MyFacadeLocal

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edu.iastate.metnet.interfaces
Interface MyFacadeLocal

All Superinterfaces:: javax.ejb.EJBLocalObject

public interface MyFacadeLocal
extends javax.ejb.EJBLocalObject
extends javax.ejb.EJBLocalObject

Local 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.
`void`	`approveCandidate(java.util.Vector blockidlist)` approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???
`void`	`attachPathway(java.lang.Integer interactionID, java.lang.Integer pathwayID)` attach the interaciton to the pathway
`void`	`attachPathwayToClass(java.lang.Integer classId, java.util.Collection pbidList)` add pathway to selected category
`void`	`batchDelete(java.util.Vector vector)` batch delete
`void`	`batchInsert(java.util.Vector vector)` batch insert
`void`	`batchUpdate(java.util.Vector vector)` batch update
`java.util.Collection`	`changeSoybeanOR()` change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.
`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`	`checkOrCreateLatestHistory(java.lang.Integer blockId, java.lang.String username)` since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation
`void`	`checkOrInsertAbbreviation(java.lang.Integer blockid, java.lang.String abbreviation)` insert the abbreviation for the blockunit
`void`	`checkOrInsertComment(java.lang.Integer blockid, java.util.Vector commentList)` check or insert comment
`java.lang.Integer`	`checkOrInsertEntity(java.lang.String name, java.lang.String entityType, java.lang.String organism, java.lang.String source, java.lang.String username)` check if the entity exists, if not, create a new one
`void`	`checkOrInsertEntitySynonym(java.lang.Integer entityid, java.util.Vector synonymList)` insert the synonym list for the entity
`void`	`checkOrInsertEntitywithcontext(java.lang.Integer blockid, java.lang.Integer entityid)` fix the entitywithcontext at background
`java.lang.Integer`	`checkOrInsertPathway(java.util.Collection ibidList, java.lang.String pathwayName, java.lang.String username, java.lang.String organism)` check or create a pathway based on the interaction list
`void`	`checkOrInsertReference(java.lang.Integer blockid, java.util.Vector refereceList)` check or insert reference
`void`	`checkOrInsertSynonym(java.lang.Integer blockid, java.util.Vector synonymList)` check or insert the synonym
`java.lang.Integer`	`checkOrInsertTransInteraction(java.lang.Integer sourceBlockid, java.lang.Integer targetBlockid, java.lang.String interactionType, java.lang.String name, java.lang.String location, java.lang.String organism, java.lang.String username)` create an transport, translation or transcription interaction and return the blockid of the interaction.
`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`	`copyCategory(java.lang.Integer newParentClassId, java.lang.Integer oldParentClassId, java.lang.Integer childClassId)` copy the category to the new position
`java.lang.Integer`	`copyPathway(java.util.Collection pbidList, java.lang.String name, java.lang.String organism, java.lang.String username, java.lang.String source)` This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism.
`void`	`createAgrisNetwork()` create the AGRIS regulatory network pathways.
`void`	`createAgrisPathway()` create the pathway for AGRIS data, must after the network is created and expanded
`java.lang.Integer`	`createBasicPathway(Blockunit blockunit, java.lang.String username)` create pathway without the structure
`void`	`createCategory(java.lang.Integer classId, java.lang.String name, java.lang.String username)` create new category
`void`	`createInitialHistory()` create initial history for all blockunits in the database
`void`	`createSoybeanLocus()` create the soybean locus
`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.
`void`	`deleteAbbreviation(java.lang.Integer blockid, java.lang.String abbreviation)` delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table
`void`	`deleteAbbreviationRule(java.lang.String shortterm, java.lang.String longterm)` delete the abbreviation rule
`void`	`deleteBlockunit(java.lang.Integer blockid, java.lang.String username, int callLevel)` delete a blockunit
`void`	`deleteCategory(java.lang.Integer classId)` delete one category from the database
`void`	`deleteComment(java.lang.Integer blockid, CommentObject commentObject)` delete the comment from the blockunit
`void`	`deleteReference(java.lang.Integer blockid, ReferenceObject referenceObject)` delete the reference from the blockunit
`void`	`deleteSynonym(java.lang.Integer blockid, java.lang.String synonym)` delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'
`void`	`detachPathway(java.lang.Integer ibid, java.lang.Integer pbid, java.lang.String username)` detach the interaction from the pathway
`void`	`detachPathwayFromClass(java.lang.Integer classId, java.util.Collection pbidList)` detach the pathway from the class
`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.
`void`	`extendLocusInPathway(java.lang.Integer pathwayid, java.lang.String username)` extend all monomers in the pathway to the gene level, add translation and transcription if necessary
`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
`void`	`findOrInsertAbbreviationRule(java.lang.String shortterm, java.lang.String longterm)` find or insert the abbreviation rule
`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
`java.util.Vector`	`findUser(User userObject)` search by example
`User`	`findUserInstance(java.lang.String username)` find the User instance based on the username
`void`	`formalizeComposition()` formalize the composition for those multi-enzyme reactions
`org.apache.commons.collections.keyvalue.MultiKey`	`fullCheckOrInsertEntitywithlocation(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)` full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also
`void`	`generateHistory(java.lang.Integer blockId)` generate the history and the version graph record.
`void`	`generateHistory(java.lang.Integer blockId, java.lang.Integer recordOldId, java.lang.String username)` generate the history and the version graph record
`void`	`generateSoybeanNetwork()` generate soybean network from arabidopsis network
`void`	`generateSynonyms()` generate the synonyms
`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
`void`	`insertBlockunitConfidence(int blockid, int locationConfidence, int functionConfidence)` insert new confidence
`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.
`void`	`mergeBlockunit(Blockunit blockunitOld, Blockunit blockunitNew, boolean replace, java.lang.String username)` merge the two blockunits in the database.
`void`	`moreSoybeanAnnotation()` create more soybean annotation
`void`	`moreSoybeanPathwayCategory()` fill the category for soybean pathway
`void`	`moveCategory(java.lang.Integer newParentClassId, java.lang.Integer oldParentClassId, java.lang.Integer childClassId)` move the category to the new position
`java.lang.Integer`	`moveInteractionHistory(Blockunit blockunit, java.lang.String username)` move the current interaction to the history
`java.lang.Integer`	`moveLiveEntityHistory(Blockunit blockunit)` move the current live entity to the history
`java.lang.Integer`	`movePathwayHistory(Blockunit blockunit, java.lang.String username)` move the current pathway to the history
`void`	`notifyPathwayStructureChange(java.util.Collection pbidList, java.lang.String username)` change the pathway structure history.
`java.util.Collection`	`permitOrganismList(java.lang.String username)` get all organism that the user allowed to edit
`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`	`realizePathwayHistory(java.lang.Integer pbid, java.lang.Integer prid, java.lang.String pathwayName, java.lang.String username)` concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway
`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.
`void`	`remoteDelete(java.lang.Object object)` remote delete a database object
`java.io.Serializable`	`remoteInsert(java.lang.Object object)` remote insert a database object
`void`	`remoteInsert(java.lang.Object object, java.io.Serializable serializable)` remote insert a database object
`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
`void`	`remoteUpdate(java.lang.Object object)` remote update a database object
`void`	`remoteUpdate(java.lang.Object oldRecord, java.lang.Object newRecord)` remote update a database object which has a natural key by itself
`void`	`removeChebiLink(EntityOntology entityOntology)` remove the entityontology
`void`	`removeGroup(java.lang.Integer groupid)` remove the selected group
`void`	`renameCategory(java.lang.Integer classId, java.lang.String name)` rename the category
`void`	`saveGraph(java.lang.Integer pbid, MetnetPathway metnetPathway, org._3pq.jgrapht.DirectedGraph network, java.util.Map dataMap, org.apache.commons.collections.map.MultiKeyMap coeffMap, java.lang.String sessionUsername, java.lang.String sessionOrganism, boolean isAracycUpdate)` save graph to the database.
`java.lang.Integer`	`saveInteractionDeletionHistory(java.lang.Integer blockId, java.lang.String username)` save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history
`java.lang.Integer`	`saveLiveEntityDeletionHistory(java.lang.Integer blockId, java.lang.String username)` save the deletion history
`void`	`saveNetwork4All()` save all compilation in the database.
`java.lang.Integer`	`savePathwayDeletionHistory(java.lang.Integer blockId, java.lang.String username)` move the current pathway to the history.
`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
`Blockunit`	`undeleteBlockunit(java.lang.Integer blockId, java.lang.String username)` undelete one history
`void`	`updateAbbreviationrules(java.util.Vector rulevec)` update the rules changed by users
`void`	`updateBlockunitConfidence(int blockid, int locationConfidence, int functionConfidence)` update existing confidence
`void`	`updateMembers(java.lang.Integer groupid, java.util.Vector memberList)` update the member list
`void`	`updateUser(User userObject)` create a new user and presume that the user does not exist

