+
+ /**
+ * Constructs an alignment consisting of the mapped exon regions in the given
+ * nucleotide sequences, and updates mappings to match.
+ *
+ * @param dna
+ * aligned dna sequences
+ * @param mappings
+ * from dna to protein; these are replaced with new mappings
+ * @return an alignment whose sequences are the exon-only parts of the dna
+ * sequences (or null if no exons are found)
+ */
+ public static AlignmentI makeExonAlignment(SequenceI[] dna,
+ Set<AlignedCodonFrame> mappings)
+ {
+ Set<AlignedCodonFrame> newMappings = new HashSet<AlignedCodonFrame>();
+ List<SequenceI> exonSequences = new ArrayList<SequenceI>();
+
+ for (SequenceI dnaSeq : dna)
+ {
+ final SequenceI ds = dnaSeq.getDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = MappingUtils
+ .findMappingsForSequence(ds, mappings);
+ if (!seqMappings.isEmpty())
+ {
+ /*
+ * We assume here that only one protein mapping is expected per dna
+ * sequence. Mapping to multiple protein sequences is conceivable but
+ * undefined. Splitting a mapping to one protein sequence across
+ * multiple mappings is possible but pathological. Need closer
+ * constraints on the contents of AlignedCodonFrame.
+ */
+ AlignedCodonFrame newMapping = new AlignedCodonFrame();
+ final SequenceI exonSequence = makeExonSequence(ds,
+ seqMappings.get(0), newMapping);
+ exonSequences.add(exonSequence);
+ newMappings.add(newMapping);
+ }
+ }
+ AlignmentI al = new Alignment(
+ exonSequences.toArray(new SequenceI[exonSequences.size()]));
+ al.setDataset(null);
+
+ /*
+ * Replace the old mappings with the new ones
+ */
+ mappings.clear();
+ mappings.addAll(newMappings);
+
+ return al;
+ }
+
+ /**
+ * Helper method to make an exon-only sequence and populate its mapping to
+ * protein
+ * <p>
+ * For example, if ggCCaTTcGAg has mappings [3, 4, 6, 7, 9, 10] to protein
+ * then generate a sequence CCTTGA with mapping [1, 6] to the same protein
+ * residues
+ *
+ * @param dnaSeq
+ * a dna dataset sequence
+ * @param mapping
+ * the current mapping of the sequence to protein
+ * @param newMapping
+ * the new mapping to populate, from the exon-only sequence
+ * @return
+ */
+ protected static SequenceI makeExonSequence(SequenceI dnaSeq,
+ AlignedCodonFrame acf, AlignedCodonFrame newMapping)
+ {
+ Mapping mapping = acf.getMappingForSequence(dnaSeq);
+ final char[] dna = dnaSeq.getSequence();
+ StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
+
+ /*
+ * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ */
+ List<int[]> exonRanges = mapping.getMap().getFromRanges();
+ for (int[] range : exonRanges)
+ {
+ for (int pos = range[0]; pos <= range[1]; pos++)
+ {
+ newSequence.append(dna[pos - 1]);
+ }
+ }
+
+ SequenceI exon = new Sequence(dnaSeq.getName(), newSequence.toString());
+
+ /*
+ * Locate any xrefs to CDS database on the protein product and attach to the
+ * CDS sequence. Also add as a sub-token of the sequence name.
+ */
+ // default to "CDS" if we can't locate an actual gene id
+ String cdsAccId = FeatureProperties.getCodingFeature(DBRefSource.EMBL);
+ DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(
+ mapping.getTo().getDBRef(), DBRefSource.CODINGDBS);
+ if (cdsRefs != null)
+ {
+ for (DBRefEntry cdsRef : cdsRefs)
+ {
+ exon.addDBRef(new DBRefEntry(cdsRef));
+ cdsAccId = cdsRef.getAccessionId();
+ }
+ }
+ exon.setName(exon.getName() + "|" + cdsAccId);
+ exon.createDatasetSequence();
+
+ /*
+ * Build new mappings - from the same protein regions, but now to contiguous
+ * exons
+ */
+ List<int[]> exonRange = new ArrayList<int[]>();
+ exonRange.add(new int[]
+ { 1, newSequence.length() });
+ MapList map = new MapList(exonRange, mapping.getMap().getToRanges(), 3, 1);
+ newMapping.addMap(exon.getDatasetSequence(), mapping.getTo(), map);
+
+ return exon;
+ }