Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace

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

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 7dd9778..b04ac13 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,13 +1,23 @@
 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;
 
   public SeqDistanceContactMatrix(int width)
@@ -75,28 +85,44 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public String getAnnotDescr()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return "Sequence distance matrix";
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public String getAnnotLabel()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return "Sequence Distance";
   }
 
   @Override
-  public String getAnnotDescr()
+  public String getType()
   {
-    return "Sequence distance matrix";
+    return SEQUENCE_DISTANCE;
   }
 
   @Override
-  public String getAnnotLabel()
+  public int getWidth()
   {
-    return "Sequence Distance";
+    return width;
+  }
+
+  @Override
+  public int getHeight()
+  {
+    return width;
+  }
+  @Override
+  public double getElementAt(int _column, int i)
+  {
+    return Math.abs(_column - i);
+  }
+  @Override
+  protected SeqDistanceContactMatrix newMappableContactMatrix(
+          SequenceI newRefSeq, MapList newFromMapList)
+  {
+
+    return new SeqDistanceContactMatrix(width);
   }
 }