private EvidenceType getEvType(ONDEXGraph aog, String str) { EvidenceType ev = aog.getMetaData().getEvidenceType(str); if (ev == null) { ev = aog.getMetaData().getFactory().createEvidenceType(str); } return ev; }
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"); }
@Override protected ConceptClass resolveExternally(String id) { return og.getMetaData().getConceptClass(id); } };
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 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); }
public synchronized ONDEXRelation getRelation ( ONDEXConcept from, ONDEXConcept to, RelationType type, EvidenceType evidence ) { String id = from.getPID () + to.getPID () + type.getId () + evidence.getId (); return this.cacheGet ( ONDEXRelation.class, id, () -> this.graph.getFactory ().createRelation ( from, to, type, evidence ) ); }
/** * 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 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; }
public AttributeName safeFetchAttributeName(String id, Class<?> type) { AttributeName an = metaData.getAttributeName(id); if (an == null) { an = metaData.getFactory().createAttributeName(id, type); } return an; }
public RelationType safeFetchRelationType(String id, String description) { RelationType rt = metaData.getRelationType(id); if (rt == null) { rt = metaData.getFactory().createRelationType(id, description); } return rt; }
public ONDEXRelation createRealtion(ONDEXConcept from, ONDEXConcept to, RelationType rt) { ONDEXRelation result = graph.getRelation(from, to, rt); if (result == null) { result = graph.getFactory().createRelation(from, to, rt, evidence); } return result; }
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; }
@Override protected RelationType resolveExternally(String id) { return og.getMetaData().getRelationType(id); } };
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; }
private static double getNumber(AttributeName an, ONDEXRelation r) { Attribute attribute = r.getAttribute(an); if (attribute == null) return 0d; else return (Double) attribute.getValue(); }
private void addAttribute(Object value, Attribute attribute, ONDEXRelation relation, AttributeName att) { if (value != null) { if (attribute == null) { relation.createAttribute(att, value, false); } else { attribute.setValue(value); } } }
@Override public int compare(ONDEXConcept o1, ONDEXConcept o2) { return o2.getElementOf().compareTo(o1.getElementOf()); } });
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 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; } }