X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=e37a5b203218335dca9eae62586837c70a725abb;hb=84ff3a3c7824890b0a201e6a4ec8fa1c9b6e9e64;hp=8f9bdf6639d4da2f44264dad72f1427db9f8091f;hpb=c3d17bf8cd43fe710f94a1111e845a0c435bb0c9;p=jalview.git

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 8f9bdf6..e37a5b2 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,5 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
 /**
  * Dummy contact matrix based on sequence distance
  * 
@@ -8,6 +13,8 @@ package jalview.datamodel;
  */
 public class SeqDistanceContactMatrix implements ContactMatrixI
 {
+  private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
   private int width = 0;
 
   public SeqDistanceContactMatrix(int width)
@@ -26,6 +33,7 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     return width;
   }
+
   @Override
   public ContactListI getContactList(final int column)
   {
@@ -60,6 +68,12 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
       }
 
       @Override
+      public int getPosition()
+      {
+        return p;
+      }
+
+      @Override
       public double getContactAt(int column)
       {
         return Math.abs(column - p);
@@ -67,4 +81,83 @@ 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()
+  {
+    return "Sequence distance matrix";
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "Sequence Distance";
+  }
+
+  @Override
+  public String getType()
+  {
+    return SEQUENCE_DISTANCE;
+  }
+
+  @Override
+  public int getWidth()
+  {
+    return width;
+  }
+
+  @Override
+  public int getHeight()
+  {
+    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);
+  }
 }