JAL-2349 allow contact map to be associated with a reference sequence

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);
+    // TODO: contact matrices could be intra or inter - more than one refseq possible! 
+    if (cm.hasReferenceSeq())
+    {
+      aa.setSequenceRef(cm.getReferenceSeq());
+    }
     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;
   }
+
+  @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();
 
+  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;
+  }
+
 }