X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FFileLoader.java;h=ce018430f358340799a956f460637c206e65740c;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=9ff3ef9cecb2f164c512069007583cbfc4e5b007;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ff3ef9..ce01843 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -31,6 +31,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -375,8 +376,8 @@ public class FileLoader implements Runnable
                       .getHiddenSequences();
               boolean showSeqFeatures = ((ComplexAlignFile) source)
                       .isShowSeqFeatures();
-              ColourSchemeI cs = ((ComplexAlignFile) source)
-                      .getColourScheme();
+              String colourSchemeName = ((ComplexAlignFile) source)
+                      .getGlobalColourScheme();
               FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                       .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
@@ -385,7 +386,12 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
               alignFrame.getViewport().setFeaturesDisplayed(fd);
-              alignFrame.changeColour(cs);
+              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                      colourSchemeName, al);
+              if (cs != null)
+              {
+                alignFrame.changeColour(cs);
+              }
             }
             else
             {