X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=f8fd750955d0861ca20606d3b4b6a7ea85ff7812;hb=a0bd24f90375fc1d4be619bf65746a912dfcfc89;hp=f6377b1605828c9b667094d1f96fb4c7374c1d38;hpb=9e40070f757fc662aba39ba6314be4937276ead4;p=jalview.git

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index f6377b1..f8fd750 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -7,14 +7,15 @@ 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 extends MappableContactMatrix<SeqDistanceContactMatrix> implements ContactMatrixI
+public class SeqDistanceContactMatrix
+        extends MappableContactMatrix<SeqDistanceContactMatrix>
+        implements ContactMatrixI
 {
   private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
   private int width = 0;
@@ -82,6 +83,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
       }
     });
   }
+
   @Override
   public String getAnnotDescr()
   {
@@ -111,53 +113,16 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
   {
     return width;
   }
-  private List<BitSet> groups=null;
-  @Override
-  public void updateGroups(List<BitSet> colGroups)
-  {
-    groups = colGroups;
-  }
-  @Override
-  public boolean hasGroups()
-  {
-    return groups!=null;
-  }
-  @Override
-  public List<BitSet> getGroups()
-  {
-    return groups;
-  }  
-
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
-  {
-    if (bs==null) {
-      return Color.white;
-    }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
-    {
-      return Color.white;
-    }
-    return groupCol;
-  }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
-  {
-    colorMap.put(bs,color);
-  }
   @Override
   protected double getElementAt(int _column, int i)
   {
-    return Math.abs(_column-i);
+    return Math.abs(_column - i);
   }
-
   @Override
   protected SeqDistanceContactMatrix newMappableContactMatrix(
           SequenceI newRefSeq, MapList newFromMapList)
   {
-    
+
     return new SeqDistanceContactMatrix(width);
   }
 }