public ONDEXConcept lookupExperiment(String id) { Holder h = lookupConcept(experimentIndex, experiment, id); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptName(id, true); return c; }
public ONDEXConcept lookupHormone(String id) { Holder h = lookupConcept(hormoneIndex, hormone, id); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptName(id, true); return c; }
public ONDEXConcept lookupMutatant(String id) { Holder h = lookupConcept(mutatnIndex, mutant, id); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptName(id, true); return c; }
public ONDEXConcept lookupTreatment(String id, String hormone) { String trueId = treatmentCode.get(id); Holder h = lookupConcept(treatmentIndex, treatment, trueId + " - " + hormone); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptName(trueId, true); return c; }
public ONDEXConcept lookupProtein(String id, String name) { String id1 = id.toUpperCase(); Holder h = lookupConcept(proteinIndex, protein, id1); ONDEXConcept c = h.concept; if (h.isNew) { if (c.getConceptNames().size() == 0 && name != null && name.length() != 0) { c.createConceptName(name, true); } } return c; }
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; }
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 ONDEXConcept lookupPhenotype(String... ids) { ArrayKey<String> key = new ArrayKey<String>(ids); Holder h = lookupConcept(phenotypeIndex, phenotype, key); ONDEXConcept c = h.concept; if (h.isNew) c.createConceptName(ids[0], true); return c; }
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; }
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; }
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; }
@Override public void parse(File file) throws IOException { pheno0 = graph.getFactory().createConcept("Phenotype", ahd, phenotype, evidence); pheno0.createConceptName("Phenotype", true); super.parse(file); }
/** * Copies all names from old concept to new concept. * * @param oldC * old ONDEXConcept * @param newC * new ONDEXConcept */ private void copyNames(ONDEXConcept oldC, ONDEXConcept newC) { // iterate over all old names for (ConceptName name : oldC.getConceptNames()) { // clone old name on new concept newC.createConceptName(name.getName(), name.isPreferred()); } }
public void createTag(String conceptClass, String name) { ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M")); c.createConceptName(name, true); this.addTag(c); } }
public static void createContext(OVTK2PropertiesAggregator viewer, String name) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); ONDEXConcept context = graph.getFactory().createConcept(name, createDataSource(graph, "unknown"), createCC(graph, "Thing"), createEvidence(graph, "manual")); context.createConceptName(name, true); for (ONDEXConcept c : graph.getConcepts()) { c.addTag(context); } }
public int getOrCreateGeneID(String geneId) { if (poplarReg.containsGene(geneId)) { return poplarReg.getGene(geneId); } else { ONDEXConcept gene = og.getFactory().createConcept(geneId, dataSourcePHYTOZOME, ccGene, etIMPD); gene.createConceptAccession(geneId, dataSourcePHYTOZOME, false); gene.createConceptName(geneId, false); Integer ondexGeneId = gene.getId(); gene.createAttribute(anTaxID, Parser.POPLAR_TAX_ID, false); poplarReg.addGene(geneId, ondexGeneId); return ondexGeneId; } }
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceAraC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceMetaC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Reaction reaction = (Reaction) node; ONDEXConcept concept = graph.getFactory().createConcept( reaction.getUniqueId(), dataSourceBioC, ccReaction, etIMPD); if (reaction.getBalancedState() != null) concept.setAnnotation(reaction.getBalancedState()); concept.createConceptName(constructFormula(reaction), false); if (reaction.getDeltaGo() != null) { concept.createAttribute(deltaGo, reaction.getDeltaGo(), false); } reaction.setConcept(concept); }
@Override public void start() throws Exception { String conceptClass = (String) args.getUniqueValue(CC); String name = (String) args.getUniqueValue(NAME); Set<ONDEXConcept> cs = graph.getConcepts(); Set<ONDEXRelation> rs = graph.getRelations(); ONDEXConcept c = graph.getFactory().createConcept(name, createDataSource(graph, "UC"), createCC(graph, conceptClass), createEvidence(graph, "M")); c.createConceptName(name, true); for (ONDEXConcept co : cs) { co.addTag(c); } for (ONDEXRelation re : rs) { re.addTag(c); } }