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JAL-2349 allow contact map to be associated with a reference sequence
author
Jim Procter
<j.procter@dundee.ac.uk>
Wed, 18 Aug 2021 15:39:35 +0000
(16:39 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Wed, 18 Aug 2021 15:39:35 +0000
(16:39 +0100)
src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/ContactMatrix.java
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src/jalview/datamodel/ContactMatrixI.java
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src/jalview/datamodel/SeqDistanceContactMatrix.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
7f73110
..
9e55911
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-2062,6
+2062,11
@@
public class Alignment implements AlignmentI, AutoCloseable
aa.editable = false;
// aa.autoCalculated = true;
contactmaps.put(aa.annotationId, cm);
aa.editable = false;
// aa.autoCalculated = true;
contactmaps.put(aa.annotationId, cm);
+ // TODO: contact matrices could be intra or inter - more than one refseq possible!
+ if (cm.hasReferenceSeq())
+ {
+ aa.setSequenceRef(cm.getReferenceSeq());
+ }
addAnnotation(aa);
return aa;
}
addAnnotation(aa);
return aa;
}
diff --git
a/src/jalview/datamodel/ContactMatrix.java
b/src/jalview/datamodel/ContactMatrix.java
index
801b292
..
07934a1
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrix.java
+++ b/
src/jalview/datamodel/ContactMatrix.java
@@
-137,4
+137,18
@@
public class ContactMatrix implements ContactMatrixI
{
return max;
}
{
return max;
}
+
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
}
}
diff --git
a/src/jalview/datamodel/ContactMatrixI.java
b/src/jalview/datamodel/ContactMatrixI.java
index
2b7b4ec
..
c16b457
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrixI.java
+++ b/
src/jalview/datamodel/ContactMatrixI.java
@@
-9,4
+9,8
@@
public interface ContactMatrixI
float getMax();
float getMax();
+ boolean hasReferenceSeq();
+
+ SequenceI getReferenceSeq();
+
}
}
diff --git
a/src/jalview/datamodel/SeqDistanceContactMatrix.java
b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index
8f9bdf6
..
bb2299b
100644
(file)
--- a/
src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/
src/jalview/datamodel/SeqDistanceContactMatrix.java
@@
-67,4
+67,18
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
});
}
});
}
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
}