edu.iastate.metnet.hiveface
Interface GraphExporter

All Known Implementing Classes:

GraphExporterImpl

public interface GraphExporter

service interface. 3rd party can get the instance by calling

 GraphExporter graphExporter = GraphExporterImpl.getInstance();
 

Author:

Jie Li

Method Summary

java.util.HashMap	bevGetAllLocationInfo() BirdsEyeView code
java.util.ArrayList	bevGetGoBioProcesses(java.lang.Integer goID) BirdsEyeView code
java.util.ArrayList	bevGetGoChildren(java.lang.Integer goNodeID) BirdsEyeView code
java.util.ArrayList	bevGetGoFunctions(java.lang.Integer goID) BirdsEyeView code
java.lang.Integer	bevGetGoGeneProductID(java.lang.String locusID) BirdsEyeView code
java.lang.String	bevGetGoNodeName(java.lang.Integer goNodeID) BirdsEyeView code
java.util.ArrayList	bevGetGoNodesWithinDistance(java.lang.Integer rootNodeID, int distance) BirdsEyeView code
java.util.ArrayList	bevGetGoTermAncestors(java.lang.Integer goTermID) BirdsEyeView code
java.util.ArrayList	bevGetLocations(java.lang.Integer entityID) BirdsEyeView code
java.util.ArrayList	bevGetLocusIDs(java.lang.String affyID) BirdsEyeView code
java.lang.Integer	bevGetMetnetEntityID(java.lang.String locusID) BirdsEyeView code
java.util.ArrayList	bevGetPathways(java.lang.Integer entityID) BirdsEyeView code
java.util.Map	bevGetPolypeptides(java.lang.Integer entityID) BirdsEyeView code
java.util.Map	bevGetProteinComplexes(java.lang.Integer entityID) BirdsEyeView code
java.util.Map	findBlockunitInstance(java.util.Collection blockIdList) get the blockunit map
java.util.Collection	findLiveEntityList(boolean exactMatch, java.lang.String name, java.lang.String location, java.lang.String entityType) find the live entities according to the specified query condition
java.util.Collection	getAllLocationList() get all location in the database
java.util.List	getAtGeneSearchAttributeList() get all attributes in the AtGeneSearch application
java.util.List	getAtGeneSearchObject(java.lang.String affyId) get one data object based on the affyId
java.util.List	getFullGeneAnnotationAttributeList() get all attributes in function getFullGeneAnnotationList()
org.apache.commons.collections.map.MultiKeyMap	getFullGeneAnnotationList() return all possible gene annnotation.
edu.uci.ics.jung.graph.DirectedGraph	getGraphModelByEntity(GobiNode gobiNode) get the graph model from the node info.
edu.uci.ics.jung.graph.DirectedGraph	getGraphModelByEntityList(java.util.Collection gobiNodeList) get the graph model from the node list.
edu.uci.ics.jung.graph.DirectedGraph	getGraphModelByPathway(java.util.Collection pbidList) return the graph model based on the pathway id list.
edu.uci.ics.jung.graph.DirectedGraph	getGraphModelByStep(java.util.Collection blockIdList, int step) get the p-neighborhood graph
org.apache.commons.collections.map.MultiKeyMap	getMetaboliteMap() get the map from metabolite blockid to name
MetaboliteObject	getMetaboliteObject(java.lang.Integer ebid) get additional metabolite information.
org.apache.commons.collections.map.MultiKeyMap	getPathwayCategoryTree() get the adjacency list of pathway category tree.
org.apache.commons.collections.map.MultiKeyMap	getPathwayElementMap() get the full mapping between the pathways and their elements
java.util.Map	getPathwayInfo(java.util.Collection pbidList) get the pathway information of
org.apache.commons.collections.map.MultiKeyMap	getPathwayLocusMap() get the full map to pathway, locus and affy probe sets
java.util.Map	getPathwayMapByEntityList(java.util.Collection gobiNodeList) get the pathways that contains the entities.
org.apache.commons.collections.map.MultiKeyMap	getPathwayMetaboliteMap() get the map from pathway blockid to metabolite blockid
java.util.Collection	pubchemCasFilter(java.util.Collection nameList) obtain CAS from a list of name.
java.util.Collection	pubchemCid2Name(java.util.Collection cidList) obtain pubchem synonym from compound id list
java.util.Collection	pubchemName2Cid(java.util.Collection nameList) obtain pubchem compound id from name.

Method Detail

getGraphModelByEntity

edu.uci.ics.jung.graph.DirectedGraph getGraphModelByEntity(GobiNode gobiNode)

get the graph model from the node info. It first collects all pathways in MetNetDB that contains the biological entity. Then, a graph model is constructed to cover all these pathways.

