JAL-1551 spotlessApply

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

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index f6377b1..89daeb2 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -14,9 +14,12 @@ import jalview.ws.datamodel.alphafold.MappableContactMatrix;
  * @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;
 
   public SeqDistanceContactMatrix(int width)
@@ -82,6 +85,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
       }
     });
   }
+
   @Override
   public String getAnnotDescr()
   {
@@ -111,53 +115,18 @@ 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);
   }
 }