Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index f6377b1..987ea36 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.awt.Color;
@@ -14,9 +34,12 @@ 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 +105,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix<SeqDistanceC
       }
     });
   }
+
   @Override
   public String getAnnotDescr()
   {
@@ -111,53 +135,18 @@ 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)
+  public 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);
   }
 }