Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b11dfd5..18ab642 100755 (executable)
--- 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