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JAL-2349 allow contact matrix to provide labels for its annotation row
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 28 Oct 2022 15:27:00 +0000
(16:27 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 28 Oct 2022 15:29:30 +0000
(16:29 +0100)
src/jalview/datamodel/ContactMapHolder.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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src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
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diff --git
a/src/jalview/datamodel/ContactMapHolder.java
b/src/jalview/datamodel/ContactMapHolder.java
index
4b46d7d
..
2b5c853
100644
(file)
--- a/
src/jalview/datamodel/ContactMapHolder.java
+++ b/
src/jalview/datamodel/ContactMapHolder.java
@@
-37,13
+37,14
@@
public class ContactMapHolder implements ContactMapHolderI
@Override
public AlignmentAnnotation addContactList(ContactMatrixI cm)
{
@Override
public AlignmentAnnotation addContactList(ContactMatrixI cm)
{
- AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
- "Contact Matrix", new Annotation[0]);
+
+ AlignmentAnnotation aa = new AlignmentAnnotation(cm.getAnnotLabel(),
+ cm.getAnnotDescr(), new Annotation[0]);
aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
aa.graphMin = cm.getMin();
aa.graphMax = cm.getMax();
aa.editable = false;
aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
aa.graphMin = cm.getMin();
aa.graphMax = cm.getMax();
aa.editable = false;
- // aa.autoCalculated = true;
+
contactmaps.put(aa.annotationId, cm);
// TODO: contact matrices could be intra or inter - more than one refseq
// possible!
contactmaps.put(aa.annotationId, cm);
// TODO: contact matrices could be intra or inter - more than one refseq
// possible!
diff --git
a/src/jalview/datamodel/ContactMatrix.java
b/src/jalview/datamodel/ContactMatrix.java
index
de7cba4
..
35ec87b
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrix.java
+++ b/
src/jalview/datamodel/ContactMatrix.java
@@
-154,4
+154,16
@@
public class ContactMatrix implements ContactMatrixI
// TODO Auto-generated method stub
return null;
}
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "Contact Matrix";
+ }
+
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Contact Matrix";
+ }
}
}
diff --git
a/src/jalview/datamodel/ContactMatrixI.java
b/src/jalview/datamodel/ContactMatrixI.java
index
c16b457
..
6860e82
100644
(file)
--- a/
src/jalview/datamodel/ContactMatrixI.java
+++ b/
src/jalview/datamodel/ContactMatrixI.java
@@
-13,4
+13,8
@@
public interface ContactMatrixI
SequenceI getReferenceSeq();
SequenceI getReferenceSeq();
+ String getAnnotDescr();
+
+ String getAnnotLabel();
+
}
}
diff --git
a/src/jalview/datamodel/SeqDistanceContactMatrix.java
b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index
4b23f04
..
7dd9778
100644
(file)
--- a/
src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/
src/jalview/datamodel/SeqDistanceContactMatrix.java
@@
-88,4
+88,15
@@
public class SeqDistanceContactMatrix implements ContactMatrixI
return null;
}
return null;
}
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Sequence distance matrix";
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "Sequence Distance";
+ }
}
}
diff --git
a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index
8fde1e8
..
0ac3e00
100644
(file)
--- a/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/
src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@
-174,4
+174,16
@@
public class PAEContactMatrix implements ContactMatrixI
return refSeq;
}
return refSeq;
}
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Predicted Alignment Error for " + refSeq.getName();
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "pAE Matrix";
+
+ }
}
}