X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FGroupSet.java;h=95d012797b6a45f9979ca6e275486d41af764f8f;hb=a3f65dbb5ba8bd470a31ba2af72db6d8ddf60546;hp=c7a73b76580e03017d7ae5a20ebecd6db17d290a;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git

diff --git a/src/jalview/datamodel/GroupSet.java b/src/jalview/datamodel/GroupSet.java
index c7a73b7..95d0127 100644
--- a/src/jalview/datamodel/GroupSet.java
+++ b/src/jalview/datamodel/GroupSet.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.awt.Color;
@@ -145,30 +165,60 @@ public class GroupSet implements GroupSetI
     return treeType;
   }
 
-  public static GroupSet makeGroups(ContactMatrixI matrix, float thresh,
-          boolean abs)
+  public static GroupSet makeGroups(ContactMatrixI matrix, boolean autoCut)
+  {
+    return makeGroups(matrix, autoCut, 0, autoCut);
+  }
+
+  public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto,
+          float thresh, boolean abs)
   {
     AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
-            matrix);
+            matrix, true);
     double height = clusterer.findHeight(clusterer.getTopNode());
+    Console.debug("Column tree height: " + height);
     String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
             true).print();
     String treeType = "UPGMA";
     Console.trace("Newick string\n" + newick);
 
     List<BinaryNode> nodegroups;
-    if (abs ? height > thresh : 0 < thresh && thresh < 1)
+    float cut = -1f;
+    if (auto)
     {
-      float cut = abs ? (float) (thresh / height) : thresh;
-      Console.debug("Threshold " + cut + " for height=" + height);
-
-      nodegroups = clusterer.groupNodes(cut);
+      double rootw = 0;
+      int p = 2;
+      BinaryNode bn = clusterer.getTopNode();
+      while (p-- > 0 & bn.left() != null)
+      {
+        if (bn.left() != null)
+        {
+          bn = bn.left();
+        }
+        if (bn.left() != null)
+        {
+          rootw = bn.height;
+        }
+      }
+      thresh = Math.max((float) (rootw / height) - 0.01f, 0);
+      cut = thresh;
+      nodegroups = clusterer.groupNodes(thresh);
     }
     else
     {
-      nodegroups = new ArrayList<BinaryNode>();
-      nodegroups.add(clusterer.getTopNode());
+      if (abs ? (height > thresh) : (0 < thresh && thresh < 1))
+      {
+        cut = abs ? thresh : (float) (thresh * height);
+        Console.debug("Threshold " + cut + " for height=" + height);
+        nodegroups = clusterer.groupNodes(cut);
+      }
+      else
+      {
+        nodegroups = new ArrayList<BinaryNode>();
+        nodegroups.add(clusterer.getTopNode());
+      }
     }
+
     List<BitSet> groups = new ArrayList<>();
     for (BinaryNode root : nodegroups)
     {
@@ -179,7 +229,8 @@ public class GroupSet implements GroupSetI
       }
       groups.add(gpset);
     }
-    GroupSet grps = new GroupSet(abs, thresh, groups, treeType, newick);
+    GroupSet grps = new GroupSet(abs, (cut == -1f) ? thresh : cut, groups,
+            treeType, newick);
     return grps;
   }