X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=84fd82f068e47112429990a5a28aa5f7cdfc4c2c;hb=d3913db54e57a595f182851af2f4043a88b0eb2a;hp=6bfea9e9493f0d86b2a0047b1fb1d3e33bb7ae77;hpb=0fd0aa9f6a7e7e4fff5d9bce03ff5734fb803e09;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 6bfea9e..84fd82f 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.util.Format;
@@ -812,8 +811,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       for (int i = 0; i < leaves.size(); i++)
       {
-        SequenceI seq = (SequenceI) leaves.elementAt(i)
-                .element();
+        SequenceI seq = (SequenceI) leaves.elementAt(i).element();
         treeSelectionChanged(seq);
       }
       av.sendSelection();
@@ -969,15 +967,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
               (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor(tree.getGroups().elementAt(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves(tree
-              .getGroups().elementAt(i));
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
       Vector<SequenceI> sequences = new Vector<SequenceI>();
 
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) l.elementAt(j)
-                .element();
+        SequenceI s1 = (SequenceI) l.elementAt(j).element();
 
         if (!sequences.contains(s1))
         {
@@ -1020,10 +1017,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (aps[a].av.getGlobalColourScheme() != null
                 && aps[a].av.getGlobalColourScheme().conservationApplied())
         {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
+          Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());
-
           c.calculate();
           c.verdict(false, aps[a].av.getConsPercGaps());
           sg.cs.setConservation(c);