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; }
private ONDEXConcept createConcept(String nodelabel, String nodeId) { ONDEXConcept concept = graph.getFactory().createConcept(nodeId, dataSource, cc, et); concept.createConceptName(nodelabel, true); nodeID2Concept.put(nodeId, concept); return concept; }
@Override public EntityFactory getFactory() { return new EntityFactory(this); }
compound = compound.toLowerCase(); if (!compound2g.containsKey(compound)) { co = g.getFactory().createConcept(compound, dataSource_brenda, compd, et); co.createConceptName(compound, false); System.out.println("Created a compound of name: " + compound); g.getFactory().createRelation(co, other_concept, r_type, et); } else { g.getFactory().createRelation(co, other_concept, r_type, et);
/** * recursively builds the output graph based on the * consensus tree. * * @param n input cluster (call this method with the root cluster) */ private ONDEXConcept buildOutput(Cluster n) { ONDEXConcept c = graph.getFactory().createConcept("hierarchy_node:" + n.toString(), dataSource_unknown, cc_hierarchy, ev); BitSet kidleaves = new BitSet(usedConcepts.size()); if (n.getChildren() != null) { for (Cluster kid : n.getChildren()) { ONDEXConcept c_kid = buildOutput(kid); kidleaves.or((BitSet) kid.getKey()); graph.getFactory().createRelation(c_kid, c, rts_isp, ev); } } BitSet leaves = (BitSet) n.getKey().clone(); leaves.andNot((BitSet) kidleaves); for (int i = leaves.nextSetBit(0); i > -1; i = leaves.nextSetBit(i + 1)) { ONDEXConcept cl = graph.getConcept(iid2cid.get(i)); graph.getFactory().createRelation(cl, c, rts_isp, ev); } return c; }
public synchronized ONDEXConcept getConcept ( String id, String annotation, String description, DataSource ds, ConceptClass conceptClass, EvidenceType evidence ) { return this.cacheGet ( ONDEXConcept.class, id, () -> this.graph.getFactory ().createConcept ( id, annotation, description, ds, conceptClass, evidence ) ); }
private static ONDEXRelation createRealtion(ONDEXGraph graph, ONDEXConcept from, ONDEXConcept to, RelationType ofType, EvidenceType ev) { ONDEXRelation result = graph.getRelation(from, to, ofType); if (result == null) { result = graph.getFactory().createRelation(from, to, ofType, ev); } return result; }
/** * recursively builds an output graph based on a * single binary tree. * * @param n input node. (call this method with the root node) */ private ONDEXConcept buildOutput(Node n) { ONDEXConcept c; if (n.isLeaf()) { c = graph.getConcept(iid2cid.get(n.getId())); } else { c = graph.getFactory().createConcept("hierarchy_node:" + n.getId(), dataSource_unknown, cc_hierarchy, ev); c.createAttribute(an_theta, new Double(n.theta), false); c.createAttribute(an_logl, new Double(n.logF), false); ONDEXConcept cl = buildOutput(n.getChild(Node.LEFT)); ONDEXConcept cr = buildOutput(n.getChild(Node.RIGHT)); graph.getFactory().createRelation(cl, c, rts_isp, ev); graph.getFactory().createRelation(cr, c, rts_isp, ev); } return c; }
public SQL3Graph(String connectionString, String user, String pass) { try { conn = DriverManager.getConnection(connectionString, user, pass); } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } ef = new EntityFactory(this); }
private ONDEXConcept createGene(String geneid, String[] additionalIdsFrom, String conceptName) { ONDEXConcept gene = graph.getFactory() .createConcept(geneid, dataSource, cc_gene, eviType); createAccessions(additionalIdsFrom, gene); if (conceptName != null && !conceptName.equalsIgnoreCase("na")) { gene.createConceptName(conceptName.trim(), true); } gene.createAttribute(taxidAn, String.valueOf(3702), false); return gene; }
protected void makeFactorInteraction() { Iterator<String> keys = factorInteraction.keySet().iterator(); while (keys.hasNext()) { String key = keys.next(); ONDEXConcept from = factorsWritten.get(key); ONDEXConcept to = factorsWritten.get(factorInteraction.get(key)); if (to != null) { aog.getFactory().createRelation(from, to, it_wi, evi); } else { Parser.propagateEventOccurred(new DataFileErrorEvent( "Factor for interaction missing: from " + from.getPID() + " to " + factorInteraction.get(from) + " (missing).", "makeFactorInteraction()")); } } }
