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add HMMER colour scheme
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
463b909
..
a1a655e
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-51,6
+51,8
@@
public class SequenceGroup implements AnnotatedCollectionI
boolean colourText = false;
boolean colourText = false;
+ HiddenMarkovModel hmm;
+
/**
* True if the group is defined as a group on the alignment, false if it is
* just a selection.
/**
* True if the group is defined as a group on the alignment, false if it is
* just a selection.
@@
-1457,4
+1459,18
@@
public class SequenceGroup implements AnnotatedCollectionI
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
{
return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
}
+
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ // TODO Auto-generated method stub
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel markov)
+ {
+ hmm = markov;
+
+ }
}
}