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; }
public AttributeName safeFetchAttributeName(String id, Class<?> type) { AttributeName an = metaData.getAttributeName(id); if (an == null) { an = metaData.getFactory().createAttributeName(id, type); } return an; }
protected static AttributeName createAttName(ONDEXGraphMetaData meta, String type, Class<?> cls) throws NullValueException, EmptyStringException{ AttributeName att = meta.getAttributeName(type); if(att == null)att = meta.getFactory().createAttributeName(type, cls); return att; } }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
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 AttributeName createAttName(ONDEXGraphMetaData meta, String type, Class<?> cls) throws NullValueException, EmptyStringException{ AttributeName att = meta.getAttributeName(type); if(att == null)att = meta.getFactory().createAttributeName(type, cls); return att; } }
public RelationType safeFetchRelationType(String id, String description) { RelationType rt = metaData.getRelationType(id); if (rt == null) { rt = metaData.getFactory().createRelationType(id, description); } return rt; }
public DataSource safeFetchDataSource(String id) { DataSource dataSource = metaData.getDataSource(id); if (dataSource == null) { dataSource = metaData.getFactory().createDataSource(id); } return dataSource; }
public EvidenceType safeFetchEvidenceType(String id) { EvidenceType et = metaData.getEvidenceType(id); if (et == null) { et = metaData.getFactory().createEvidenceType(id); } return et; }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
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 ) ); }
/** * Get cv * * @param graph * @param type * @return */ public static DataSource createDataSource(final ONDEXGraph graph, final String type) { ONDEXGraphMetaData meta = graph.getMetaData(); DataSource dataSource = meta.getDataSource(type); if (dataSource == null) dataSource = meta.getFactory().createDataSource(type); return dataSource; }
/** * 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; }
private EvidenceType getEvType(ONDEXGraph aog, String str) { EvidenceType ev = aog.getMetaData().getEvidenceType(str); if (ev == null) { ev = aog.getMetaData().getFactory().createEvidenceType(str); } return ev; }
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); } }
@Override public void init(OVTK2PropertiesAggregator v, Set<ONDEXConcept> e) { super.init(v, e); ONDEXJUNGGraph graph = this.viewer.getONDEXJUNGGraph(); anFlag = graph.getMetaData().getAttributeName(AppearanceSynchronizer.FLAGGED); if (anFlag == null) anFlag = graph.getMetaData().getFactory().createAttributeName(AppearanceSynchronizer.FLAGGED, "flagged concept", Boolean.class); }
@Override public void init(OVTK2PropertiesAggregator v, Set<ONDEXConcept> e) { super.init(v, e); ONDEXJUNGGraph graph = this.viewer.getONDEXJUNGGraph(); anFlag = graph.getMetaData().getAttributeName(AppearanceSynchronizer.FLAGGED); if (anFlag == null) anFlag = graph.getMetaData().getFactory().createAttributeName(AppearanceSynchronizer.FLAGGED, "flagged concept", Boolean.class); }
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"); }