JAL-4134 column grouping model and methods moved to their own object held by by Conta...

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

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index f2e207c..8f0afdf 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,7 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
 import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Spliterator;
 import java.util.StringTokenizer;
@@ -147,29 +150,26 @@ public abstract class ContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public String getAnnotLabel()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return "Contact Matrix";
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public String getAnnotDescr()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return "Contact Matrix";
   }
-
+  GroupSet grps = new GroupSet();
   @Override
-  public String getAnnotLabel()
+  public GroupSetI getGroupSet()
   {
-    return "Contact Matrix";
+    return grps;
   }
-
   @Override
-  public String getAnnotDescr()
+  public void setGroupSet(GroupSet makeGroups)
   {
-    return "Contact Matrix";
+    grps = makeGroups;
   }
 
   public static String contactToFloatString(ContactMatrixI cm)