Set user colours same as global

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 075d8cb..9483436 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -480,9 +480,25 @@ public class TreeCanvas
               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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e9e9358..2f5ddf4 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -704,19 +704,31 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                         }\r
                     }\r
 \r
-                    ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,\r
-                            av.alignment.getWidth(),\r
-                            ColourSchemeProperty.getColourName(\r
-                                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
 \r
                     SequenceGroup sg = new SequenceGroup(sequences,\r
                             "TreeGroup", cs, true, true, false, 0,\r
                             av.alignment.getWidth());\r
 \r
-                    if (sg.cs != null)\r
-                    {\r
-                        sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());\r
-                    }\r
 \r
                     if (  av.getGlobalColourScheme()!=null\r
                        && av.getGlobalColourScheme().conservationApplied())\r