Parameters:

gobiNode - the node info from gene gobi

Returns:

the graph model

getGraphModelByEntityList

edu.uci.ics.jung.graph.DirectedGraph getGraphModelByEntityList(java.util.Collection gobiNodeList)

get the graph model from the node list. This function returns a combination of pathways that contains one or more entities provided by users.

Parameters:

gobiNodeList - the node list

Returns:

the graph model which contains all the nodes

getAtGeneSearchAttributeList

java.util.List getAtGeneSearchAttributeList()

get all attributes in the AtGeneSearch application

Returns:

list of attribute name

getAtGeneSearchObject

java.util.List getAtGeneSearchObject(java.lang.String affyId)

get one data object based on the affyId

Parameters:

affyId - the affyID regardless Affy25K or Affy8K. If there are multiple affyIDs, separate them by comma or semicolon

Returns:

a list of AtGeneSearchObject

getMetaboliteObject

MetaboliteObject getMetaboliteObject(java.lang.Integer ebid)

get additional metabolite information. Users can get the blockid from the vertex of the graph model. It's better to detect if the entity type of the vertex is a metabolite or not before call this function. It's OK if not to do so but some fields in the object will have null values.

Parameters:

ebid - the blockid of the metabolite.

Returns:

the metabolite information

pubchemName2Cid

java.util.Collection pubchemName2Cid(java.util.Collection nameList)

obtain pubchem compound id from name.

Parameters:

nameList - the name list

Returns:

pubchem compound id list

pubchemCid2Name

java.util.Collection pubchemCid2Name(java.util.Collection cidList)

obtain pubchem synonym from compound id list

Parameters:

cidList - the pubchem compound id list

Returns:

the synonym from pubchem

pubchemCasFilter

java.util.Collection pubchemCasFilter(java.util.Collection nameList)

obtain CAS from a list of name. This function look at the format of each name to see if it satisfies the CAS format.

Parameters:

nameList - the name or synonym list

Returns:

the CAS list in that synonym list

getPathwayMapByEntityList

java.util.Map getPathwayMapByEntityList(java.util.Collection gobiNodeList)

get the pathways that contains the entities.

Parameters:

gobiNodeList - the entity list.

Returns:

the pathway mapping, the key is the pathway id, and the value is pathway name of the pathway.

See Also:

getGraphModelByPathway(Collection)

getGraphModelByPathway

edu.uci.ics.jung.graph.DirectedGraph getGraphModelByPathway(java.util.Collection pbidList)

return the graph model based on the pathway id list.

Parameters:

pbid - the pathway blockid list

Returns:

the graph model

See Also:

getPathwayMapByEntityList(Collection)

getPathwayCategoryTree

org.apache.commons.collections.map.MultiKeyMap getPathwayCategoryTree()

get the adjacency list of pathway category tree. Suppose the tree is like "Pathways" > "Super-pathways" > "Amino acid biosynthesis", the multikey map contains entries like {key = ("Pathways", "Super-pathways"), value = 1} and {key = ("Super-pathways", "Amino acid biosynthesis"), value=1}. The directed acyclic graph represented by the adjacency list contains both category information and pathway information. The direction of the edge is always from the parent node in the DAG to the child node.

Returns:

the adjacency list of pathway category tree.

See Also:

PathwayCategoryNode

getPathwayInfo

java.util.Map getPathwayInfo(java.util.Collection pbidList)

get the pathway information of

Parameters:

pbidList - the list of pathway blockid

Returns:

the map from blockid to the pathway info

getGraphModelByStep

edu.uci.ics.jung.graph.DirectedGraph getGraphModelByStep(java.util.Collection blockIdList,
                                                         int step)

get the p-neighborhood graph

Parameters:

blockIdList - the blockid list, which can be obtained from various ways

step - the neighbor list is in the 1st step, then 2nd, and so on.

Returns:

the whole community JUNG graph

findLiveEntityList

java.util.Collection findLiveEntityList(boolean exactMatch,
                                        java.lang.String name,
                                        java.lang.String location,
                                        java.lang.String entityType)

find the live entities according to the specified query condition

Parameters:

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

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

location - subcellular compartment, can be null if not known

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

Returns:

the blockunit object list

getAllLocationList

java.util.Collection getAllLocationList()

get all location in the database

Returns:

the location in the database

findBlockunitInstance

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

get the blockunit map

Parameters:

blockIdList - the id list

Returns:

the map of blockid=>blockunitobject

getPathwayElementMap

org.apache.commons.collections.map.MultiKeyMap getPathwayElementMap()

get the full mapping between the pathways and their elements

Returns:

