X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FTreeModel.java;h=b6c9caad68488ec9401c6e33193cd5de92d1f573;hb=89f0bcb459ed6acff9f7da0842bf967b8f941dee;hp=a50634ecf6178632561e498458857b969fe19a46;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index a50634e..b6c9caa 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -80,8 +80,8 @@ public class TreeModel
   public TreeModel(SequenceI[] seqs, AlignmentView odata,
           NewickFile treefile)
   {
-    this(seqs, treefile.getTree(), treefile.HasDistances(),
-            treefile.HasBootstrap(), treefile.HasRootDistance());
+    this(seqs, treefile.getTree(), treefile.hasDistances(),
+            treefile.hasBootstrap(), treefile.hasRootDistance());
     seqData = odata;
 
     associateLeavesToSequences(seqs);
@@ -97,6 +97,7 @@ public class TreeModel
     this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
             tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
+
   }
 
   /**
@@ -136,7 +137,7 @@ public class TreeModel
     SequenceNode j;
     SequenceI nam;
     String realnam;
-    Vector<SequenceI> one2many = new Vector<SequenceI>();
+    Vector<SequenceI> one2many = new Vector<>();
     // int countOne2Many = 0;
     while (i < leaves.size())
     {
@@ -295,7 +296,7 @@ public class TreeModel
    */
   public Vector<SequenceNode> findLeaves(SequenceNode nd)
   {
-    Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+    Vector<SequenceNode> leaves = new Vector<>();
     findLeaves(nd, leaves);
     return leaves;
   }
@@ -389,7 +390,7 @@ public class TreeModel
    */
   public List<SequenceNode> groupNodes(float threshold)
   {
-    List<SequenceNode> groups = new ArrayList<SequenceNode>();
+    List<SequenceNode> groups = new ArrayList<>();
     _groupNodes(groups, getTopNode(), threshold);
     return groups;
   }