X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=3510ed135f9809b4dd8c5f2d060fffb2c6926f3a;hb=173c541c3bdef7cee4f72a76cc8e23e8902a8614;hp=6860e820529a57ddf93ebffcda80dc25750556ca;hpb=059c891e783721341341b71ef222559c9f68fe31;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 6860e82..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
 {
 
@@ -17,4 +22,58 @@ public interface ContactMatrixI
 
   String getAnnotLabel();
 
+  /**
+   * 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;};
 }