Methods inherited from interface javax.ejb.EJBLocalObject
`getEJBLocalHome, getPrimaryKey, isIdentical, remove`

Method Detail

approveCandidate

void approveCandidate(java.util.Vector blockidlist)
                      throws javax.ejb.EJBException

approve the candidate maybe we need lock the table to prevent any concurrent approve procedure???

Parameters:: blockidlist - the id list of the candidates
Throws:: EJBException - Throw if the instance could not perform the function requested by the container because of an system-level error

generateSynonyms

void generateSynonyms()
                      throws javax.ejb.EJBException

generate the synonyms

Throws:: EJBException - Throw if the instance could not perform the function requested by the container because of an system-level error

getAbbreviationRules

java.util.Vector getAbbreviationRules()
                                      throws javax.ejb.EJBException

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

Returns:: the list of the class abbreviationrules
Throws:: javax.ejb.EJBException

updateAbbreviationrules

void updateAbbreviationrules(java.util.Vector rulevec)
                             throws javax.ejb.EJBException

update the rules changed by users

Throws:: javax.ejb.EJBException

getCoderules

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

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

Returns:: the list of the class coderule
Throws:: javax.ejb.EJBException

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

getGroupMemberList

java.util.List getGroupMemberList(java.lang.Integer groupid)
                                  throws javax.ejb.EJBException

get the member of the specified group

Parameters:: groupid -
Returns:: the user list of the group
Throws:: EJBException - any remote call exception

findEntitywithlocation

java.util.Vector findEntitywithlocation(java.lang.String name)
                                        throws javax.ejb.EJBException

get the entity with location contains the similar name

Parameters:: name - the search string
Returns:: the entity list
Throws:: EJBException - any remote call exception

findAmbiguousEntitywithlocation

java.util.Vector findAmbiguousEntitywithlocation(java.lang.String name)
                                                 throws javax.ejb.EJBException

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

findExactEntitywithlocation

java.util.Vector findExactEntitywithlocation(java.lang.String name)
                                             throws javax.ejb.EJBException

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

findAmbiguousEntitywithlocationIDList

java.util.Vector findAmbiguousEntitywithlocationIDList(java.lang.String name)
                                                       throws javax.ejb.EJBException

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

findBlockunitInstance

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

get the map id->blockunit

Parameters:: blockIdList - the list of blockid
Returns:: the map of id->blockunit
Throws:: EJBException - any remote call exception

findEntityInstance

java.util.Map findEntityInstance(java.util.Vector entityidvec)
                                 throws javax.ejb.EJBException

get the map id->entity

Parameters:: blockidvec - the list of entityid
Returns:: the map of id->entity
Throws:: EJBException - any remote call exception

findBrendaProduct

java.util.Vector findBrendaProduct(java.lang.String ecid)
                                   throws javax.ejb.EJBException

get the product based on the ec number

Parameters:: ecid - ec number
Returns:: list of product
Throws:: EJBException

findBrendaSubstrate

java.util.Vector findBrendaSubstrate(java.lang.String ecid)
                                     throws javax.ejb.EJBException

get the substrate based on the ec number

Parameters:: ecid - ec number
Returns:: list of substrate
Throws:: EJBException

findBrendaName

java.util.Vector findBrendaName(java.lang.String ecid)
                                throws javax.ejb.EJBException

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

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

findEntityInstance

Entity findEntityInstance(java.lang.Integer entityid)
                          throws javax.ejb.EJBException

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

findUser

java.util.Vector findUser(User userObject)
                          throws javax.ejb.EJBException

search by example

Parameters:: userObject -
Returns:: the list similar to the example case
Throws:: EJBException - any remote call exception

findUserInstance

User findUserInstance(java.lang.String username)
                      throws javax.ejb.EJBException

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

createUser

void createUser(User userObject)
                throws javax.ejb.EJBException

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

Parameters:: userObject - new user
Throws:: EJBException - any remote call exception

updateUser

void updateUser(User userObject)
                throws javax.ejb.EJBException

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

Parameters:: userObject - new user
Throws:: EJBException - any remote call exception

getCodelocationList

java.util.Vector getCodelocationList()
                                     throws javax.ejb.EJBException

get the codelocation

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodeconfidenceList

java.util.Vector getCodeconfidenceList()
                                       throws javax.ejb.EJBException

get the codeconfidence

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodedatasourceList

java.util.Vector getCodedatasourceList()
                                       throws javax.ejb.EJBException

get the codeconfidence

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodeentitytypeList

java.util.Vector getCodeentitytypeList()
                                       throws javax.ejb.EJBException

get the codeentitytype

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodeinteractiontypeList

java.util.Vector getCodeinteractiontypeList()
                                            throws javax.ejb.EJBException

get the codeinteractiontype

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodeorganismList

java.util.Vector getCodeorganismList()
                                     throws javax.ejb.EJBException

get the codeorganism

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCodereferencetypeList

java.util.Vector getCodereferencetypeList()
                                          throws javax.ejb.EJBException

get the codereferencetype

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

getCoderuleList

java.util.Vector getCoderuleList()
                                 throws javax.ejb.EJBException

get the coderule

Returns:: the list of codelocation
Throws:: any - remote call exception; javax.ejb.EJBException

mergeBlockunit

void mergeBlockunit(Blockunit blockunitOld,
                    Blockunit blockunitNew,
                    boolean replace,
                    java.lang.String username)
                    throws javax.ejb.EJBException

merge the two blockunits in the database.

