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JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
755abbb
..
9464c74
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-343,13
+343,9
@@
public class Sequence extends ASequence implements SequenceI
this.addPDBId(new PDBEntry(pdb));
}
}
this.addPDBId(new PDBEntry(pdb));
}
}
- if (seq.isHMMConsensusSequence())
- {
- this.isHMMConsensusSequence = true;
- }
if (seq.getHMM() != null)
{
if (seq.getHMM() != null)
{
- this.hmm = new HiddenMarkovModel(seq.getHMM());
+ this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
}
}
}
}
@@
-1916,18
+1912,6
@@
public class Sequence extends ASequence implements SequenceI
}
@Override
}
@Override
- public boolean isHMMConsensusSequence()
- {
- return isHMMConsensusSequence;
- }
-
- @Override
- public void setIsHMMConsensusSequence(boolean value)
- {
- this.isHMMConsensusSequence = value;
- }
-
- @Override
public boolean hasHMMAnnotation()
{
if (this.annotation == null) {
public boolean hasHMMAnnotation()
{
if (this.annotation == null) {
@@
-2107,4
+2091,10
@@
public class Sequence extends ASequence implements SequenceI
// otherwise, sequence was completely hidden
return 0;
}
// otherwise, sequence was completely hidden
return 0;
}
+
+ @Override
+ public boolean hasHMMProfile()
+ {
+ return hmm != null;
+ }
}
}