X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=1d20987117ba409ebb79782c9453ca51acf03f19;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=1c169ef31e19cf6fb6d4e050c74ddc8b28b1993f;hpb=e122bcdde6d11fd3711eda525924d0d737a4f62a;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 1c169ef..1d20987 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -14,63 +14,112 @@ public interface ContactMatrixI
 
   float getMax();
 
-  boolean hasReferenceSeq();
-
-  SequenceI getReferenceSeq();
-
   String getAnnotDescr();
 
   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;
+  public GroupSetI getGroupSet();
+
+  /// proxy methods to simplify use of the interface
+  /// Mappable contact matrices can override these to perform mapping
+
+  default public boolean hasGroupSet()
+  {
+    return getGroupSet() != null;
   }
-  default BitSet getGroupsFor(int column) {
-    BitSet colbitset  = new BitSet();
-    colbitset.set(column);
-    return colbitset;
+
+  default boolean hasGroups()
+  {
+    return hasGroupSet() && getGroupSet().hasGroups();
   }
 
-  default List<BitSet> getGroups() {
-    return Arrays.asList();
+  default BitSet getGroupsFor(int column)
+  {
+    if (!hasGroupSet())
+    {
+      BitSet colbitset = new BitSet();
+      colbitset.set(column);
+      return colbitset;
+    }
+    return getGroupSet().getGroupsFor(column);
   }
 
-  default boolean hasTree() {
-    return false;
+  default List<BitSet> getGroups()
+  {
+    if (!hasGroupSet())
+    {
+      return Arrays.asList();
+    }
+    return getGroupSet().getGroups();
+  }
+
+  default boolean hasTree()
+  {
+    return hasGroupSet() ? getGroupSet().hasTree() : false;
   }
 
   /**
    * Newick representation of clustered matrix
+   * 
    * @return null unless hasTree is true
    */
-  default String getNewick() {
-    return null;
+  default String getNewick()
+  {
+    return hasGroupSet() ? getGroupSet().getNewick() : null;
   }
 
-  default String getTreeMethod() {
-    return null;
+  default String getTreeMethod()
+  {
+    return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
   }
 
-  default boolean hasCutHeight() {
-    return false;
+  default boolean hasCutHeight()
+  {
+    return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
   }
 
-  default double getCutHeight() {
-    return 0;
+  default double getCutHeight()
+  {
+    return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
   }
 
-  void updateGroups(List<BitSet> colGroups);
+  default void updateGroups(List<BitSet> colGroups)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().updateGroups(colGroups);
+    }
+  }
 
-  void setColorForGroup(BitSet bs, Color color);
+  default void setColorForGroup(BitSet bs, Color color)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().setColorForGroup(bs, color);
+    }
+  }
+
+  default Color getColourForGroup(BitSet bs)
+  {
+    if (hasGroupSet())
+    {
+      return getGroupSet().getColourForGroup(bs);
+    }
+    else
+    {
+      return Color.white;
+    }
+  }
 
-  default Color getColourForGroup(BitSet bs) { return Color.white;};
+  void setGroupSet(GroupSet makeGroups);
 }