X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=18ab642be987901d19a54679c0f5ba8e98ec774f;hb=7703a6a091c65e45bfb8f4d056cd2cbdb19b3535;hp=b11dfd55554b0556ad71408c4364d89d1da173ab;hpb=3b1a35f953ef3bcfd8c0dd8a00919212b69ba25d;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b11dfd5..18ab642 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.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
@@ -356,11 +357,14 @@ public class FileLoader implements Runnable
                       .isShowSeqFeatures();
               ColourSchemeI cs = ((ComplexAlignFile) source)
                       .getColourScheme();
+              FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                      .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
               alignFrame.changeColour(cs);
             }
             else