public Collection<IdentifiedObject> getAllOBOObjects() { Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); Collection<IdentifiedObject> allOBOObjectsCol = new ArrayList<IdentifiedObject>(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject instanceof OBOObject ) { allOBOObjectsCol.add( identifiedObject ); } else { log.debug( "----Not Oboobject---" + identifiedObject.getID() ); } } return allOBOObjectsCol; }
public Collection<IdentifiedObject> getInvalidOBOObjects() { Collection<IdentifiedObject> invalidOboObjects = new ArrayList<IdentifiedObject>(); Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject instanceof OBOObject ) { if ( !identifiedObject.getID().startsWith( "MI:" ) ) { invalidOboObjects.add( identifiedObject ); if ( log.isTraceEnabled() ) log.trace( "invalidCv## " + identifiedObject.getID() + " " + identifiedObject.getName() ); } } } return invalidOboObjects; }
public Collection<IdentifiedObject> getAllMIOBOObjects() { int obsoleteCounter = 0; ArrayList<IdentifiedObject> allMIObjects = new ArrayList<IdentifiedObject>(); Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject.getID().equalsIgnoreCase( MI_ROOT_IDENTIFIER ) ) { continue; } if ( identifiedObject.getID().startsWith( "MI:" ) ) { if ( identifiedObject instanceof OBOObject ) { OBOObject obj = ( OBOObject ) identifiedObject; if ( obj.isObsolete() ) obsoleteCounter++; allMIObjects.add( identifiedObject ); } } } log.info( "obsoleteCounter " + obsoleteCounter ); return allMIObjects; }
/** * returns all the terms parsed from an ontology * * @return a set of OBOClass/Instance objects, or null if session is not initialized */ public Set<OBOObject> getTerms() { LinkDatabase lnkDb = session.getLinkDatabase(); HashSet<OBOObject> terms = new HashSet<OBOObject>(); for (IdentifiedObject io : lnkDb.getObjects()) { //do not return built-in obo: constructs if ((io instanceof OBOClass || io instanceof Instance) && !io.getID().toLowerCase().startsWith("obo:")) { terms.add((OBOObject) io); } } return terms; }
public Collection<IdentifiedObject> getOrphanOBOObjects() { Collection<IdentifiedObject> orphanOboObjects = new ArrayList<IdentifiedObject>(); Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject.getID().startsWith( "MI:" ) ) { if ( identifiedObject instanceof OBOObject ) { OBOObject obj = ( OBOObject ) identifiedObject; Class<? extends CvObject> cvClass = findCvClassforMI( obj.getID() ); //if CvClass is null then no parent if ( cvClass == null ) { if ( !identifiedObject.getID().startsWith( MI_ROOT_IDENTIFIER ) ) { orphanOboObjects.add( identifiedObject ); } } } } } return orphanOboObjects; }
/** * returns all the terms parsed from an ontology * * @return a set of OBOClass/Instance objects, or null if session is not initialized */ public Set<OBOObject> getTerms() { LinkDatabase lnkDb = session.getLinkDatabase(); HashSet<OBOObject> terms = new HashSet<OBOObject>(); for (IdentifiedObject io : lnkDb.getObjects()) { //do not return built-in obo: constructs if ((io instanceof OBOClass || io instanceof Instance) && !io.getID().startsWith("obo:")) { terms.add((OBOObject) io); } // else { // if (io instanceof OBOProperty){ // System.out.println(((OBOProperty) io).getID()); // } // } } return terms; }
public Collection<IdentifiedObject> getObsoleteOBOObjects() { Collection<IdentifiedObject> ObsoloteOboObjects = new ArrayList<IdentifiedObject>(); Collection<IdentifiedObject> allOBOObjects = oboSession.getObjects(); for ( IdentifiedObject identifiedObject : allOBOObjects ) { if ( identifiedObject.getID().startsWith( "MI:" ) ) { if ( identifiedObject instanceof OBOObject ) { OBOObject obj = ( OBOObject ) identifiedObject; String defText = obj.getDefinition(); if ( obj.isObsolete() || defText.contains( "\nOBSOLETE" ) ) { ObsoloteOboObjects.add( identifiedObject ); } } } } return ObsoloteOboObjects; }
/** * returns all the terms parsed from an ontology * * @return a set of OBOClass/Instance objects, or null if session is not initialized */ public Set<OBOObject> getTerms() { LinkDatabase lnkDb = session.getLinkDatabase(); HashSet<OBOObject> terms = new HashSet<OBOObject>(); for (IdentifiedObject io : lnkDb.getObjects()) { //do not return built-in obo: constructs if ((io instanceof OBOClass || io instanceof Instance) && !io.getID().startsWith("obo:")) { terms.add((OBOObject) io); } // else { // if (io instanceof OBOProperty){ // System.out.println(((OBOProperty) io).getID()); // } // } } return terms; }
public OboOntologyIterator(String ontology, URL path) throws OBOParseException, IOException { this.ontology = ontology; DefaultOBOParser parser = new DefaultOBOParser(); OBOParseEngine engine = new OBOParseEngine(parser); engine.setPaths(Arrays.asList(path.toString())); engine.parse(); OBOSession session = parser.getSession(); List<OBOClassImpl> filteredList = new ArrayList<OBOClassImpl>(session.getObjects().size()); for (IdentifiedObject idObj : session.getObjects()) { if (idObj instanceof OBOClassImpl && !idObj.getID().startsWith("obo:")) { filteredList.add((OBOClassImpl)idObj); } } this.oboClassesIterator = filteredList.iterator(); }