phenote.dataadapter
Class OntologyDataAdapter

java.lang.Object
  phenote.dataadapter.OntologyDataAdapter

public class OntologyDataAdapter
extends java.lang.Object

is this really a data adapter? - OntologyLoader? this isnt a data adapter it doesnt load & commit character data - just loads ontologies. rename OntologyLoader for now can stay in dataadapter package this is specifically a OboFileLoader - other kinds of ontology loading may com along OntologyDataAdapter and OntologyDataAdapter2 desperately need to be merged! theres a lot of cut&paste code between them and maintaining both is very tedious the parts that are different in ODA2 should just be done with a flag, the duplicated classes is not the way to go

Method Summary

static OntologyDataAdapter	getInstance() synchronized so cant reload an ontology while ontologies are being initialized getInstance calls initOntologies - in other words you have to call getInstance to initialize the ontologies
long	getOboDate(java.net.URL oboUrl) Get the date of the file from the header of the obo file - just read header dont read in whole file.
static void	initialize() just calls getInstance - but more intuitive for initialization
void	reloadOntologies() The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one
static void	reset()

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static OntologyDataAdapter getInstance()

synchronized so cant reload an ontology while ontologies are being initialized getInstance calls initOntologies - in other words you have to call getInstance to initialize the ontologies

reset

public static void reset()

initialize

public static void initialize()

just calls getInstance - but more intuitive for initialization

getOboDate

public long getOboDate(java.net.URL oboUrl)
                throws OntologyException

Get the date of the file from the header of the obo file - just read header dont read in whole file. should it also query urlConnection for date first? throws OntologyException if unable to parse date DateEx?

Throws:

OntologyException

reloadOntologies

public void reloadOntologies()
                      throws OntologyException

The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one

Throws:

OntologyException