+ return translateCodingRegion(selection, seqstring, viscontigs, codons,
+ gapCharacter, product, false);
+ }
+
+ /**
+ * Translate a na sequence
+ *
+ * @param selection
+ * sequence displayed under viscontigs visible columns
+ * @param seqstring
+ * ORF read in some global alignment reference frame
+ * @param viscontigs
+ * mapping from global reference frame to visible seqstring ORF read
+ * @param codons
+ * Definition of global ORF alignment reference frame
+ * @param gapCharacter
+ * @param starForStop
+ * when true stop codons will translate as '*', otherwise as 'X'
+ * @return sequence ready to be added to alignment.
+ */
+ public static SequenceI translateCodingRegion(SequenceI selection,
+ String seqstring, int[] viscontigs, AlignedCodonFrame codons,
+ char gapCharacter, DBRefEntry product, final boolean starForStop)
+ {