X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=f8fd750955d0861ca20606d3b4b6a7ea85ff7812;hb=c956ba7ae40dd7f269aa372044ed4ed5f28fb042;hp=731948b3b8be489e41b92fd2640eba84792b51fb;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 731948b..f8fd750 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,12 +1,21 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
+import jalview.util.MapList;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
 /**
  * Dummy contact matrix based on sequence distance
  * 
  * @author jprocter
  *
  */
-public class SeqDistanceContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix
+        extends MappableContactMatrix<SeqDistanceContactMatrix>
+        implements ContactMatrixI
 {
   private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
   private int width = 0;
@@ -76,20 +85,6 @@ 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;
-  }
-
-  @Override
   public String getAnnotDescr()
   {
     return "Sequence distance matrix";
@@ -118,4 +113,16 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     return width;
   }
+  @Override
+  protected double getElementAt(int _column, int i)
+  {
+    return Math.abs(_column - i);
+  }
+  @Override
+  protected SeqDistanceContactMatrix newMappableContactMatrix(
+          SequenceI newRefSeq, MapList newFromMapList)
+  {
+
+    return new SeqDistanceContactMatrix(width);
+  }
 }