{
static final String HMMALIGN = "hmmalign";
- static final String ARG_TRIM = "--trim";
-
private final AlignmentI dataset;
/**
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
msgId);
+ // ensure alignments are the same length
+ alignment.padGaps();
+
AlignmentView msa = af.gatherSequencesForAlignment();
SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());