- // map is from dna seq to a protein product
- cf.addMap(sequenceI, nxt, map);
- }
- else
- {
- // map should be from protein seq to its coding dna
- cf.addMap(nxt, sequenceI, map.getInverse());
+ // get sense of map correct for adding to product
+ // alignment.
+ if (dna)
+ {
+ // map is from dna seq to a protein product
+ cf.addMap(sequenceI, nxt, map);
+ }
+ else
+ {
+ // map should be from protein seq to its coding dna
+ cf.addMap(nxt, sequenceI, map.getInverse());
+ }