JAL-1831 updated json schema doc

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

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 16b2647..6612db3 100644 (file)
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -98,7 +98,8 @@ public class HtmlSvgOutput
               .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
       if (isEmbbedBioJSON)
       {
-      AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+        AlignmentExportData exportData = jalview.gui.AlignFrame
+                .getAlignmentForExport(
               JSONFile.FILE_DESC, av);
       if (exportData.getSettings().isCancelled())
       {
@@ -107,8 +108,8 @@ public class HtmlSvgOutput
         jsonData = new FormatAdapter(ap, exportData.getSettings())
               .formatSequences(JSONFile.FILE_DESC, exportData
                       .getAlignment(), exportData.getOmitHidden(),
-                      exportData.getStartEndPostions(), ap
-                              .getAlignViewport().getColumnSelection());
+                        exportData.getStartEndPostions(),
+                        av.getColumnSelection());
       }
       String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
       FileOutputStream out = new FileOutputStream(file);