X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=94834363056bfa073c0acff835e1bf330022c8aa;hb=064f2fdaa463367f8bf7e6aea5e7fc6a32170138;hp=15c4bfa9f62af1f7b952c2c92c6a03c15150d269;hpb=085727a32930d9a05becd66686ed001f50331bc6;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 15c4bfa..9483436 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -82,10 +82,9 @@ public class TreeCanvas
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth());
+    selected.setEndRes(av.alignment.getWidth()-1);
     selected.addOrRemove(sequence, true);
 
-System.out.println("called here");
     PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }
@@ -481,19 +480,34 @@ System.out.println("called here");
               sequences.addElement(s1);
           }
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
-              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
+          ColourSchemeI cs = null;
 
+          if (av.getGlobalColourScheme() != null)
+          {
+            if (av.getGlobalColourScheme() instanceof UserColourScheme)
+            {
+              cs = new UserColourScheme(
+                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+            }
+            else
+              cs = ColourSchemeProperty.getColour(sequences,
+                                                  av.alignment.getWidth(),
+                                                  ColourSchemeProperty.getColourName(
+                                                      av.getGlobalColourScheme()));
+
+              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                                                   av.getIgnoreGapsConsensus());
+          }
 
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
                                                cs, true, true,
-                                               false, 0, av.alignment.getWidth());
+                                               false, 0, av.alignment.getWidth()-1);
 
 
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-          {
-            ConservationColourScheme ccs = (ConservationColourScheme) av.
-                getGlobalColourScheme();
+          if (  av.getGlobalColourScheme()!=null
+             && av.getGlobalColourScheme().conservationApplied())
+            {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
                                               sg.sequences, sg.getStartRes(),
@@ -501,9 +515,9 @@ System.out.println("called here");
 
             c.calculate();
             c.verdict(false, av.ConsPercGaps);
-            ccs = new ConservationColourScheme(c, ccs.cs);
+            cs.setConservation(c);
 
-            sg.cs = ccs;
+            sg.cs = cs;
 
           }