From beaa65409fc4cf865392c4e6e57116b64af37dfc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 30 Aug 2005 15:24:57 +0000
Subject: [PATCH] Set user colours same as global

---
 src/jalview/appletgui/TreeCanvas.java |   20 ++++++++++++++++++--
 src/jalview/gui/TreeCanvas.java       |   28 ++++++++++++++++++++--------
 2 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 075d8cb..9483436 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -480,9 +480,25 @@ public class TreeCanvas
               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,
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index e9e9358..2f5ddf4 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -704,19 +704,31 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                         }
                     }
 
-                    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());
 
-                    if (sg.cs != null)
-                    {
-                        sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());
-                    }
 
                     if (  av.getGlobalColourScheme()!=null
                        && av.getGlobalColourScheme().conservationApplied())
-- 
1.7.10.2