JAL-2964 missed branch for restore link tree to all views

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 1797fb7..02b405e 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -3859,7 +3859,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     jGroup.getColour());
           }
         }
@@ -4187,10 +4187,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-          // FIXME: should we use safeBoolean here ?
-          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
         }
+        tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
           warn("There was a problem recovering stored Newick tree: \n"
@@ -4973,7 +4971,8 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+                view.getBgColour());
       }
     }
 
@@ -5271,7 +5270,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.getViewport(), al,
                       viewAnnColour.getColourScheme()),
               safeInt(viewAnnColour.getAboveThreshold()));
     }