- /*
- * map from peptide position to all variant features of the codon for it
- * LinkedHashMap ensures we add the peptide features in sequence order
- */
- LinkedHashMap<Integer, String[][]> variants = new LinkedHashMap<Integer, String[][]>();
- SequenceOntology so = SequenceOntology.getInstance();
-
- SequenceFeature[] dnaFeatures = dnaSeq.getSequenceFeatures();
- if (dnaFeatures == null)
- {
- return variants;
- }
-
- int dnaStart = dnaSeq.getStart();
- int[] lastCodon = null;
- int lastPeptidePostion = 0;
-
- /*
- * build a map of codon variations for peptides
- */
- for (SequenceFeature sf : dnaFeatures)
- {
- int dnaCol = sf.getBegin();
- if (dnaCol != sf.getEnd())
- {
- // not handling multi-locus variant features
- continue;
- }
- if (so.isSequenceVariant(sf.getType()))
- {
- int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
- if (mapsTo == null)
- {
- // feature doesn't lie within coding region
- continue;
- }
- int peptidePosition = mapsTo[0];
- String[][] codonVariants = variants.get(peptidePosition);
- if (codonVariants == null)
- {
- codonVariants = new String[3][];
- variants.put(peptidePosition, codonVariants);
- }
-
- /*
- * extract dna variants to a string array
- */
- String alls = (String) sf.getValue("alleles");
- if (alls == null)
- {
- continue;
- }
- String[] alleles = alls.split(",");
-
- /*
- * get this peptides codon positions e.g. [3, 4, 5] or [4, 7, 10]
- */
- int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
- : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
- peptidePosition, peptidePosition));
- lastPeptidePostion = peptidePosition;
- lastCodon = codon;
-
- /*
- * save nucleotide (and this variant) for each codon position
- */
- for (int codonPos = 0; codonPos < 3; codonPos++)
- {
- String nucleotide = String.valueOf(dnaSeq
- .getCharAt(codon[codonPos] - dnaStart));
- if (codon[codonPos] == dnaCol)
- {
- /*
- * record current dna base and its alleles
- */
- String[] dnaVariants = new String[alleles.length + 1];
- dnaVariants[0] = nucleotide;
- System.arraycopy(alleles, 0, dnaVariants, 1, alleles.length);
- codonVariants[codonPos] = dnaVariants;
- }
- else if (codonVariants[codonPos] == null)
- {
- /*
- * record current dna base only
- * (at least until we find any variation and overwrite it)
- */
- codonVariants[codonPos] = new String[] { nucleotide };
- }
- }
- }
- }
- return variants;
- }