X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b449d19aba7692a4481264805f97c784584dd8f1;hb=f3392c352962c6827674ada5948500725e4eed1e;hp=b1944b45e6c22b6b9fb23e2de2991c406ead46ac;hpb=d9c02118b8e03e6f102a46d316b6e52a41c41a27;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b1944b4..b449d19 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
@@ -362,8 +363,14 @@ public class FileLoader implements Runnable
             }
           }
 
+          FeatureSettingsModelI proxyColourScheme = source
+                  .getFeatureColourScheme();
           if (viewport != null)
           {
+            if (proxyColourScheme != null)
+            {
+              viewport.applyFeaturesStyle(proxyColourScheme);
+            }
             // append to existing alignment
             viewport.addAlignment(al, title);
           }
@@ -407,7 +414,11 @@ public class FileLoader implements Runnable
             {
               alignFrame.setFileName(file, format);
             }
-
+            if (proxyColourScheme != null)
+            {
+              alignFrame.getViewport()
+                      .applyFeaturesStyle(proxyColourScheme);
+            }
             alignFrame.statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_loaded_file",
                     new String[] { title }));