Merge branch 'develop' into features/JAL-1759jmolUpdate

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

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 74fb147..089f50b 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
 import jalview.json.binding.v1.BioJSReleasePojo;
 import jalview.json.binding.v1.BioJSRepositoryPojo;
@@ -51,7 +52,20 @@ public class BioJsHTMLOutput
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignmentExportData exportData = jalview.gui.AlignFrame
+              .getAlignmentForExport(
+              JSONFile.FILE_DESC, ap.getAlignViewport());
+      if (exportData.getSettings().isCancelled())
+      {
+        return;
+      }
+      String jalviewAlignmentJson = new FormatAdapter(ap,
+              exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
+              exportData.getAlignment(), exportData.getOmitHidden(),
+              exportData.getStartEndPostions(), ap.getAlignViewport()
+                      .getColumnSelection());
+
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll(