SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
Hashtable sequencesHash = stashSequences(copyArray);
- exportStockholm(copyArray, alignmentFile, ac);
+ exportStockholm(copyArray, alignmentFile, ac, false);
recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));