X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=1d7391b617a009807695ac995693130c1c20e6dd;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=bac3abf05acb9eb36fa42b7349b1312aa85ab93c;hpb=a0ac724dba7d556966b546d4a0093449c397be84;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index bac3abf..1d7391b 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -1,5 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
 public interface ContactMatrixI
 {
 
@@ -29,4 +34,59 @@ public interface ContactMatrixI
 
   int getHeight();
 
+  default boolean hasGroups()
+  {
+    return false;
+  }
+
+  default BitSet getGroupsFor(int column)
+  {
+    BitSet colbitset = new BitSet();
+    colbitset.set(column);
+    return colbitset;
+  }
+
+  default List<BitSet> getGroups()
+  {
+    return Arrays.asList();
+  }
+
+  default boolean hasTree()
+  {
+    return false;
+  }
+
+  /**
+   * Newick representation of clustered matrix
+   * 
+   * @return null unless hasTree is true
+   */
+  default String getNewick()
+  {
+    return null;
+  }
+
+  default String getTreeMethod()
+  {
+    return null;
+  }
+
+  default boolean hasCutHeight()
+  {
+    return false;
+  }
+
+  default double getCutHeight()
+  {
+    return 0;
+  }
+
+  void updateGroups(List<BitSet> colGroups);
+
+  void setColorForGroup(BitSet bs, Color color);
+
+  default Color getColourForGroup(BitSet bs)
+  {
+    return Color.white;
+  };
 }