns:

the graph structure of the small interaction cluster

Throws:

java.rmi.RemoteException

findNormalInteractionStructureX

java.util.Collection findNormalInteractionStructureX(java.util.Map leftX,
                                                     java.util.Map rightX)
                                                     throws java.rmi.RemoteException

an extension version of finding interaction structure. The input structure contains the coeffcient information.

Parameters:

leftX - the substrate list. It is a map of [ebid, coeff].

rightX - the product list. It is a map of [ebid, coeff].

Returns:

the blockid list of interaction

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

pubchemCasFilter

java.util.Collection pubchemCasFilter(java.util.Collection nameList)
                                      throws java.rmi.RemoteException

filter out the cas number from synonyms

Parameters:

nameList - the synonym list

Returns:

the cas list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

pubchemName2Cid

java.util.Collection pubchemName2Cid(java.util.Collection nameList)
                                     throws java.rmi.RemoteException

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

java.rmi.RemoteException

pubchemCid2Name

java.util.Collection pubchemCid2Name(java.util.Collection cidList)
                                     throws java.rmi.RemoteException

get the pubchem synonym from pubchem cid

Parameters:

cidList - cid list

Returns:

name list pubchem synonym list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getBiologicalType

java.lang.String getBiologicalType(java.lang.Integer blockId)
                                   throws java.rmi.RemoteException

get thebiological type like entitywithcontext, interaction or pathway

Parameters:

blockId - the blockid

Returns:

the type obtained from table blockunit

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getPathwayElementMap

org.apache.commons.collections.map.MultiKeyMap getPathwayElementMap()
                                                                    throws java.rmi.RemoteException

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

java.rmi.RemoteException

getPathwayLocusMap

org.apache.commons.collections.map.MultiKeyMap getPathwayLocusMap()
                                                                  throws java.rmi.RemoteException

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

java.rmi.RemoteException

getPathwayMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getPathwayMetaboliteMap()
                                                                       throws java.rmi.RemoteException

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

java.rmi.RemoteException

getMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getMetaboliteMap()
                                                                throws java.rmi.RemoteException

get the map from metabolite blockid to name

Returns:

the collection of [blockId, name, 1].

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getEntityIdListOfPathway

java.util.Collection getEntityIdListOfPathway(java.lang.Integer pbid)
                                              throws java.rmi.RemoteException

get the entity id list of specified pathway

Parameters:

pbid - the blockid of the pathway

Returns:

the entityid list

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getEntityIdOfUniqueId

java.util.Collection getEntityIdOfUniqueId(java.util.Collection blockunitList)
                                           throws java.rmi.RemoteException

collection version of getEntityIdOfUniqueId().

Parameters:

blockunitList - the blockunit list

Returns:

the entity id list, not all aracyc entry has a entityid in the database in advance

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getEntityIdOfUniqueId

java.lang.Integer getEntityIdOfUniqueId(Blockunit blockunit)
                                        throws java.rmi.RemoteException

this function is used to test if the given AraCyc entry has a corresponding entity id in MetNetDB. The function first look at the unique id. Then look at the name. Finally, it tries to look at the synonym? However, the name and synonym may not be reliable and should be curated by expert. Thus function finally get a possible entity id or null for pathway similarity computing. It totally depends on the entity node.

Parameters:

blockunit - AraCyc entry. This is not a concrete blockunit in database. Instead, it is a data holder for AraCyc entry.

Returns:

a possible matching entity

Throws:

EJBException - any remote call exception

java.rmi.RemoteException

getEntityIdListOfPathway

org.apache.commons.collections.map.MultiKeyMap getEntityIdListOfPathway()
                                                                        throws java.rmi.RemoteException

collection version of getEntityIdListOfPathway()

Returns:

the map from the pbid to entityid

Throws:

EJBException - any remote call exception

java.rmi.RemoteException