+ * Insert a gap into the aligned proteins and the codon mapping array.
+ *
+ * @param pos
+ * @param gapCharacter
+ * @param alignedCodons
+ * @param proteinSeqs
+ */
+ protected static void insertAAGap(int pos, char gapCharacter,
+ int[][] alignedCodons, List<SequenceI> proteinSeqs)
+ {
+ System.out.println("insertAAGap " + pos + "/" + proteinSeqs.size());
+ // aaWidth++;
+ for (SequenceI seq : proteinSeqs)
+ {
+ seq.insertCharAt(pos, gapCharacter);
+ }
+
+ // if (pos < aaWidth)
+ // {
+ // aaWidth++;
+ System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
+ alignedCodons.length - pos - 1);
+ alignedCodons[pos] = null; // clear so new codon position can be marked.
+ // }
+ }
+
+ /**