From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 28 Oct 2022 15:27:00 +0000 (+0100)
Subject: JAL-2349 allow contact matrix to provide labels for its annotation row
X-Git-Tag: Release_2_11_3_0~23^2~18^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=059c891e783721341341b71ef222559c9f68fe31

JAL-2349 allow contact matrix to provide labels for its annotation row
---

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
index 4b46d7d..2b5c853 100644
--- 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)
   {
-    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.autoCalculated = true;
+
     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
--- 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;
   }
+
+  @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
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -13,4 +13,8 @@ public interface ContactMatrixI
 
   SequenceI getReferenceSeq();
 
+  String getAnnotDescr();
+
+  String getAnnotLabel();
+
 }
diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 4b23f04..7dd9778 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -88,4 +88,15 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
     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
--- 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;
   }
 
+  @Override
+  public String getAnnotDescr()
+  {
+    return "Predicted Alignment Error for " + refSeq.getName();
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "pAE Matrix";
+
+  }
 }