X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;fp=src%2Fjalview%2Fio%2FBioJsHTMLOutput.java;h=50486f229d9d2bd77bb37ba9a70ae35a416c5ba4;hb=1fcd6eb366ba3d4c1a0f41c881ad6f6357be240f;hp=6c8d2df4e20c1d0ae0fe30c8780b6b9595d875ba;hpb=c2998dd409165095887a3aec405837ecbb3b4ffe;p=jalview.git

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 6c8d2df..50486f2 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,5 +1,6 @@
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
@@ -53,9 +54,49 @@ public class BioJsHTMLOutput
     {
       String outputFile = getOutputFile();
       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignExportSettingI exportSettings = new AlignExportSettingI()
+      {
+        @Override
+        public boolean isExportHiddenSequences()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportHiddenColumns()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportAnnotations()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportFeatures()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isExportGroups()
+        {
+          return true;
+        }
+
+        @Override
+        public boolean isCancelled()
+        {
+          return false;
+        }
+
+      };
       AlignmentExportData exportData = jalview.gui.AlignFrame
               .getAlignmentForExport(
-              JSONFile.FILE_DESC, ap.getAlignViewport());
+JSONFile.FILE_DESC,
+                      ap.getAlignViewport(), exportSettings);
       if (exportData.getSettings().isCancelled())
       {
         return;