JAL-2277 bug fix for mis-alligned graphics output for scrolled annotations

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 763b10b..bcb4e7b 100755 (executable)
--- 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;
@@ -650,10 +651,33 @@ public class Jalview
           {
             File imageFile = new File(file);
             imageName = imageFile.getName();
-            new HtmlSvgOutput(new File(file), af.alignPanel);
+            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+            htmlSVG.exportHTML(file);
+
             System.out.println("Creating HTML image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("biojsmsa"))
+          {
+            if (file == null)
+            {
+              System.err.println("The output html file must not be null");
+              return;
+            }
+            try
+            {
+              BioJsHTMLOutput
+                      .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+            } catch (URISyntaxException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+            bjs.exportHTML(file);
+            System.out.println("Creating BioJS MSA Viwer HTML file: "
+                    + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new File(file), imageName);
@@ -789,6 +813,7 @@ public class Jalview
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
                     + "-html FILE\tCreate HTML file from alignment.\n"
+                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
                     + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                     + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"