JAL-1780 JAL-653 moved AlignExportSettings reference on AlignViewportI to FileParse...

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

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index a026c57..74fb147 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,9 +1,7 @@
 package jalview.io;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.exceptions.NoFileSelectedException;
-import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
 import jalview.json.binding.v1.BioJSReleasePojo;
 import jalview.json.binding.v1.BioJSRepositoryPojo;
 import jalview.util.MessageManager;
@@ -23,7 +21,7 @@ import java.util.TreeMap;
 
 public class BioJsHTMLOutput
 {
-  private AlignViewport av;
+  private AlignmentViewPanel ap;
 
   private static File currentBJSTemplateFile;
 
@@ -40,12 +38,11 @@ public class BioJsHTMLOutput
                   "biojs_template_git_repo",
                   "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
 
-  public BioJsHTMLOutput(AlignmentPanel ap, FeatureRenderer fr1)
+  public BioJsHTMLOutput(AlignmentViewPanel ap)
   {
     if (ap != null)
     {
-      this.av = ap.av;
-      av.setFeatureRenderer(new FeatureRenderer(ap));
+      this.ap = ap;
     }
   }
 
@@ -54,7 +51,7 @@ public class BioJsHTMLOutput
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(av);
+      String jalviewAlignmentJson = JSONFile.getJSONData(ap);
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll(