AlignViewportI viewport)
{
List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+ boolean foundArg = false;
+
for (ArgumentI arg : params)
{
String name = arg.getName();
if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
+ foundArg = true;
String value = arg.getValue();
if (MessageManager.getString("label.alignment").equals(value))
{
}
}
}
+
+ /*
+ * default is to build for the whole alignment
+ */
+ if (!foundArg)
+ {
+ runBuildFor.add(alignment);
+ }
+
return runBuildFor;
}
boolean ran = runCommand(alignmentFile, hmmFile, ac);
if (!ran)
{
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmbuild"));
return;
}
importData(hmmFile, ac);
*/
void deleteHmmSequences(AnnotatedCollectionI ac)
{
- SequenceI hmmSeq = ac.getHmmConsensus();
- if (hmmSeq != null)
+ List<SequenceI> hmmSeqs = ac.getHmmSequences();
+ for (SequenceI hmmSeq : hmmSeqs)
{
if (ac instanceof SequenceGroup)
{
alignment.insertSequenceAt(topIndex, hmmSeq);
ac.setSeqrep(hmmSeq);
grp.addSequence(hmmSeq, false);
- grp.setHmmConsensus(hmmSeq);
}
else
{
alignment.insertSequenceAt(0, hmmSeq);
- alignment.setHmmConsensus(hmmSeq);
- }
-
- if (af.getSelectedHMM() == null)
- {
- af.setSelectedHMMSequence(hmmSeq);
}
}
}