JAL-2277 Refactored out duplicated method - printUnwrapped() in HtmlSvgOutput, extern...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ce29f01..d0cabb2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -291,9 +291,10 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model unless preferences say not to
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
      */
-    if (!Cache.getDefault("USE_SO_LITE", false))
+    if (Cache.getDefault("USE_FULL_SO", false))
     {
       SequenceOntologyFactory.setInstance(new SequenceOntology());
     }
@@ -649,10 +650,28 @@ 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.generateHtmlSvgOutput(new File(file));
+
             System.out.println("Creating HTML image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("biojsmsa"))
+          {
+            BioJsHTMLOutput.updateBioJS();
+            try
+            {
+              Thread.sleep(1500);
+            } catch (InterruptedException e)
+            {
+              e.printStackTrace();
+            }
+            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel, af);
+            bjs.exportJalviewAlignmentAsBioJsHtmlFile(file);
+            System.out.println("Creating BioJS MSA Viwer HTML file: "
+                    + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new File(file), imageName);
@@ -788,6 +807,7 @@ 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"