@Override protected ConceptClass resolveExternally(String id) { return og.getMetaData().getConceptClass(id); } };
private ConceptClass getConceptClass(ONDEXGraph aog, String str) { ConceptClass cc; cc = aog.getMetaData().getConceptClass(str); if (cc == null) { cc = thing; } return cc; }
@Override public ConceptClass getSpecialisationOf() { String ccName = MetaDataHelper.fetchString(sg, tableName, "specOf", mid); if (ccName == null || ccName.isEmpty()) { return null; } return sg.getMetaData().getConceptClass(ccName); }
public static void createContextId(ONDEXGraph graph, String conceptClass, String prefix) throws Exception { ConceptClass cc = graph.getMetaData().getConceptClass(conceptClass); if (cc == null) { throw new Exception("Incorrect concept class specified: " + conceptClass); } Integer i = 0; for (ONDEXConcept c : graph.getConceptsOfConceptClass(cc)) { c.createConceptName(prefix + "_" + i.toString(), true); i++; } } /*
@Override public ConceptClass getOfType() { String a = EntityHelper.fetchString(sg, "concept", "conceptClass", id); return sg.getMetaData().getConceptClass(a); }
protected static ConceptClass createCC(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ ConceptClass cc = meta.getConceptClass(type); if(cc == null)cc = meta.getFactory().createConceptClass(type); return cc; }
protected static ConceptClass createCC(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ ConceptClass cc = meta.getConceptClass(type); if(cc == null)cc = meta.getFactory().createConceptClass(type); return cc; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public ConceptClass requireConceptClass(String id) throws ConceptClassMissingException { ConceptClass cc = graph.getMetaData().getConceptClass(id); if (cc == null) throw new ConceptClassMissingException("Concept Class " + id + " missing"); else return cc; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public ConceptClass requireConceptClass(String id) throws ConceptClassMissingException { ConceptClass cc = graph.getMetaData().getConceptClass(id); if (cc == null) throw new ConceptClassMissingException("concept class " + id + " missing"); else return cc; }
/** * Get concpet class * * @param graph * @param type * @return */ public static ConceptClass createCC(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); ConceptClass cc = meta.getConceptClass(type); if (cc == null) cc = meta.getFactory().createConceptClass(type); return cc; }
/** * Get concpet class * * @param graph * @param type * @return */ public static ConceptClass createCC(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); ConceptClass cc = meta.getConceptClass(type); if (cc == null) cc = meta.getFactory().createConceptClass(type); return cc; }
public Blast(String blastDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(blastDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.ccPfam = graph.getMetaData().getConceptClass(MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource( MetaData.CV_PFAM); this.blast = graph.getMetaData().getEvidenceType(EV_BLAST); }
/** * initialise Ondex meta-data */ private void initMetaData() { // basic concept meta data dsCHEMBL = graph.getMetaData().getDataSource(DS_CHEMBL); dsVO = graph.getMetaData().getDataSource(DS_VO); ccComp = graph.getMetaData().getConceptClass(CC_COMP); ccThing = graph.getMetaData().getConceptClass(CC_THING); evidencetype = graph.getMetaData().getEvidenceType(ET_IMPD); rtIsa = graph.getMetaData().getRelationType(RT_ISA); }
public void start() { FileFilter filter = setupFilters(graph.getConceptsOfConceptClass(graph .getMetaData().getConceptClass(MetaData.CC_ProtFam)), graph .getMetaData().getDataSource(MetaData.CV_PDB)); try { transformer = new ProteinTransformer(graph); ReadFiles(filter); } catch (Exception e) { e.printStackTrace(); } } }
public Decypher(String programDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(programDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.hmmer = graph.getMetaData().getEvidenceType(EV_HMMER); this.ccPfam = graph.getMetaData().getConceptClass( MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource(MetaData.CV_PFAM); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); cc = metaData.getConceptClass("Taxon"); et = metaData.getEvidenceType("IMPD"); external = metaData.getDataSource("TX"); // as used by NCBI Taxonomy parser taxidAttributeName = metaData.getAttributeName("TAXID"); }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }