fr.curie.BiNoM.pathways.utils
Class BioPAXGraphQueryEngine

java.lang.Object
  fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

public class BioPAXGraphQueryEngine
extends java.lang.Object

The actual implementation of the standard query

Field Summary

Graph	database The index with which the query is performed
Graph	databaseCopyForPathAnalysis Copy of the database to perform index path analysis
java.util.HashMap	entitySynonym Map from node names and synonyms to the Vector of Node objects
java.util.HashMap	entityXREF Map from node xrefs to the Vector of Node objects
boolean	excludeSmallMolecules If false, all smallMolecules are excluded in queries
BioPAXGraphQuery	query The query to be made

Constructor Summary

BioPAXGraphQueryEngine()

Method Summary

void	countEntities(java.util.Vector entities, java.util.Vector numbers)
void	doQuery(BioPAXGraphQuery q, int queryType) Performs a query of queryType
void	prepareDatabaseCopyForIndexPathAnalysis() Prepares a copy of database for Index Path Analysis.
edu.rpi.cs.xgmml.GraphDocument	resultAsXgmml() Result of the query as GraphDocument object
void	setDatabase(Graph graph) Setting the BioPAX index file for performing the query
void	setDatabase(edu.rpi.cs.xgmml.GraphDocument xgml) Setting the BioPAX index file for performing the query

Methods inherited from class java.lang.Object

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

Field Detail

query

public BioPAXGraphQuery query

The query to be made

database

public Graph database

The index with which the query is performed

databaseCopyForPathAnalysis

public Graph databaseCopyForPathAnalysis

Copy of the database to perform index path analysis

entitySynonym

public java.util.HashMap entitySynonym

Map from node names and synonyms to the Vector of Node objects

entityXREF

public java.util.HashMap entityXREF

Map from node xrefs to the Vector of Node objects

excludeSmallMolecules

public boolean excludeSmallMolecules

If false, all smallMolecules are excluded in queries

Constructor Detail

BioPAXGraphQueryEngine

public BioPAXGraphQueryEngine()

Method Detail

doQuery

public void doQuery(BioPAXGraphQuery q,
                    int queryType)

Performs a query of queryType

setDatabase

public void setDatabase(edu.rpi.cs.xgmml.GraphDocument xgml)

Setting the BioPAX index file for performing the query

setDatabase

public void setDatabase(Graph graph)

Setting the BioPAX index file for performing the query

Parameters:

graph -

resultAsXgmml

public edu.rpi.cs.xgmml.GraphDocument resultAsXgmml()

Result of the query as GraphDocument object

Returns:

countEntities

public void countEntities(java.util.Vector entities,
                          java.util.Vector numbers)

Parameters:

entities - List of entities

numbers - Empty vector in which after Integer numbers are found

prepareDatabaseCopyForIndexPathAnalysis

public void prepareDatabaseCopyForIndexPathAnalysis()

Prepares a copy of database for Index Path Analysis. Removes publications, pathways, pathwaySteps, revert direction of some edges.