X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=3510ed135f9809b4dd8c5f2d060fffb2c6926f3a;hb=173c541c3bdef7cee4f72a76cc8e23e8902a8614;hp=2367414c32e9c8a0853bb20e29e4d4db422fa5b2;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 2367414..3510ed1 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
 {
 
@@ -18,12 +23,57 @@ public interface ContactMatrixI
   String getAnnotLabel();
 
   /**
-   * string indicating how the contactMatrix should be rendered - stored in calcId
-   * @return 
+   * string indicating how the contactMatrix should be rendered - stored in
+   * calcId
+   * 
+   * @return
    */
   String getType();
 
   int getWidth();
+
   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;};
 }