Parameters:: blockunitOld - the old blockunit; blockunitNew - the new blockunit; replace - if true, all old blockunits in the database are replaced by the new blockunit. if false, old blockunit information are not deleted, only the interaction parts are replaced while the old information is merged to new blockunit information set
Throws:: EJBException - any remote call exception

deleteBlockunit

void deleteBlockunit(java.lang.Integer blockid,
                     java.lang.String username,
                     int callLevel)
                     throws javax.ejb.EJBException

delete a blockunit

Parameters:: blockid - the blockid of the blockunit
Throws:: EJBException - any remote call exception

findDownstreamInteraction

java.util.Vector findDownstreamInteraction(Blockunit blockunit)
                                           throws javax.ejb.EJBException

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

filterCatalysis

java.util.Vector filterCatalysis(java.util.Vector vector)
                                 throws javax.ejb.EJBException

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

findUpstreamInteraction

java.util.Vector findUpstreamInteraction(Blockunit blockunit)
                                         throws javax.ejb.EJBException

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

attachPathway

void attachPathway(java.lang.Integer interactionID,
                   java.lang.Integer pathwayID)
                   throws javax.ejb.EJBException

attach the interaciton to the pathway

Parameters:: interactionID - the blokid of the interaction; pathwayID - the blockid of the pathway
Throws:: EJBException - any remote call exception

detachPathway

void detachPathway(java.lang.Integer ibid,
                   java.lang.Integer pbid,
                   java.lang.String username)
                   throws javax.ejb.EJBException

detach the interaction from the pathway

Parameters:: ibid - the blockid of the interaction; pbid - the blockid of the pathway
Throws:: EJBException - any remote call exception

remoteInsert

java.io.Serializable remoteInsert(java.lang.Object object)
                                  throws javax.ejb.EJBException

remote insert a database object

Parameters:: object - the DAO
Throws:: EJBException - any remote call exception

remoteInsert

void remoteInsert(java.lang.Object object,
                  java.io.Serializable serializable)
                  throws javax.ejb.EJBException

remote insert a database object

Parameters:: object - the DAO; serializable - the id of the object
Throws:: EJBException - any remote call exception

batchInsert

void batchInsert(java.util.Vector vector)
                 throws javax.ejb.EJBException

batch insert

Parameters:: vector - the list of object
Throws:: EJBException - any remote call exception

remoteUpdate

void remoteUpdate(java.lang.Object object)
                  throws javax.ejb.EJBException

remote update a database object

Parameters:: object - the DAO
Throws:: EJBException - any remote call exception

remoteUpdate

void remoteUpdate(java.lang.Object oldRecord,
                  java.lang.Object newRecord)
                  throws javax.ejb.EJBException

remote update a database object which has a natural key by itself

Parameters:: oldRecord - the old DAO; newRecord - the new DAO
Throws:: EJBException - any remote call exception

remoteDelete

void remoteDelete(java.lang.Object object)
                  throws javax.ejb.EJBException

remote delete a database object

Parameters:: object - the DAO
Throws:: EJBException - any remote call exception

remoteSelect

java.util.Vector remoteSelect(java.lang.String hql)
                              throws javax.ejb.EJBException

let hibernate run at remote side

Parameters:: hql - the HQL to do the select
Returns:: the object lists
Throws:: EJBException - any remote call exception

batchDelete

void batchDelete(java.util.Vector vector)
                 throws javax.ejb.EJBException

batch delete

Parameters:: vector - list of the object
Throws:: EJBException - any remote call exception

batchUpdate

void batchUpdate(java.util.Vector vector)
                 throws javax.ejb.EJBException

batch update

Parameters:: vector - list of the object
Throws:: EJBException - any remote call exception

findConfidenceList

java.util.Vector findConfidenceList()
                                    throws javax.ejb.EJBException

get the confidence object list

Returns:: the confidence object list
Throws:: EJBException - any remote call exception

findChebiCompoundsList

java.util.Vector findChebiCompoundsList()
                                        throws javax.ejb.EJBException

get the chebi compounds list

Returns:: the object list
Throws:: EJBException - any remote call exception

findChebiNamesList

java.util.Vector findChebiNamesList()
                                    throws javax.ejb.EJBException

get the chebi names list

Returns:: the object list
Throws:: EJBException - any remote call exception

findSimilarEntitywithlocationIDByName

java.util.Vector findSimilarEntitywithlocationIDByName(java.lang.String name)
                                                       throws javax.ejb.EJBException

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

findDatasourceList

java.util.Vector findDatasourceList()
                                    throws javax.ejb.EJBException

get the data source object list

Returns:: the data source object list
Throws:: EJBException - any remote call exception

findOrganismList

java.util.Vector findOrganismList()
                                  throws javax.ejb.EJBException

get the organism object list

Returns:: the organism object list
Throws:: EJBException - any remote call exception

findEntityTypeList

java.util.Vector findEntityTypeList()
                                    throws javax.ejb.EJBException

get the entity type object list

Returns:: the entity type object list
Throws:: EJBException - any remote call exception

findInteractionTypeList

java.util.Vector findInteractionTypeList()
                                         throws javax.ejb.EJBException

get the interaction type object list

Returns:: the interaction type object list
Throws:: EJBException - any remote call exception

findLocationList

java.util.Vector findLocationList()
                                  throws javax.ejb.EJBException

get the location object list

Returns:: the location object list
Throws:: EJBException - any remote call exception

findCodelocationList

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

get the codelocation object list

Returns:: the codelocation object list
Throws:: EJBException - any remote call exception

findReferenceTypeList

java.util.Vector findReferenceTypeList()
                                       throws javax.ejb.EJBException

get the reference type object list

Returns:: the reference type object list
Throws:: EJBException - any remote call exception

findRuleList

java.util.Vector findRuleList()
                              throws javax.ejb.EJBException

get the rule object list

Returns:: the rule object list
Throws:: EJBException - any remote call exception

findExactBlockunit

java.util.Vector findExactBlockunit(java.lang.String name)
                                    throws javax.ejb.EJBException

find the blockunit match the name exactly

Parameters:: name - the name
Returns:: the list of the blockunit
Throws:: EJBException - any remote cal exception

findExactEntity

java.util.Vector findExactEntity(java.lang.String name)
                                 throws javax.ejb.EJBException

find the entityt match the name exactly

Parameters:: name - the name
Returns:: the list of the entity
Throws:: EJBException - any remote cal exception

getCandidate

java.util.Map getCandidate()
                           throws javax.ejb.EJBException

Throws:: javax.ejb.EJBException

getCandidate

java.util.Map getCandidate(int limit)
                           throws javax.ejb.EJBException

Throws:: javax.ejb.EJBException

findExactEntity

java.util.Vector findExactEntity(java.lang.String name,
                                 java.lang.String entityType)
                                 throws javax.ejb.EJBException

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

findEnzyme

java.util.Vector findEnzyme(java.lang.Integer blockid)
                            throws javax.ejb.EJBException

