X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=9931f32ee8f57e222aab21f64c66ab941523ae73;hb=4513bd826c54623c14aa8946a51a2382f64e98f3;hp=9ff3ef9cecb2f164c512069007583cbfc4e5b007;hpb=39439812058a1c48ccec89eb80fb139888519d46;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ff3ef9..9931f32 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -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,
@@ -385,6 +386,8 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
               alignFrame.getViewport().setFeaturesDisplayed(fd);
+              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                      colourSchemeName, al);
               alignFrame.changeColour(cs);
             }
             else