public void parseLine(String[] data) throws FileNotFoundException, IOException { ONDEXConcept prot = lookup.lookupProtein(data[1], data[2]); ONDEXConcept h = lookup.lookupHormone(data[3]); ONDEXRelation rel = createRealtion(prot, h, r); ONDEXConcept anno = graph.getFactory().createConcept(data[4], ahd, annotation, evidence); if (!data[4].equals("-")) { anno.createConceptName(data[4], true); } if (data[5].length() != 0) { anno.createAttribute(description, data[5], false); } anno.createAttribute(micro, data[7], false); String z = "Mutant"; if (data.length == 9) { z = data[8]; } anno.createAttribute(annoSource, z, false); rel.addTag(anno); String[] ids = data[6].split(";"); for (String id1 : ids) { id1 = id1.trim(); if (id1 == null || id1.length() == 0) continue; ONDEXConcept pub = lookup.lookupPublication(id1); graph.getFactory().createRelation(anno, pub, pub_in, evidence); createHormoneContext(data[3], pub); } createHormoneContext(data[3], prot, rel, anno); } });
private ONDEXConcept createTranscriptionFactor( String tfid, String[] additionalIdsFrom, String conceptName ) { ONDEXConcept tf = graph.getFactory().createConcept(tfid, dataSource, cc_tf, eviType); createAccessions(additionalIdsFrom, tf); if (conceptName != null && !conceptName.equalsIgnoreCase("na")) { tf.createConceptName(conceptName.trim(), true); } tf.createAttribute(taxidAn, String.valueOf(3702), false); return tf; }
private void parseEdge() throws XMLStreamException, ParsingFailedException { // <edge label="YGL028C (pp) YML058W-A" source="-15" target="-59"> Map<String, String> attributes = getAttributes(); ONDEXConcept fromConcept = nodeID2Concept.get(attributes.get("source")); ONDEXConcept toConcept = nodeID2Concept.get(attributes.get("target")); ONDEXRelation relation = graph.getFactory().createRelation(fromConcept, toConcept, rt, et); boolean more = true; for (int event = r.next(); more; event = r.next()) { switch (event) { case XMLStreamConstants.END_DOCUMENT: r.close(); more = false; break; case XMLStreamConstants.START_ELEMENT: String elementName = r.getLocalName(); if (elementName.equals("att")) { parseRelationAttribute(relation); } else if (elementName.equals("graphics")) { parseRelationGraphics(relation); } break; case XMLStreamConstants.END_ELEMENT: if (r.getLocalName().equals("edge")) { more = false; break; } } } }
if (!poplarReg.containsProtein(pAcc)) { count_proteins_fasta++; ONDEXConcept c = graph.getFactory().createConcept(pAcc, dataSourcePHYTOZOME, ccProt, etIMPD); c.createConceptName(geneId, true); c.createConceptAccession(pAcc, dataSourcePHYTOZOME, false); graph.getFactory().createRelation(protein, gene, rt_encodedBy, etIMPD);
@SuppressWarnings("unchecked") private Holder lookupConcept(Map index, ConceptClass cc, Object o) { ONDEXConcept c = (ONDEXConcept) index.get(o); if (c == null) { if (o instanceof String) { String pid = (String) o; c = graph.getFactory().createConcept(pid, ahd, cc, evidence); index.put(pid, c); } else if (o instanceof ArrayKey) { ArrayKey key = (ArrayKey) o; c = graph.getFactory().createConcept((String) key.getArray()[0], ahd, cc, evidence); index.put(key, c); } return new Holder(c, true); } return new Holder(c, false); } }
ONDEXConcept enzyme = g.getConcept(eid2g.get(enzyme_id)); publication_list = check_publistToGid(g, null, refToPublidetails, publist2g, publi2g, compound.references, null); g.getFactory().createRelation(comp, enzyme, rel, et);
ONDEXConcept c = graph.getFactory().createConcept(acc, dataSourcePHYTOZOME, ccProt, etIMPD); c.createConceptName(locus, true); c.createConceptAccession(acc, accDataSource, false); graph.getFactory().createRelation(gene, protein, rt_encodes, etIMPD); graph.getFactory().createRelation(cds, protein, rt_encodes, etIMPD);
private ONDEXConcept createProtein( String proteinid, String[] additionalIdsFrom, String conceptName ) { ONDEXConcept tf_prot = graph.getFactory() .createConcept(proteinid, dataSource, cc_protein, eviType); createAccessions(additionalIdsFrom, tf_prot); if (conceptName != null && !conceptName.equalsIgnoreCase("na")) { tf_prot.createConceptName(conceptName.trim(), true); } tf_prot.createAttribute(taxidAn, String.valueOf(3702), false); return tf_prot; }
g.getFactory().createRelation(g.getConcept(protein_id), g.getConcept(enzyme_id), is_a, et);