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

findEntity

java.util.Vector findEntity(java.lang.String name)
                            throws javax.ejb.EJBException

get all entity which contain "similar" name

Parameters:: name - the search string
Returns:: the vector of the entity
Throws:: EJBException - any remote exception

findEntity

java.util.Vector findEntity(java.util.Vector nameList)
                            throws javax.ejb.EJBException

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

findExactEntitywithlocation

java.util.Vector findExactEntitywithlocation(java.lang.String name,
                                             java.lang.String entityType,
                                             java.lang.String location)
                                             throws javax.ejb.EJBException

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

findDownstreamEntitywithlocation

java.util.Vector findDownstreamEntitywithlocation(java.lang.Integer blockid)
                                                  throws javax.ejb.EJBException

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

findUpstreamEntitywithlocation

java.util.Vector findUpstreamEntitywithlocation(java.lang.Integer blockid)
                                                throws javax.ejb.EJBException

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

checkOrInsertEntitywithcontext

void checkOrInsertEntitywithcontext(java.lang.Integer blockid,
                                    java.lang.Integer entityid)
                                    throws javax.ejb.EJBException

fix the entitywithcontext at background

Parameters:: blockid - the blockid of the blockunit; entityid - the entityid of the entity
Throws:: EJBException - any remote call exception

fullCheckOrInsertEntitywithlocation

org.apache.commons.collections.keyvalue.MultiKey fullCheckOrInsertEntitywithlocation(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 javax.ejb.EJBException

full insert blockunit and entity and entitywithcontext, since the data can be from expert data or aracyc, so source and username are parameters also

Parameters:: name - name of the entitywithlocation; entityType - entity type of the entitywithlocation; location - location of the entitywithlocation; organism - organism of the entitywithlocation; source - source of the data; username - username of the data source
Returns:: blockid, entityid and insertion flag of the live entity
Throws:: EJBException - any remote call exception

checkOrInsertSynonym

void checkOrInsertSynonym(java.lang.Integer blockid,
                          java.util.Vector synonymList)
                          throws javax.ejb.EJBException

check or insert the synonym

Parameters:: blockid - the id of the blockunit; synonymList - the synonym list
Throws:: EJBException - any remote call exception

checkOrInsertAbbreviation

void checkOrInsertAbbreviation(java.lang.Integer blockid,
                               java.lang.String abbreviation)
                               throws javax.ejb.EJBException

insert the abbreviation for the blockunit

Parameters:: blockid - the id of the blockunit; synonymList - the synonym list
Throws:: EJBException - any remote call exception

deleteSynonym

void deleteSynonym(java.lang.Integer blockid,
                   java.lang.String synonym)

delete the synonym for the blockunit and potential entity, if the synonym exists in the entity's table, move the synonym to all other blockunit'

Parameters:: blockid - id of the blockunit; synonym - the synonym of the blockunit to be removed

deleteAbbreviation

void deleteAbbreviation(java.lang.Integer blockid,
                        java.lang.String abbreviation)

delete the abbreviation for the blockunit and potential entity, if the abbreviation exists in the entity's table, move the abbreviation to all other blockunit' synonym table

Parameters:: blockid - id of the blockunit; abbreviation - the abbreviation of the blockunit

checkOrInsertReference

void checkOrInsertReference(java.lang.Integer blockid,
                            java.util.Vector refereceList)
                            throws javax.ejb.EJBException

check or insert reference

Parameters:: blockid - blockid of the blockunit; refereceList - the list of reference object
Throws:: EJBException - any remote call exception

checkOrInsertComment

void checkOrInsertComment(java.lang.Integer blockid,
                          java.util.Vector commentList)
                          throws javax.ejb.EJBException

check or insert comment

Parameters:: blockid - id of the blockunit; commentList - the list of comment object
Throws:: EJBException - any remote call exception

deleteReference

void deleteReference(java.lang.Integer blockid,
                     ReferenceObject referenceObject)
                     throws javax.ejb.EJBException

delete the reference from the blockunit

Parameters:: blockid - the id of the blockunit; referenceObject - the reference object
Throws:: EJBException - any remote call exception

deleteComment

void deleteComment(java.lang.Integer blockid,
                   CommentObject commentObject)
                   throws javax.ejb.EJBException

delete the comment from the blockunit

Parameters:: blockid - the id of hte blockunit; commentObject - the comment object
Throws:: EJBException - any remote call exeption

detectWrongInteraction

java.util.Vector detectWrongInteraction()
                                        throws javax.ejb.EJBException

detect the wrong interaction which contains entitywithcontext

Returns:: the blockid list of the wrong interaction
Throws:: EJBException - any remote call exception

findInteractionIDByEntitywithlocationID

java.util.Vector findInteractionIDByEntitywithlocationID(java.lang.Integer blockid)
                                                         throws javax.ejb.EJBException

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

findInteractionIDByName

java.util.Vector findInteractionIDByName(java.lang.String name)
                                         throws javax.ejb.EJBException

find all associated interaction for the name

Parameters:: name - the search string
Returns:: the interaction id list
Throws:: EJBException - any remote call exception

findInteractionInformation

InteractionInformation findInteractionInformation(java.lang.Integer blockid)
                                                  throws javax.ejb.EJBException

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

findInteractionInformation

java.util.Vector findInteractionInformation(java.lang.String name)
                                            throws javax.ejb.EJBException

search the interaction according to the entitywithlocation name

Parameters:: name - entitywithlocation name
Returns:: the involved interaction list
Throws:: EJBException - any remote call exception

findExactInteractionInformation

java.util.Vector findExactInteractionInformation(java.lang.String name)
                                                 throws javax.ejb.EJBException

search the interaction according to the entitywithlocation name

Parameters:: name - entitywithlocation name
Returns:: the involved interaction list
Throws:: EJBException - any remote call exception

findInteractionInformationByEntitywithlocationID

java.util.Vector findInteractionInformationByEntitywithlocationID(java.lang.Integer entitywithlocationid)
                                                                  throws javax.ejb.EJBException

find all involved interaction except catalysis type

Parameters:: blockid - the entitywithlocation's blockid
Returns:: the involved interactions
Throws:: EJBException - any remote call exception

iterateCompositionInteraction

java.util.Vector iterateCompositionInteraction(java.lang.Integer complexid)
                                               throws javax.ejb.EJBException

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

findChebiOntologyName

java.util.Vector findChebiOntologyName(java.lang.String name)
                                       throws javax.ejb.EJBException

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

getAllPathwayObjectList2

java.util.ArrayList getAllPathwayObjectList2(java.lang.String searchString)
                                             throws javax.ejb.EJBException

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

getPathwayObjectList

java.util.List getPathwayObjectList(java.util.Collection pbidList,
                                    boolean includeEmpty)
                                    throws javax.ejb.EJBException

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

findInvolvedPathways

java.util.List findInvolvedPathways(java.util.Collection ebidList,
                                    java.util.Collection pbidList)
                                    throws javax.ejb.EJBException

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

findChebiOntologyName

ChebiOntologyName findChebiOntologyName(java.lang.Integer chebiid)
                                        throws javax.ejb.EJBException

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

checkOrInsertEntitySynonym

void checkOrInsertEntitySynonym(java.lang.Integer entityid,
                                java.util.Vector synonymList)
                                throws javax.ejb.EJBException

insert the synonym list for the entity

Parameters:: entityid - the id of the entity; synonymList - the synonym list
Throws:: EJBException - any remote call exception

removeChebiLink

void removeChebiLink(EntityOntology entityOntology)
                     throws javax.ejb.EJBException

remove the entityontology

Parameters:: entityOntology - the entityonlogy not contain the serial id
Throws:: EJBException - any remote call exception

getChebiidName

BidiMultiHashMap getChebiidName()
                                throws javax.ejb.EJBException

get the map of id and name

Returns:: the mapping
Throws:: EJBException - any remote call exception

findPubchemID

java.util.Vector findPubchemID(java.util.Vector names)
                               throws javax.ejb.EJBException

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

findPubchemSynonym

java.util.Vector findPubchemSynonym(java.util.Vector names)
                                    throws javax.ejb.EJBException

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

findPubchemEntityID

java.util.Vector findPubchemEntityID(java.util.Vector names)
                                     throws javax.ejb.EJBException

find the entity id list for the name

Parameters:: names - the search name
Returns:: the entityid list
Throws:: EJBException

findStrictPubchemEntityID

java.util.Vector findStrictPubchemEntityID(java.util.Vector names)
                                           throws javax.ejb.EJBException

find the entity id list for the name

Parameters:: names - the search name
Returns:: the entityid list
Throws:: EJBException

findStrictPubchemID

java.util.Vector findStrictPubchemID(java.util.Vector names)
                                     throws javax.ejb.EJBException

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

findStrictPubchemSynonym

java.util.Vector findStrictPubchemSynonym(java.util.Vector names)
                                          throws javax.ejb.EJBException

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

findAssociatedInteraction

Blockunit findAssociatedInteraction(java.lang.Integer leftid,
                                    java.lang.Integer rightid)
                                    throws javax.ejb.EJBException

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

getA

java.util.Vector getA()
                      throws javax.ejb.EJBException

get the account name

Returns:: the account name
Throws:: EJBException

getP

java.util.Vector getP()
                      throws javax.ejb.EJBException

get the password

Returns:: the password
Throws:: EJBException

findGroupOfOwner

java.util.Vector findGroupOfOwner(java.lang.String username)
                                  throws javax.ejb.EJBException

find the group of the owner

Parameters:: username - the owner
Returns:: the list of the group object
Throws:: EJBException - any remote call exception

removeGroup

void removeGroup(java.lang.Integer groupid)
                 throws javax.ejb.EJBException

remove the selected group

Parameters:: groupid - the id of the group
Throws:: EJBException - any remote call exception

updateMembers

void updateMembers(java.lang.Integer groupid,
                   java.util.Vector memberList)
                   throws javax.ejb.EJBException

update the member list

Parameters:: groupid - the id of the group; memberList - member list only contain the username key
Throws:: EJBException - any remote call exception

isVisibleBlockunit

boolean isVisibleBlockunit(java.lang.Integer blockid,
                           java.lang.String username)
                           throws javax.ejb.EJBException

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

isVisibleBlockunit

boolean isVisibleBlockunit(Blockunit blockunit,
                           java.lang.String username)
                           throws javax.ejb.EJBException

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

findEntitywithlocation

java.util.Vector findEntitywithlocation(boolean exactMatch,
                                        java.lang.String name,
                                        java.lang.String location,
                                        java.lang.String entityType,
                                        java.lang.String source)
                                        throws javax.ejb.EJBException

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

isOrphanInteraction

boolean isOrphanInteraction(java.lang.Integer blockid)
                            throws javax.ejb.EJBException

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

detectOrphanInteraction

java.util.Vector detectOrphanInteraction()
                                         throws javax.ejb.EJBException

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

detectOrphanInteraction2

java.util.Vector detectOrphanInteraction2()
                                          throws javax.ejb.EJBException

detect all orphan interaction in the database

Returns:: the pathway name where orphan exists
Throws:: EJBException - any remote call exception

getCounter

int getCounter()
               throws javax.ejb.EJBException

a test of state in stateless session bean

Throws:: javax.ejb.EJBException

detectDuplicationInteractions

java.util.Map detectDuplicationInteractions()
                                            throws javax.ejb.EJBException

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:: javax.ejb.EJBException

checkOrInsertEntity

java.lang.Integer checkOrInsertEntity(java.lang.String name,
                                      java.lang.String entityType,
                                      java.lang.String organism,
                                      java.lang.String source,
                                      java.lang.String username)
                                      throws javax.ejb.EJBException

check if the entity exists, if not, create a new one

Parameters:: name - entity name; entityType - entity type like gene, rna or polypeptide; organism - entity organism like human, mouse or arabidopsis; source - source of the data; username - username of the data owner
Returns:: the entity id
Throws:: EJBException - any remote call exception

detectAbnormalEntitywithcontext

java.util.Vector detectAbnormalEntitywithcontext()
                                                 throws javax.ejb.EJBException

detect abnormal record in the table entitywithcontext.

Returns:: list of distinct blockname, this is for manually caration, so blockid is not useful
Throws:: EJBException

checkInteraction

java.lang.Integer checkInteraction(java.util.Vector leftPart,
                                   java.util.Vector rightPart)
                                   throws javax.ejb.EJBException

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

getCoefficientMap

org.apache.commons.collections.map.MultiKeyMap getCoefficientMap(java.util.ArrayList interactionIDList,
                                                                 java.util.ArrayList intermediumIDList)
                                                                 throws javax.ejb.EJBException

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

extendLocusInPathway

void extendLocusInPathway(java.lang.Integer pathwayid,
                          java.lang.String username)
                          throws javax.ejb.EJBException

extend all monomers in the pathway to the gene level, add translation and transcription if necessary

Parameters:: pathwayid - the blockid of pathway; username - user name since new interaction may be created
Throws:: EJBException - any remote call exception

formalizeComposition

void formalizeComposition()
                          throws javax.ejb.EJBException

formalize the composition for those multi-enzyme reactions

Throws:: EJBException - any remote call exception

findAtGeneLocusObject

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

extract locus only information

Parameters:: locusid - the locus id from the input
Returns:: the locus information object
Throws:: EJBException - any remote call exception

findInvolvedPathway

java.util.Vector findInvolvedPathway(Blockunit blockunit)
                                     throws javax.ejb.EJBException

find the involved pathway from the blockunit

Parameters:: blockunit - interaction or entityeithlocation
Returns:: the list of pathway object
Throws:: EJBException - any remote call exception

findAtGeneLocusObjectList

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

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

findAtGeneLocusObjectListByFulltext

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

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

deleteAbbreviationRule

void deleteAbbreviationRule(java.lang.String shortterm,
                            java.lang.String longterm)
                            throws javax.ejb.EJBException

delete the abbreviation rule

Parameters:: shortterm - short term; longterm - long term
Throws:: EJBException - any remote call exception

findOrInsertAbbreviationRule

void findOrInsertAbbreviationRule(java.lang.String shortterm,
                                  java.lang.String longterm)
                                  throws javax.ejb.EJBException

find or insert the abbreviation rule

Parameters:: shortterm - short term; longterm - long term
Throws:: EJBException - any remote call exception

