org.biopax.paxtools.persistence.level2
Class HiRDB

java.lang.Object
  org.biopax.paxtools.persistence.level2.HiRDB

public class HiRDB
extends java.lang.Object

RDB hibernation context class

Field Summary

boolean

bPrintTime

Constructor Summary

HiRDB()
contructor

HiRDB(java.lang.String puName, java.lang.String connectionURL, java.lang.String user, java.lang.String password, java.lang.String indexBase)
contructor

Method Summary

InteractionSearch	createInteractionSearch() create interaction search
KeywordSearch	createKeywordSearch() create keyword search
MiscSearch	createMiscSearch() create misc search
PathwaySearch	createPathwaySearch() create pathway search
PhysicalEntitySearch	createPhysicalEntitySearch() create physicalEntity search
HiRDBConnect	getConnect() connect
BioPAXElement	getElementByRDFID(java.lang.String rdfID) get element by rdf:ID
javax.persistence.EntityManager	getEntityManager()
HiRDBSession	getSession() session
void	setConnect(HiRDBConnect connect)
void	setSession(HiRDBSession session)
boolean	setup() setup before upload / download

Methods inherited from class java.lang.Object

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

Field Detail

bPrintTime

public boolean bPrintTime

Constructor Detail

HiRDB

public HiRDB()

contructor

HiRDB

public HiRDB(java.lang.String puName,
             java.lang.String connectionURL,
             java.lang.String user,
             java.lang.String password,
             java.lang.String indexBase)

contructor

Parameters:

puName - persistence unit name. "PaxtoolsForPostgreSQL" / "PaxtoolsForMySQL"

connectionURL - jdbc connection path. e.g. "jdbc:postgresql://localhost/PAXTOOLS"

user - jdbc user

password - jdbc password

indexBase - Lucene index base directory path

Method Detail

getConnect

public HiRDBConnect getConnect()

connect

setConnect

public void setConnect(HiRDBConnect connect)

getSession

public HiRDBSession getSession()

session

setSession

public void setSession(HiRDBSession session)

setup

public boolean setup()

setup before upload / download

Returns:

true is OK

getElementByRDFID

public BioPAXElement getElementByRDFID(java.lang.String rdfID)

get element by rdf:ID

Parameters:

rdfID - rdf:ID

Returns:

BioPAXElement

getEntityManager

public javax.persistence.EntityManager getEntityManager()

createKeywordSearch

public KeywordSearch createKeywordSearch()

create keyword search

Returns:

KeywordSearch

createMiscSearch

public MiscSearch createMiscSearch()

create misc search

Returns:

MiscSearch

createPathwaySearch

public PathwaySearch createPathwaySearch()

create pathway search

Returns:

PathwaySearch

createInteractionSearch

public InteractionSearch createInteractionSearch()

create interaction search

Returns:

InteractionSearch

createPhysicalEntitySearch

public PhysicalEntitySearch createPhysicalEntitySearch()

create physicalEntity search

Returns:

PhysicalEntitySearch