+ List<Feature> features = entry.getFeature();
+ if (features != null)
+ {
+ for (Feature feature : features)
+ {
+ if (FeatureProperties.isCodingFeature(sourceDb,
+ feature.getName()))
+ {
+ parseCodingFeature(entry, feature, sourceDb, dna, peptides,
+ matcher);
+ }
+ }
+ }
+ } catch (Exception e)
+ {
+ System.err.println("EMBL Record Features parsing error!");
+ System.err
+ .println("Please report the following to help@jalview.org :");
+ System.err.println("EMBL Record " + accession);
+ System.err.println("Resulted in exception: " + e.getMessage());
+ e.printStackTrace(System.err);
+ }
+
+ return dna;
+ }
+
+ /**
+ * Extracts coding region and product from a CDS feature and decorates it with
+ * annotations
+ *
+ * @param entry
+ * @param feature
+ * @param sourceDb
+ * @param dna
+ * @param peptides
+ * @param matcher
+ */
+ void parseCodingFeature(EntryType entry, Feature feature, String sourceDb,
+ SequenceI dna, List<SequenceI> peptides,
+ SequenceIdMatcher matcher)
+ {
+ final boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
+ final String accession = entry.getAccession();
+ final String sequenceVersion = entry.getVersion().toString();
+
+ int[] exons = getCdsRanges(entry.getAccession(), feature);
+
+ String translation = null;
+ String proteinName = "";
+ String proteinId = null;
+ Map<String, String> vals = new Hashtable<>();
+
+ /*
+ * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
+ * (phase is required for CDS features in GFF3 format)
+ */
+ int codonStart = 1;
+
+ /*
+ * parse qualifiers, saving protein translation, protein id,
+ * codon start position, product (name), and 'other values'
+ */
+ if (feature.getQualifier() != null)
+ {
+ for (Qualifier q : feature.getQualifier())
+ {
+ String qname = q.getName();
+ String value = q.getValue();
+ value = value == null ? ""
+ : value.trim().replace(" ", "").replace("\n", "")
+ .replace("\t", "");
+ if (qname.equals("translation"))
+ {
+ translation = value;
+ }
+ else if (qname.equals("protein_id"))
+ {
+ proteinId = value;
+ }
+ else if (qname.equals("codon_start"))
+ {
+ try
+ {
+ codonStart = Integer.parseInt(value.trim());
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Invalid codon_start in XML for "
+ + entry.getAccession() + ": " + e.getMessage());
+ }
+ }
+ else if (qname.equals("product"))
+ {
+ // sometimes name is returned e.g. for V00488
+ proteinName = value;
+ }
+ else
+ {
+ // throw anything else into the additional properties hash
+ if (!"".equals(value))
+ {
+ vals.put(qname, value);
+ }
+ }
+ }
+ }
+
+ DBRefEntry proteinToEmblProteinRef = null;
+ exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
+
+ SequenceI product = null;
+ Mapping dnaToProteinMapping = null;
+ if (translation != null && proteinName != null && proteinId != null)
+ {
+ int translationLength = translation.length();
+
+ /*
+ * look for product in peptides list, if not found, add it
+ */
+ product = matcher.findIdMatch(proteinId);
+ if (product == null)
+ {
+ product = new Sequence(proteinId, translation, 1,
+ translationLength);
+ product.setDescription(((proteinName.length() == 0)
+ ? "Protein Product from " + sourceDb
+ : proteinName));
+ peptides.add(product);
+ matcher.add(product);
+ }
+
+ // we have everything - create the mapping and perhaps the protein
+ // sequence
+ if (exons == null || exons.length == 0)
+ {
+ /*
+ * workaround until we handle dna location for CDS sequence
+ * e.g. location="X53828.1:60..1058" correctly
+ */
+ System.err.println(
+ "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ + sourceDb + ":" + entry.getAccession() + ")");
+ int dnaLength = dna.getLength();
+ if (translationLength * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Not allowing for additional stop codon at end of cDNA fragment... !");
+ // this might occur for CDS sequences where no features are marked
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
+ {
+ System.err.println(
+ "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+ exons = new int[] { dna.getStart() + (codonStart - 1),
+ dna.getEnd() - 3 };
+ dnaToProteinMapping = new Mapping(product, exons,
+ new int[]
+ { 1, translationLength }, 3, 1);
+ }
+ }
+ else