insertBlockunitConfidence

void insertBlockunitConfidence(int blockid,
                               int locationConfidence,
                               int functionConfidence)
                               throws javax.ejb.EJBException

insert new confidence

Parameters:: blockid - the blockid of the blockunit; locationConfidence - confidence of the location; functionConfidence - confidence of the function
Throws:: EJBException - any remote call exception

updateBlockunitConfidence

void updateBlockunitConfidence(int blockid,
                               int locationConfidence,
                               int functionConfidence)
                               throws javax.ejb.EJBException

update existing confidence

Parameters:: blockid - the blockid of the blockunit; locationConfidence - confidence of the location; functionConfidence - confidence of the function
Throws:: EJBException - any remote call 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

getInteractionObject

InteractionObject getInteractionObject(java.lang.Integer blockid)
                                       throws javax.ejb.EJBException

get more interaction information

Parameters:: blockid - the blockid of the interaction
Returns:: the interaction infomation data object
Throws:: EJBException - any remote call exception

getAllElementNodeBlockIDList

java.util.ArrayList getAllElementNodeBlockIDList(java.lang.Integer pbid)
                                                 throws javax.ejb.EJBException

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

constructMultiPathwayGraph

MultiPathwayGraph constructMultiPathwayGraph(java.util.ArrayList pbidList)
                                             throws javax.ejb.EJBException

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

findTrivialMetabolite

java.util.List findTrivialMetabolite(java.lang.Integer degreeThreshold,
                                     java.lang.Integer limit)
                                     throws javax.ejb.EJBException

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

remoteLayout

java.lang.Object[] remoteLayout(java.lang.String bitstream)
                                throws javax.ejb.EJBException

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

eaQuery

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

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

aaQuery

java.lang.Object[] aaQuery(java.util.Collection ebidList,
                           java.util.Collection pbidList,
                           java.util.Collection eidList)
                           throws javax.ejb.EJBException

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

esQuery

java.util.List esQuery(org._3pq.jgrapht.DirectedGraph directedGraph)
                       throws javax.ejb.EJBException

esQuery.

Parameters:: directedGraph - directed graph model, vertex is the blockid
Returns:: sorted shrinked alignment list
Throws:: EJBException - any remote call exception

esQuery

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

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

sortAlignmentList

java.util.List sortAlignmentList(java.util.Collection alignList)

sort the alignment list

Parameters:: alignList - the alignment list
Returns:: sorted list

moveLiveEntityHistory

java.lang.Integer moveLiveEntityHistory(Blockunit blockunit)
                                        throws javax.ejb.EJBException

move the current live entity to the history

Parameters:: blockId - the block id of the live entity
Returns:: the history record Id
Throws:: EJBException - any remote exception

moveInteractionHistory

java.lang.Integer moveInteractionHistory(Blockunit blockunit,
                                         java.lang.String username)
                                         throws javax.ejb.EJBException

move the current interaction to the history

Parameters:: blockunit - the block id of the interaction; username - session username
Returns:: the history record Id
Throws:: EJBException - any remote exception

movePathwayHistory

java.lang.Integer movePathwayHistory(Blockunit blockunit,
                                     java.lang.String username)
                                     throws javax.ejb.EJBException

move the current pathway to the history

Parameters:: blockId - the block id of the pathway; username - session username
Returns:: the history record Id
Throws:: EJBException - any remote exception

findHistoryAsGraph

MyVersionGraph findHistoryAsGraph(java.lang.Integer blockId,
                                  java.lang.String username)
                                  throws javax.ejb.EJBException

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

generateHistory

void generateHistory(java.lang.Integer blockId,
                     java.lang.Integer recordOldId,
                     java.lang.String username)
                     throws javax.ejb.EJBException

generate the history and the version graph record

Parameters:: blockId - the blockid which has just been updated; recordNewId - new record id; recordOldId - old record id; username - session username
Throws:: EJBException - any remote exception

createInitialHistory

void createInitialHistory()
                          throws javax.ejb.EJBException

create initial history for all blockunits in the database

Parameters:: username - session username
Throws:: EJBException - any remote exception

checkOrCreateLatestHistory

java.lang.Integer checkOrCreateLatestHistory(java.lang.Integer blockId,
                                             java.lang.String username)
                                             throws javax.ejb.EJBException

since things are complicated to create all initial history in advance, we move this step to the action on the normal blockunit operation

Parameters:: blockId - the blockid of the blockunit; username - session username
Throws:: EJBException - any remote call exception

generateHistory

void generateHistory(java.lang.Integer blockId)
                     throws javax.ejb.EJBException

generate the history and the version graph record. By default use the latest two

Parameters:: blockId - the blockid which has just been updated
Throws:: EJBException - any remote exception

findLatestPathwayPart

java.util.Map findLatestPathwayPart(java.lang.Integer pbid,
                                    java.lang.Integer prid)
                                    throws javax.ejb.EJBException

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:: javax.ejb.EJBException

findLatestInteractionPart

java.util.Map findLatestInteractionPart(java.lang.Integer ibid,
                                        java.lang.Integer irid)
                                        throws javax.ejb.EJBException

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:: javax.ejb.EJBException

findHistoryFlatInteraction

HistoryFlatInteraction findHistoryFlatInteraction(java.lang.Integer blockId,
                                                  java.lang.Integer recordId)
                                                  throws javax.ejb.EJBException

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:: javax.ejb.EJBException

findHistoryFlatLiveEntity

HistoryFlatLiveEntity findHistoryFlatLiveEntity(java.lang.Integer blockId,
                                                java.lang.Integer recordId)
                                                throws javax.ejb.EJBException

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:: javax.ejb.EJBException

findHistoryFlatPathway

HistoryFlatPathway findHistoryFlatPathway(java.lang.Integer blockId,
                                          java.lang.Integer recordId)
                                          throws javax.ejb.EJBException

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:: javax.ejb.EJBException

findLatestControlLiveEntity

org.apache.commons.collections.keyvalue.MultiKey findLatestControlLiveEntity(java.lang.Integer ibid,
                                                                             java.lang.Integer irid)
                                                                             throws javax.ejb.EJBException

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

notifyPathwayStructureChange

void notifyPathwayStructureChange(java.util.Collection pbidList,
                                  java.lang.String username)
                                  throws javax.ejb.EJBException

change the pathway structure history. If nothing is changed in the structure, then skip this

Parameters:: pbidList - the blockid list of the pathway; username - session username
Throws:: EJBException - any remote call exception

createAgrisNetwork

void createAgrisNetwork()
                        throws javax.ejb.EJBException

create the AGRIS regulatory network pathways. each pathway contains one locus and its neighbors.

