/** * Creates a new EvidenceType with the given id, fullname and description. * Adds the new EvidenceType to the list of EvidenceTypes of this graph. * * @param id * id of the new EvidenceType * @param fullname * fullname of the new EvidenceType * @param description * description of the new EvidenceType * @return EvidenceType * @throws NullValueException * if any parameter is null. * @throws EmptyStringException * if id parameter is an empty string. * @throws UnsupportedOperationException * for read-only graphs */ public EvidenceType createEvidenceType(String id, String fullname, String description) throws NullValueException, EmptyStringException, UnsupportedOperationException { return md.createEvidenceType(id, fullname, description); }
/** * Creates a new EvidenceType with the given id, fullname and empty * description. Adds the new EvidenceType to the list of EvidenceTypes of * this graph. * * @param id * id of the new EvidenceType * @param fullname * fullname of the new EvidenceType * @return EvidenceType * @throws NullValueException * if any parameter is null. * @throws EmptyStringException * if id parameter is an empty string. * @throws UnsupportedOperationException * for read-only graphs */ public EvidenceType createEvidenceType(String id, String fullname) throws NullValueException, EmptyStringException, UnsupportedOperationException { return md.createEvidenceType(id, fullname, ""); }
public synchronized EvidenceType getEvidenceType ( String id, String fullName, String description ) { return this.cacheGet ( EvidenceType.class, id, () -> this.graph.getMetaData ().createEvidenceType ( id, fullName, description ) ); }
ev = og.getMetaData().createEvidenceType(nameS, fullnameS, descriptionS);
aog.getMetaData().createEvidenceType(id.getText(), fullname.getText(), description.getText()); try { this.setClosed(true);
private EvidenceType getIMPDEvidenceType() throws InvalidPluginArgumentException{ EvidenceType evidenceType = graph.getMetaData().getEvidenceType("IMPD");; if (evidenceType != null) { return evidenceType; } return graph.getMetaData().createEvidenceType("IMPD", ((String) args.getUniqueValue(IMPD_FULLNAME_ARG)), ((String) args.getUniqueValue(IMPD_DESCRIPTION_ARG))); }
evidence = graph.getMetaData().getEvidenceType(ev); } else { evidence = graph.getMetaData().createEvidenceType(ev, ev, ev);
@Override public void start() throws Exception { Set<ONDEXConcept> conceptsWithNT = graph.getConceptsOfAttributeName(graph.getMetaData().getAttributeName("NA")); Set<ONDEXConcept> conceptsWithProteins = graph.getConceptsOfAttributeName(graph.getMetaData().getAttributeName("AA")); DecypherAlignment dcAlign = new DecypherAlignment( net.sourceforge.ondex.config.Config.ondexDir, getArguments().getUniqueValue(PROGRAM_DIR_ARG).toString(), 0, //cutff 0f, //% 0001f, //evalue 0, //bitscore Integer.MAX_VALUE, //max alignments false); Collection<Match> hits = dcAlign.query(graph, conceptsWithNT, conceptsWithProteins, BLASTAlignmentProgram.ALGO_BLASTX); RelationType h_s_s = graph.getMetaData().getRelationType("h_s_s"); EvidenceType ev = graph.getMetaData().createEvidenceType("BLASTx", "BLASTx", "BLASTx"); Set<EvidenceType> evs = new HashSet<EvidenceType>(); for (Match hit : hits) { //you might prefer to build an index query-->Hit if you want to take the best n ONDEXConcept query = graph.getConcept(hit.getQueryId()); ONDEXConcept hitTarget = graph.getConcept(hit.getTargetId()); ONDEXRelation relation = graph.createRelation(query, hitTarget, h_s_s, evs); //add some properties to the relations...etc } }
nomd.createEvidenceType(et.getId(), et.getFullname(), et .getDescription());