public void parseLine(String[] data) throws FileNotFoundException, IOException { ONDEXConcept exp = lookup.lookupExperiment(data[0]); if (exp.getAttributes().size() == 0) { exp.createAttribute(ecoCont, data[1], false); exp.createAttribute(ecoTest, data[2], false); exp.createAttribute(cell, data[3], false); exp.createAttribute(age, data[5], false); exp.createAttribute(treatments, data[8], false); exp.createAttribute(description, data[7], false); exp.createAttribute(hormoneTreat, data[4], false); exp.createAttribute(hormoneConc, data[6], false); } createHormoneContext(data[4], exp); }
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 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; }
/** * Creates the corresponding ONDEXConcept on the given graph. * * @return created publication ONDEXConcept */ public ONDEXConcept createONDEXConcept(int index) { if (!taxids[index].isEmpty()) { ONDEXConcept c = graph.getFactory().createConcept(taxids[index], dataSource, cc, et); // publication associated Attribute c.createAttribute(taxidAttributeName, taxids[index], false); c.createConceptAccession(taxids[index], external, false); return c; } else { throw new RuntimeException("Organism without valid taxid tag!"); } } }
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; }
@Override protected void doAction() { // set flagged attribute to true on all concepts for (ONDEXConcept c : entities) { if (c.getAttribute(anFlag) == null) { c.createAttribute(anFlag, Boolean.TRUE, false); } else { c.getAttribute(anFlag).setValue(Boolean.TRUE); } } }
@Override public void nodeToConcept(AbstractNode node) { Gene gene = (Gene) node; ONDEXConcept concept = graph.getFactory().createConcept(gene.getUniqueId(), dataSourceAraC, ccGene, etIMPD); concept.createAttribute(attTaxId, MetaData.TAXID, false); gene.setConcept(concept); //super.addCommonDetailsToConcept(concept, node); }
@Override public void nodeToConcept(AbstractNode node) { Gene gene = (Gene) node; ONDEXConcept concept = graph.getFactory().createConcept(gene.getUniqueId(), dataSourceBioC, ccGene, etIMPD); concept.createAttribute(attTaxId, Parser.taxidToUse, false); gene.setConcept(concept); //super.addCommonDetailsToConcept(concept, node); }
/** * Copies all Attribute from old concept to new concept. * * @param oldC * old ONDEXConcept * @param newC * new ONDEXConcept */ private void copyGDS(ONDEXConcept oldC, ONDEXConcept newC) { // iterate over all old Attribute for (Attribute attribute : oldC.getAttributes()) { // clone old Attribute on new concept newC.createAttribute(attribute.getOfType(), attribute.getValue(), attribute.isDoIndex()); } }
public void parseLine(String[] data) throws FileNotFoundException, IOException { ONDEXConcept protein = lookup.lookupProtein(data[1], data[2]); ONDEXConcept mut = lookup.lookupMutatant(data[4]); if (data.length > 5 && mut.getAttribute(description) == null) { mut.createAttribute(description, data[5], false); } ONDEXRelation rr = createRealtion(protein, mut, r); createHormoneContext(data[3], rr, protein, mut); } });
@Override public void nodeToConcept(AbstractNode node) { Protein protein = (Protein) node; ConceptClass cc = null; if (protein.isComplex()) cc = ccProteinComplex; else cc = ccProtein; ONDEXConcept concept = graph.getFactory().createConcept( protein.getUniqueId(), dataSourceBioC, cc, etIMPD); concept.createAttribute(attTaxId, Parser.taxidToUse, false); protein.setConcept(concept); }
public static void countMembers(OVTK2PropertiesAggregator viewer, String clsOfConctext, String clsOfMemeber) { ONDEXGraph graph = viewer.getONDEXJUNGGraph(); AttributeName an = createAttName(graph, clsOfMemeber + "_members", Double.class); ConceptClass cls = createCC(graph, clsOfMemeber); for (ONDEXConcept c : graph.getConceptsOfConceptClass(createCC(graph, clsOfConctext))) { Double count = 0d; for (ONDEXConcept oc : graph.getConceptsOfTag(c)) { if (oc.getOfType().equals(cls)) { count++; } } c.createAttribute(an, count, false); } }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
@Override public void nodeToConcept(AbstractNode node) { Publication pub = (Publication) node; if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD)) return; ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD); if (pub.getPubMedId() != 0){ concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false); } if (pub.getTitle() != null && !pub.getTitle().equals("")){ concept.createAttribute(attTitle, pub.getTitle(), false); } pub.setConcept(concept); }
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); }