public class BioPAXGraphQueryEngine
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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 and Description |
---|
BioPAXGraphQueryEngine() |
Modifier and Type | Method and Description |
---|---|
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.
|
GraphDocument |
resultAsXgmml()
Result of the query as GraphDocument object
|
void |
setDatabase(edu.rpi.cs.xgmml.GraphDocument xgml)
Setting the BioPAX index file for performing the query
|
public BioPAXGraphQuery query
public Graph database
public Graph databaseCopyForPathAnalysis
public java.util.HashMap entitySynonym
public java.util.HashMap entityXREF
public boolean excludeSmallMolecules
public void doQuery(BioPAXGraphQuery q, int queryType)
public void setDatabase(edu.rpi.cs.xgmml.GraphDocument xgml)
public GraphDocument resultAsXgmml()
public void countEntities(java.util.Vector entities, java.util.Vector numbers)
entities
- List of entitiesnumbers
- Empty vector in which after Integer numbers are foundpublic void prepareDatabaseCopyForIndexPathAnalysis()