X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=3a0f1696a914612706288559278973816e775da7;hb=02d6b4895305788dbf460a6e0334dba93b0b3423;hp=6612db3d99ec77389534cec1df24355471531f56;hpb=3e0acd768b9b0a35aff4d5a4e862473c70e50100;p=jalview.git

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 6612db3..3a0f169 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,5 +1,6 @@
 package jalview.io;
 
+import jalview.api.AlignExportSettingI;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.SequenceI;
@@ -98,13 +99,47 @@ public class HtmlSvgOutput
               .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
       if (isEmbbedBioJSON)
       {
+        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, av);
-      if (exportData.getSettings().isCancelled())
-      {
-        return;
-      }
+                .getAlignmentForExport(JSONFile.FILE_DESC, av,
+                        exportSettings);
         jsonData = new FormatAdapter(ap, exportData.getSettings())
               .formatSequences(JSONFile.FILE_DESC, exportData
                       .getAlignment(), exportData.getOmitHidden(),