JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE...

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

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 4e2076d..9eabb10 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -1,6 +1,8 @@
 package jalview.datamodel;
 
+import java.util.Arrays;
 import java.util.BitSet;
+import java.util.List;
 
 public interface ContactMatrixI
 {
@@ -37,4 +39,31 @@ public interface ContactMatrixI
     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;
+  }
 }