X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=54eed1a73c9dcf6b049a5e872c85f97ad072061a;hb=7c19c72efd3433b14f845c265747010d9dc596cc;hp=6bfea9e9493f0d86b2a0047b1fb1d3e33bb7ae77;hpb=0fd0aa9f6a7e7e4fff5d9bce03ff5734fb803e09;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 6bfea9e..54eed1a 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))
         {
@@ -1000,17 +997,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
-                  .getColourName(av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(sg,
+                  ColourSchemeProperty.getColourName(av
+                          .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs != null)
-        {
-          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.isIgnoreGapsConsensus());
-        }
+        // if (cs != null)
+        // {
+        // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+        // av.isIgnoreGapsConsensus());
+        // }
       }
-      sg.cs = cs;
+      sg.setColourScheme(cs);
+      sg.getGroupColourScheme().setThreshold(
+              av.getResidueShading().getThreshold(),
+              av.isIgnoreGapsConsensus());
       // sg.recalcConservation();
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -1018,12 +1019,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
-                && aps[a].av.getGlobalColourScheme().conservationApplied())
+                && aps[a].av.getResidueShading()
+                        .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);