Throws:: EJBException - any remote call exception

checkOrInsertTransInteraction

java.lang.Integer checkOrInsertTransInteraction(java.lang.Integer sourceBlockid,
                                                java.lang.Integer targetBlockid,
                                                java.lang.String interactionType,
                                                java.lang.String name,
                                                java.lang.String location,
                                                java.lang.String organism,
                                                java.lang.String username)
                                                throws javax.ejb.EJBException

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; interactionType - the interaction type, only be trasnportation, transcription, or translation; name - the name of the interaction, used for insertion only; location - the location of the interaction, used for insertion only; organism - the organism of the interaction, used for insertion only; username - user name since new interaction may be created
Returns:: the blockid of the trans-interaction
Throws:: EJBException - any remote call exception

checkOrInsertPathway

java.lang.Integer checkOrInsertPathway(java.util.Collection ibidList,
                                       java.lang.String pathwayName,
                                       java.lang.String username,
                                       java.lang.String organism)
                                       throws javax.ejb.EJBException

check or create a pathway based on the interaction list

Parameters:: ibidList - the blockid list of interaction; pathwayName - the name of the pathway if it needs creation; username - the user who input the pathway
Returns:: the block id of the pathway
Throws:: EJBException - any remote call exception

createAgrisPathway

void createAgrisPathway()
                        throws javax.ejb.EJBException

create the pathway for AGRIS data, must after the network is created and expanded

Throws:: EJBException - any remote call exception

saveInteractionDeletionHistory

java.lang.Integer saveInteractionDeletionHistory(java.lang.Integer blockId,
                                                 java.lang.String username)
                                                 throws javax.ejb.EJBException

save the deletion history, who delete it and when it is deleted, we can use null name to determine this is a saved deletion history

Parameters:: blockId - the block id of the interaction; username - session username
Returns:: the history record Id
Throws:: EJBException - any remote exception

saveLiveEntityDeletionHistory

java.lang.Integer saveLiveEntityDeletionHistory(java.lang.Integer blockId,
                                                java.lang.String username)
                                                throws javax.ejb.EJBException

save the deletion history

Parameters:: blockId - the block id of the live entity
Returns:: the history record Id
Throws:: EJBException - any remote exception

savePathwayDeletionHistory

java.lang.Integer savePathwayDeletionHistory(java.lang.Integer blockId,
                                             java.lang.String username)
                                             throws javax.ejb.EJBException

move the current pathway to the history.

Parameters:: blockunit - the blockunit instance of the pathway; username - session username
Returns:: the history record Id
Throws:: EJBException - any remote exception

getLiveEntityChange

java.lang.String getLiveEntityChange(HistoryFlatLiveEntity history)
                                     throws javax.ejb.EJBException

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

getInteractionChange

java.lang.String getInteractionChange(HistoryFlatInteraction history)
                                      throws javax.ejb.EJBException

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

getPathwayChange

java.lang.String getPathwayChange(HistoryFlatPathway history)
                                  throws javax.ejb.EJBException

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

getHistoryReport

java.util.List getHistoryReport(java.util.Date fromDate,
                                java.util.Date toDate,
                                java.lang.Integer numLimit)
                                throws javax.ejb.EJBException

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

undeleteBlockunit

Blockunit undeleteBlockunit(java.lang.Integer blockId,
                            java.lang.String username)
                            throws javax.ejb.EJBException

undelete one history

Parameters:: blockId - the block id of the blockunit to be undeleted
Returns:: the block id of the undeleted stuff
Throws:: EJBException - any remote call exception

getInvolvedPbidSet

java.util.Set getInvolvedPbidSet(java.lang.Integer ebid)
                                 throws javax.ejb.EJBException

get the involved pathway list

Parameters:: ebid - the blockid of the live entity
Returns:: the pbid set
Throws:: EJBException - any remote call exception

testPathwayName

boolean testPathwayName(java.lang.String name,
                        java.lang.String organism)
                        throws javax.ejb.EJBException

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

realizePathwayHistory

java.lang.Integer realizePathwayHistory(java.lang.Integer pbid,
                                        java.lang.Integer prid,
                                        java.lang.String pathwayName,
                                        java.lang.String username)
                                        throws javax.ejb.EJBException

concrete one history of the pathway into the database so we can use it for comparison or other purposed like a normal pathway

Parameters:: pbid - the blockid of the pathway; prid - the record id of the history; pathwayName - new pathway name; username - session username
Returns:: the blockid of the new pathway
Throws:: EJBException - any remote call exception

getLatestHistory

HistoryBlockunit getLatestHistory(java.lang.Integer blockId)
                                  throws javax.ejb.EJBException

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

constructAlignmentMode

java.lang.Object[] constructAlignmentMode(AlignmentObject alignment)
                                          throws javax.ejb.EJBException

(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

saveNetwork4All

void saveNetwork4All()
                     throws javax.ejb.EJBException

save all compilation in the database. this must be called after any changes in the data structure of matching network

Throws:: EJBException - any remote call exception

getPbidList

java.util.List getPbidList()

get the pbid list

Returns:: the pbid list

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

getPbidList4Class

java.util.Collection getPbidList4Class(java.lang.Integer classId)
                                       throws javax.ejb.EJBException

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

moveCategory

void moveCategory(java.lang.Integer newParentClassId,
                  java.lang.Integer oldParentClassId,
                  java.lang.Integer childClassId)
                  throws javax.ejb.EJBException

move the category to the new position

Parameters:: newParentClassId - the new parent category; oldParentClassId - the old parent category; childClassId - the child category
Throws:: EJBException - remote call exception

copyCategory

void copyCategory(java.lang.Integer newParentClassId,
                  java.lang.Integer oldParentClassId,
                  java.lang.Integer childClassId)
                  throws javax.ejb.EJBException

copy the category to the new position

Parameters:: newParentClassId - the new parent category; oldParentClassId - the old parent category; childClassId - the child category
Throws:: EJBException - any remote call exception

renameCategory

void renameCategory(java.lang.Integer classId,
                    java.lang.String name)
                    throws javax.ejb.EJBException

rename the category

Parameters:: classId - the class id of the category; name - the new name of the category
Throws:: EJBException - any remote call exception

detachPathwayFromClass

void detachPathwayFromClass(java.lang.Integer classId,
                            java.util.Collection pbidList)
                            throws javax.ejb.EJBException

detach the pathway from the class

Parameters:: classId - the class id of the class; pbidList - the pathway blockid list
Throws:: EJBException - any remote call exception

deleteCategory

void deleteCategory(java.lang.Integer classId)
                    throws javax.ejb.EJBException

delete one category from the database

Parameters:: classId - the class id of the category
Throws:: EJBException - any remote call exception

createCategory

void createCategory(java.lang.Integer classId,
                    java.lang.String name,
                    java.lang.String username)
                    throws javax.ejb.EJBException

create new category

Parameters:: classId - the class id of current category; name - the new category name; username - the user who provides the data
Throws:: EJBException - any remote call exception

attachPathwayToClass

void attachPathwayToClass(java.lang.Integer classId,
                          java.util.Collection pbidList)
                          throws javax.ejb.EJBException

add pathway to selected category

Parameters:: classId - the class id of the selected category; pbidList - the pathway blockid list
Throws:: EJBException - any remote call exception

createUserRequest

void createUserRequest(java.lang.String username,
                       java.lang.String organism)
                       throws javax.ejb.EJBException

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

findNormalInteractionStructure

java.util.Collection findNormalInteractionStructure(java.util.Collection leftList,
                                                    java.util.Collection rightList)
                                                    throws javax.ejb.EJBException

