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JAL-2629 update spikes/mungo to latest
[jalview.git]
/
src
/
jalview
/
analysis
/
SeqsetUtils.java
diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
2c077b6
..
921ab2a
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-53,7
+53,7
@@
public class SeqsetUtils
sqinfo.put("Description", seq.getDescription());
}
sqinfo.put("Description", seq.getDescription());
}
- Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+ Vector<SequenceFeature> sfeat = new Vector<>();
List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
sfeat.addAll(sfs);
List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
sfeat.addAll(sfs);
@@
-70,7
+70,7
@@
public class SeqsetUtils
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
}
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
}
- if (seq.isHMMConsensusSequence())
+ if (seq.hasHMMProfile())
{
sqinfo.put("HMM", seq.getHMM());
}
{
sqinfo.put("HMM", seq.getHMM());
}
@@
-143,8
+143,7
@@
public class SeqsetUtils
if (hmm != null)
{
if (hmm != null)
{
- sq.setHMM(new HiddenMarkovModel(hmm));
- sq.setIsHMMConsensusSequence(true);
+ sq.setHMM(new HiddenMarkovModel(hmm, sq));
}
return namePresent;
}
}
return namePresent;
}