/** * @return * @see net.sourceforge.ondex.core.ONDEXGraph#getMetaData() */ public ONDEXGraphMetaData getMetaData() { return og.getMetaData(); }
@Override protected ConceptClass resolveExternally(String id) { return og.getMetaData().getConceptClass(id); } };
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); }
@Override protected RelationType resolveExternally(String id) { return og.getMetaData().getRelationType(id); } };
@Override protected AttributeName resolveExternally(String id) { return og.getMetaData().getAttributeName(id); } };
/** * @param og * ONDEXGraph to wrap */ LuceneONDEXGraph(ONDEXGraph og) { this(og.getName(), og.getMetaData()); this.parent = og; super.readOnly = true; }
/** * Constructor. */ public TaxidPlugin(ONDEXGraph aog) { super(aog); taxid_an = aog.getMetaData().getAttributeName("TAXID"); }
private RelationType getRelationType(ONDEXGraph aog, String str) { RelationType rt; rt = aog.getMetaData().getRelationType(str); if (rt == null) { rt = rtype; } return rt; }
private EvidenceType getEvType(ONDEXGraph aog, String str) { EvidenceType ev = aog.getMetaData().getEvidenceType(str); if (ev == null) { ev = aog.getMetaData().getFactory().createEvidenceType(str); } return ev; }
@Override public void start() { for (ConceptClass conceptClass : graph.getMetaData().getConceptClasses()) { Set<ONDEXConcept> concepts = graph.getConceptsOfConceptClass(conceptClass); System.out.println("ConceptClassId\tNumber of instances"); if (concepts.size() > 0) { System.out.println(conceptClass.getId() + "\t" + concepts.size()); } } }
@Override public void start() { for (DataSource dataSource : graph.getMetaData().getDataSources()) { Set<ONDEXConcept> concepts = graph.getConceptsOfDataSource(dataSource); System.out.println("Data source C.V. id\tNumber of instances"); if (concepts.size() > 0) { System.out.println(dataSource.getId() + "\t" + concepts.size()); } } }
public synchronized ConceptClass getConceptClass ( String id, String fullName, String description, ConceptClass specialisationOf ) { return this.cacheGet ( ConceptClass.class, id, () -> this.graph.getMetaData ().createConceptClass ( id, fullName, description, specialisationOf ) ); }
public synchronized DataSource getDataSource ( String id, String fullName, String description ) { return this.cacheGet ( DataSource.class, id, () -> this.graph.getMetaData ().createDataSource ( id, fullName, description ) ); }
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++; } } /*
public WrapperModel(ONDEXGraph og, OntModelSpec spec) { om = createOntModel(og.getMetaData(), spec); im = createModel(og); om.addSubModel(im); }
public synchronized RelationType getRelationType ( String id, boolean isAntisymmetric, boolean isReflexive, boolean isSymmetric, boolean isTransitive ) { return this.cacheGet ( RelationType.class, id, () -> this.graph.getMetaData ().getFactory ().createRelationType ( id, isAntisymmetric, isReflexive, isSymmetric, isTransitive ) ); }
private static void assignCoexWeight(ONDEXGraph graph) { AttributeName an = graph.getMetaData().getFactory().createAttributeName("COEX_WEIGHT", Double.class); for (ONDEXRelation r : graph.getRelations()) { Attribute attribute = r.getAttribute(graph.getMetaData().getAttributeName("Correlation")); if (attribute == null) continue; Double score = (Double) attribute.getValue(); r.createAttribute(an, (Math.abs(score) - 0.6) / 0.4, false); } }
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())); } }