JAL-2349 allow PAE or other contact matrices to hold a coordinate mapping allowing...

[jalview.git] / src / jalview / datamodel / SeqDistanceContactMatrix.java

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index c3f3670..f6377b1 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -5,13 +5,16 @@ 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;
@@ -79,21 +82,6 @@ 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()
   {
@@ -159,4 +147,17 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     colorMap.put(bs,color);
   }
+  @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);
+  }
 }