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JAL-3666 SequenceI.*HMM methods look to dataset sequence for HMM profile. Initial...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
25e9611
..
d1f13c1
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-1609,6
+1609,8
@@
public class Sequence extends ASequence implements SequenceI
datasetSequence.addAlignmentAnnotation(_aa);
}
}
datasetSequence.addAlignmentAnnotation(_aa);
}
}
+ datasetSequence.setHMM(hmm);
+ hmm=null;
}
return datasetSequence;
}
}
return datasetSequence;
}
@@
-1888,13
+1890,23
@@
public class Sequence extends ASequence implements SequenceI
@Override
public HiddenMarkovModel getHMM()
{
@Override
public HiddenMarkovModel getHMM()
{
+ if (datasetSequence!=null)
+ {
+ return datasetSequence.getHMM();
+ }
return hmm;
}
@Override
public void setHMM(HiddenMarkovModel hmm)
{
return hmm;
}
@Override
public void setHMM(HiddenMarkovModel hmm)
{
- this.hmm = hmm;
+ if (datasetSequence!=null)
+ {
+ datasetSequence.setHMM(hmm);
+ } else {
+ this.hmm=hmm;
+ }
+
}
@Override
}
@Override
@@
-2081,6
+2093,6
@@
public class Sequence extends ASequence implements SequenceI
@Override
public boolean hasHMMProfile()
{
@Override
public boolean hasHMMProfile()
{
- return hmm != null;
+ return hmm != null || (datasetSequence!=null && datasetSequence.hasHMMProfile());
}
}
}
}