JAL-1641 fixed broken functionalities after refactor

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

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 7e02118..781eace 100644 (file)
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.api.FeatureRenderer;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
@@ -93,13 +94,26 @@ public class HtmlSvgOutput
       }
       printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
               g2);
-      FileOutputStream out = new FileOutputStream(file);
 
       String titleSvgData = g1.getSVGDocument();
       String alignSvgData = g2.getSVGDocument();
-      String jsonData = JSONFile.getJSONData(ap);
+
+      AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+              JSONFile.FILE_DESC, av);
+      if (exportData.getSettings().isCancelled())
+      {
+        return;
+      }
+      String jsonData = new FormatAdapter(ap, exportData.getSettings())
+              .formatSequences(JSONFile.FILE_DESC, exportData
+                      .getAlignment(), exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(), ap
+                              .getAlignViewport().getColumnSelection());
+
+      // String jsonData = JSONFile.getJSONData(ap);
       String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
 
+      FileOutputStream out = new FileOutputStream(file);
       out.write(htmlData.getBytes());
       out.flush();
       out.close();