protected List<String> getProteinAccessions(Protein protein) { Set<ProteinXref> crossReferences = protein.getCrossReferences(); List<String> proteinXRefs = new ArrayList<>(crossReferences.size()); for (ProteinXref crossReference : crossReferences) { proteinXRefs.add(crossReference.getIdentifier()); } return proteinXRefs; }
protected String getProteinAccession(Protein protein) { StringBuilder proteinXRef = new StringBuilder(); Set<ProteinXref> crossReferences = protein.getCrossReferences(); for (ProteinXref crossReference : crossReferences) { if (proteinXRef.length() > 0) proteinXRef.append(VALUE_SEPARATOR); proteinXRef.append(crossReference.getIdentifier()); } return proteinXRef.toString(); }
protected String getProteinAccession(Protein protein) { StringBuilder proteinXRef = new StringBuilder(); Set<ProteinXref> crossReferences = protein.getCrossReferences(); for (ProteinXref crossReference : crossReferences) { if (proteinXRef.length() > 0) proteinXRef.append(VALUE_SEPARATOR); proteinXRef.append(crossReference.getIdentifier()); } return proteinXRef.toString(); }
protected List<String> getProteinAccessions(Protein protein) { Set<ProteinXref> crossReferences = protein.getCrossReferences(); List<String> proteinXRefs = new ArrayList<>(crossReferences.size()); for (ProteinXref crossReference : crossReferences) { proteinXRefs.add(crossReference.getIdentifier()); } return proteinXRefs; }
for (ProteinXref xref : proteinXrefs) { counter++; xref.setIdentifier(xref.getIdentifier() + "_" + counter); updates.add(xref);
LOGGER.trace("Has " + protein.getMatches().size() + " matches"); for (ProteinXref xref : protein.getCrossReferences()) { LOGGER.trace("Xref: " + xref.getIdentifier());
LOGGER.trace(xref.getIdentifier()); LOGGER.trace("Adding " + xref.getIdentifier() + " and setting updateRequired = true");
String urlFriendlyId = gen.generate(xref.getIdentifier()); final Path newResultFile = Paths.get(tempDirectory + urlFriendlyId + ".svg"); resultFiles.add(newResultFile);
String urlFriendlyId = gen.generate(xref.getIdentifier()); final Path newResultFile = Paths.get(tempDirectory + urlFriendlyId + ".html"); resultFiles.add(newResultFile);
"getCrossReferences: " + (System.currentTimeMillis() - startPersistProtein ) + " millis "); for (ProteinXref xref : xrefs) { String nucleotideId = xref.getIdentifier(); String description = xref.getDescription(); Long startNewOrf = System.currentTimeMillis();
String strippedProteinId = XrefParser.stripOfFinalUnderScore(proteinXref.getIdentifier());
String strippedProteinId = XrefParser.stripOfFinalUnderScore(proteinXref.getIdentifier());
String strippedProteinId = XrefParser.stripOfFinalUnderScore(proteinXref.getIdentifier());
String strippedProteinId = XrefParser.stripOfFinalUnderScore(proteinXref.getIdentifier());