JAL-4134 allow tree groups to be stored/recovered on contact matrix for groupwise...

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

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index c16b457..4e2076d 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -1,5 +1,7 @@
 package jalview.datamodel;
 
+import java.util.BitSet;
+
 public interface ContactMatrixI
 {
 
@@ -13,4 +15,26 @@ public interface ContactMatrixI
 
   SequenceI getReferenceSeq();
 
+  String getAnnotDescr();
+
+  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;
+  }
+
 }