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

copyPathway

java.lang.Integer copyPathway(java.util.Collection pbidList,
                              java.lang.String name,
                              java.lang.String organism,
                              java.lang.String username,
                              java.lang.String source)

This funciton copy the pathway specified by the blockid to a new pathway belongs to the specified organism. By default, the organism is not identical so we only copy all metabolite only interactions

Parameters:: pbid - the blockid of the pathway; name - new pathway name; organism - the new organism, normally should be different with the old organism of the pathway; username - user name; source - data source
Returns:: the new blockid of the pathway

createSoybeanLocus

void createSoybeanLocus()
                        throws javax.ejb.EJBException

create the soybean locus

Throws:: EJBException - any remote call exception

generateSoybeanNetwork

void generateSoybeanNetwork()
                            throws javax.ejb.EJBException

generate soybean network from arabidopsis network

Throws:: EJBException - any remote call exception

moreSoybeanAnnotation

void moreSoybeanAnnotation()
                           throws javax.ejb.EJBException

create more soybean annotation

Throws:: EJBException - any remote call exception

moreSoybeanPathwayCategory

void moreSoybeanPathwayCategory()
                                throws javax.ejb.EJBException

fill the category for soybean pathway

Throws:: EJBException - any remote call exception

permitOrganismList

java.util.Collection permitOrganismList(java.lang.String username)
                                        throws javax.ejb.EJBException

get all organism that the user allowed to edit

Parameters:: username -
Returns:: the organism list that the user can edit
Throws:: EJBException - any remote call exception

createBasicPathway

java.lang.Integer createBasicPathway(Blockunit blockunit,
                                     java.lang.String username)
                                     throws javax.ejb.EJBException

create pathway without the structure

Parameters:: blockunit - the blockunit information; username - user name
Returns:: the blockid of the pathway
Throws:: EJBException - any remote call exception

findPbidList

java.util.Collection findPbidList(java.lang.String searchString,
                                  boolean includeEmpty)
                                  throws javax.ejb.EJBException

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

getPathwayCoverList

java.util.List getPathwayCoverList(java.util.Collection ibidList)
                                   throws javax.ejb.EJBException

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

getPathwayComponentSet

java.util.Set getPathwayComponentSet(java.util.Collection pbidList)
                                     throws javax.ejb.EJBException

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

changeSoybeanOR

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

change the duplicate soybean probes in the network to the OR relation except for those exising OR relation, use flattern OR relation.

Throws:: EJBException - any remote call exception

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 javax.ejb.EJBException

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

recognizeNormalInteraction

java.lang.Integer recognizeNormalInteraction()
                                             throws javax.ejb.EJBException

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

recognizeControlInteraction

java.lang.Integer recognizeControlInteraction()
                                              throws javax.ejb.EJBException

depends on the controlled interaction?

Returns:: the blockid of the control interaction
Throws:: EJBException - any remote call exception

findPbidListX

java.util.Collection findPbidListX(java.lang.String nameS,
                                   java.lang.String organism)
                                   throws javax.ejb.EJBException

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

findEbidListX

java.util.Collection findEbidListX(java.lang.String nameS,
                                   java.lang.String organism,
                                   java.lang.String entityType,
                                   java.lang.String location)
                                   throws javax.ejb.EJBException

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

findIbidListX

java.util.Collection findIbidListX(java.lang.String nameS,
                                   java.lang.String organism,
                                   java.lang.String interactionType,
                                   java.lang.String location)
                                   throws javax.ejb.EJBException

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

checkTransInteraction

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.

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

adjacentIbidList

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

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

saveGraph

void saveGraph(java.lang.Integer pbid,
               MetnetPathway metnetPathway,
               org._3pq.jgrapht.DirectedGraph network,
               java.util.Map dataMap,
               org.apache.commons.collections.map.MultiKeyMap coeffMap,
               java.lang.String sessionUsername,
               java.lang.String sessionOrganism,
               boolean isAracycUpdate)
               throws javax.ejb.EJBException

save graph to the database. The pathway must have already been in te database. Otherwise, manually create the basic information of the pathway without structure information.

Parameters:: pbid - blockid of the pathway to be saved; metnetPathway - pathway information; network - the network; dataMap - the data map; coeffMap - the coefficient map; sessionUsername - session username; sessionOrganism - session organism
Throws:: EJBException - any remote call exception

findNormalInteractionStructureX

java.util.Collection findNormalInteractionStructureX(java.util.Map leftX,
                                                     java.util.Map rightX)
                                                     throws javax.ejb.EJBException

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

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

getBiologicalType

java.lang.String getBiologicalType(java.lang.Integer blockId)
                                   throws javax.ejb.EJBException

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

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

getEntityIdListOfPathway

java.util.Collection getEntityIdListOfPathway(java.lang.Integer pbid)
                                              throws javax.ejb.EJBException

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

getEntityIdOfUniqueId

java.util.Collection getEntityIdOfUniqueId(java.util.Collection blockunitList)
                                           throws javax.ejb.EJBException

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

getEntityIdOfUniqueId

java.lang.Integer getEntityIdOfUniqueId(Blockunit blockunit)
                                        throws javax.ejb.EJBException

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

getEntityIdListOfPathway

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

collection version of getEntityIdListOfPathway()

Returns:: the map from the pbid to entityid
Throws:: EJBException - any remote call exception

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edu.iastate.metnet.interfaces Interface MyFacadeLocal

approveCandidate

generateSynonyms

getAbbreviationRules

updateAbbreviationrules

getCoderules

getAllUserList

getGroupMemberList

findEntitywithlocation

findAmbiguousEntitywithlocation

findExactEntitywithlocation

findAmbiguousEntitywithlocationIDList

findBlockunitInstance

findEntityInstance

findBrendaProduct

findBrendaSubstrate

findBrendaName

findBlockunitInstance

findEntityInstance

findUser

findUserInstance

createUser

updateUser

getCodelocationList

getCodeconfidenceList

getCodedatasourceList

getCodeentitytypeList

getCodeinteractiontypeList

getCodeorganismList

getCodereferencetypeList

getCoderuleList

mergeBlockunit

deleteBlockunit

findDownstreamInteraction

filterCatalysis

findUpstreamInteraction

attachPathway

detachPathway

remoteInsert

remoteInsert

batchInsert

remoteUpdate

remoteUpdate

remoteDelete

remoteSelect

batchDelete

batchUpdate

findConfidenceList

findChebiCompoundsList

findChebiNamesList

findSimilarEntitywithlocationIDByName

findDatasourceList

findOrganismList

findEntityTypeList

findInteractionTypeList

findLocationList

findCodelocationList

findReferenceTypeList

findRuleList

findExactBlockunit

findExactEntity

getCandidate

getCandidate

findExactEntity

findEnzyme

findEntity

findEntity

findExactEntitywithlocation

findDownstreamEntitywithlocation

findUpstreamEntitywithlocation

checkOrInsertEntitywithcontext

fullCheckOrInsertEntitywithlocation

checkOrInsertSynonym

checkOrInsertAbbreviation

deleteSynonym

deleteAbbreviation

checkOrInsertReference

checkOrInsertComment

deleteReference

deleteComment

edu.iastate.metnet.interfaces
Interface MyFacadeLocal