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; }
LOGGER.trace("Protein ID: " + protein.getId() + " MD5: " + protein.getMd5()); LOGGER.trace("Has " + protein.getMatches().size() + " matches"); for (ProteinXref xref : protein.getCrossReferences()) { LOGGER.trace("Xref: " + xref.getIdentifier());
if (candidate.getCrossReferences() != null) { if (LOGGER.isTraceEnabled()) { LOGGER.trace("Protein TO BE STORED has xrefs:"); for (ProteinXref xref : candidate.getCrossReferences()) { if (LOGGER.isTraceEnabled()) { LOGGER.trace(xref.getIdentifier()); if (!existingProtein.getCrossReferences().contains(xref)) { if (LOGGER.isTraceEnabled()) { LOGGER.trace("Adding " + xref.getIdentifier() + " and setting updateRequired = true");
for (ProteinXref xref : protein.getCrossReferences()) { final SimpleProtein simpleProtein = SimpleProtein.valueOf(protein, xref, entryHierarchy); if (simpleProtein != null) {
checkEntryHierarchy(); if (entryHierarchy != null) { for (ProteinXref xref : protein.getCrossReferences()) { final SimpleProtein simpleProtein = SimpleProtein.valueOf(protein, xref, entryHierarchy); if (simpleProtein != null) {
proteinCount ++; Long startPersistProtein = System.currentTimeMillis(); Set<ProteinXref> xrefs = newProtein.getCrossReferences(); if (LOGGER.isDebugEnabled()) { LOGGER.debug("Protein with ID " + newProtein.getId() + " has " + xrefs.size() + " cross references.");
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier(); for (ProteinXref proteinXref : protein.getCrossReferences()) {
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier(); for (ProteinXref proteinXref : protein.getCrossReferences()) {
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier(); for (ProteinXref proteinXref : protein.getCrossReferences()) {
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier(); for (ProteinXref proteinXref : protein.getCrossReferences()) {