If vconsensus is null, return

[jalview.git] / src / jalview / appletgui / TreeCanvas.java

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