X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=bcb4e7b50fcb9b017fa5a17f4cc75d94f08d917d;hb=e60cacff9260c47c12cf34a7e191678cfc97d265;hp=d0cabb263a341add9ae62d248f21c0011c8b54b7;hpb=a8362b85de4f21440433bc9385bd9b3a24354532;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index d0cabb2..bcb4e7b 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -51,6 +51,7 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.security.AllPermission;
 import java.security.CodeSource;
@@ -651,23 +652,28 @@ public class Jalview
             File imageFile = new File(file);
             imageName = imageFile.getName();
             HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-            htmlSVG.generateHtmlSvgOutput(new File(file));
+            htmlSVG.exportHTML(file);
 
             System.out.println("Creating HTML image: " + file);
             continue;
           }
           else if (format.equalsIgnoreCase("biojsmsa"))
           {
-            BioJsHTMLOutput.updateBioJS();
+            if (file == null)
+            {
+              System.err.println("The output html file must not be null");
+              return;
+            }
             try
             {
-              Thread.sleep(1500);
-            } catch (InterruptedException e)
+              BioJsHTMLOutput
+                      .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
             {
               e.printStackTrace();
             }
-            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
-            bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(file);
             System.out.println("Creating BioJS MSA Viwer HTML file: "
                     + file);
             continue;