/** * Creates a new EvidenceType with the given id and empty description. Adds * the new EvidenceType to the list of EvidenceTypes of this graph. * * @param id * id 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) throws NullValueException, EmptyStringException, UnsupportedOperationException { return createEvidenceType(id, ""); }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
public EvidenceType safeFetchEvidenceType(String id) { EvidenceType et = metaData.getEvidenceType(id); if (et == null) { et = metaData.getFactory().createEvidenceType(id); } return et; }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
/** * Get evidence type * * @param graph * @param type * @return */ public static EvidenceType createEvidence(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); EvidenceType evidence = meta.getEvidenceType(type); if (evidence == null) evidence = meta.getFactory().createEvidenceType(type); return evidence; }
/** * Get evidence type * * @param graph * @param type * @return */ public static EvidenceType createEvidence(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); EvidenceType evidence = meta.getEvidenceType(type); if (evidence == null) evidence = meta.getFactory().createEvidenceType(type); return evidence; }
errorReport.append(arguments[2]); et = aog.getMetaData().getFactory() .createEvidenceType(arguments[2]); errorReport.append("\n"); errorReport.append("parseRelation: Dummy EvidenceType "
private EvidenceType getEvType(ONDEXGraph aog, String str) { EvidenceType ev = aog.getMetaData().getEvidenceType(str); if (ev == null) { ev = aog.getMetaData().getFactory().createEvidenceType(str); } return ev; }
errorReport.append(arguments[4]); et = aog.getMetaData().getFactory() .createEvidenceType(arguments[4]); errorReport.append("\n"); errorReport.append("parseConcept: Dummy EvidenceType "
et = og.getMetaData().getFactory().createEvidenceType("IMPD");
if (evidencetype == null) evidencetype = graph.getMetaData().getFactory() .createEvidenceType(ET); AttributeName conf = graph.getMetaData().getAttributeName(ATTR_CONF); RelationType relationtype = graph.getMetaData().getRelationType(RT);
targetET = meta.getFactory().createEvidenceType(MetaData.ET);
public void start() throws JAXBException, XMLStreamException, PluginConfigurationException, ClassNotFoundException, InstantiationException, IllegalAccessException { // configure XML parser xmlif = (XMLInputFactory2) XMLInputFactory2.newInstance(); xmlif.configureForXmlConformance(); // define meta data TODO: have this as argument to parser graph.getMetaData().createDataSource(CV_SBML, "SBML", "Imported from SBML file"); graph.getMetaData().getFactory() .createEvidenceType(ET_SBML, "Imported from SBML model"); // mapping of SBML id to Ondex concept Map<String, ONDEXConcept> nodeIDToConcept = new HashMap<String, ONDEXConcept>(); XmlParser parser = new XmlParser(); // parsing of compartments parser.registerParser(Export.COMPARTMENT, new CompartmentParser(graph, nodeIDToConcept)); // parsing of species parser.registerParser(Export.SPECIES, new SpeciesParser(graph, nodeIDToConcept)); // parsing of reactions parser.registerParser(Export.REACTION, new ReactionParser(graph, nodeIDToConcept)); parser.parse(getXMLStreamReader()); // 2nd pass for reactions }
.getMetaData() .getFactory() .createEvidenceType(EVI_GDSEQUAL, "A specified Attribute value was equal", getName());
EvidenceType etWGS = graph.getMetaData().getFactory().createEvidenceType("WGS", "Whole Genome Scan", "This information was inferred from the results of a Whole Genome Scan");
getCurrentMethodName())); eviType = graph.getMetaData().getFactory() .createEvidenceType(MetaData.evidence);
EvidenceType etQTL = graph.getMetaData().getFactory().createEvidenceType("EQTL", "Expression Quantitative Trait Loci", "This information was inferred from the results of a Expression Quantitative Trait Loci Experiment");
m = (M) md.getEvidenceType(id); if (m == null) { m = (M) md.getFactory().createEvidenceType(id);
et = graph.getMetaData().getEvidenceType(id); if (et == null) { et = graph.getMetaData().getFactory().createEvidenceType(id);
if (evidencetype == null) evidencetype = graph.getMetaData().getFactory() .createEvidenceType(ET_IMPD);