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

getPathwayLocusMap

org.apache.commons.collections.map.MultiKeyMap getPathwayLocusMap()

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

Returns:

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

getPathwayMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getPathwayMetaboliteMap()

get the map from pathway blockid to metabolite blockid

Returns:

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

getMetaboliteMap

org.apache.commons.collections.map.MultiKeyMap getMetaboliteMap()

get the map from metabolite blockid to name

Returns:

the collection of [blockId (int), name, 1].

bevGetAllLocationInfo

java.util.HashMap bevGetAllLocationInfo()

BirdsEyeView code

Returns:

na

bevGetGoBioProcesses

java.util.ArrayList bevGetGoBioProcesses(java.lang.Integer goID)

BirdsEyeView code

Parameters:

goID - na

Returns:

na

bevGetGoChildren

java.util.ArrayList bevGetGoChildren(java.lang.Integer goNodeID)

BirdsEyeView code

Parameters:

goNodeID - na

Returns:

na

bevGetGoFunctions

java.util.ArrayList bevGetGoFunctions(java.lang.Integer goID)

BirdsEyeView code

Parameters:

goID - na

Returns:

na

bevGetGoGeneProductID

java.lang.Integer bevGetGoGeneProductID(java.lang.String locusID)

BirdsEyeView code

Parameters:

locusID - na

Returns:

na

bevGetGoNodeName

java.lang.String bevGetGoNodeName(java.lang.Integer goNodeID)

BirdsEyeView code

Parameters:

goNodeID - na

Returns:

na

bevGetGoNodesWithinDistance

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

BirdsEyeView code

Parameters:

rootNodeID - na

distance - na

Returns:

na

bevGetGoTermAncestors

java.util.ArrayList bevGetGoTermAncestors(java.lang.Integer goTermID)

BirdsEyeView code

Parameters:

goTermID - na

Returns:

na

bevGetLocations

java.util.ArrayList bevGetLocations(java.lang.Integer entityID)

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

bevGetLocusIDs

java.util.ArrayList bevGetLocusIDs(java.lang.String affyID)

BirdsEyeView code

Parameters:

affyID - na

Returns:

na

bevGetMetnetEntityID

java.lang.Integer bevGetMetnetEntityID(java.lang.String locusID)

BirdsEyeView code

Parameters:

locusID - na

Returns:

na

bevGetPathways

java.util.ArrayList bevGetPathways(java.lang.Integer entityID)

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

bevGetPolypeptides

java.util.Map bevGetPolypeptides(java.lang.Integer entityID)

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

bevGetProteinComplexes

java.util.Map bevGetProteinComplexes(java.lang.Integer entityID)

BirdsEyeView code

Parameters:

entityID - na

Returns:

na

getFullGeneAnnotationList

org.apache.commons.collections.map.MultiKeyMap getFullGeneAnnotationList()

return all possible gene annnotation. The annotation is organized like ('ATMG00690', 'affy25k_id', '244906_at', 1), ('AT3G56800', 'go_term_proc', 'calcium-mediated signaling'), etc. The value of this map is always integer 1. The key is a 3-tuple. The first element is the locus ID, the second element is attribute, the third element is the corresponding value. In previous example, '244906_at' is the 'affy25k_id' of the locus 'ATMG00690', 'calcium-mediated signaling' is the 'go_term_proc' of the locus 'AT3G56800'. Here is all possible attributes:

• affy25k_id: Affymetrix 22K probe set ID
• affy8k_id: Affymetrix 8K probe set ID
• - afgc_id: AFGC probe set ID
• - go_term_comp: cellular component ontology term
• - go_term_func: molecular function ontology term
• - go_term_proc: biological process ontology term
• - target_location: TargetP location
• - uniprot_id: UniProt ID
• aracyc_pathway: pathway in AraCyc
• - tair_annotation: annotation from TAIR
• - comment: comment
• - metnet_location: location in MetNetDB
• metnet_pathway: pathway in MetNetDB
• gene_name: gene name
• - mapman_bin_id: MapMan BIN ID
• - mapman_category: MapMan function category
• - mapman_description: MapMan description
• - agris_activates: regulation from AGRIS
• - agris_activatedBy: regulation from AGRIS
• - agris_represses: regulation from AGRIS
• - agris_repressedBy: regulation from AGRIS
• - agris_affects: regulation from AGRIS
• - agris_affectedBy: regulation from AGRIS
• - agris_reference: reference from AGRIS

Returns:

all possible gene annotation

getFullGeneAnnotationAttributeList

java.util.List getFullGeneAnnotationAttributeList()

get all attributes in function getFullGeneAnnotationList()

Returns:

all attributes in function getFullGeneAnnotationList()