JAL-2284 basic support for exporting BioJS MSA viewer via CLI

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 763b10b..164ba27 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -654,6 +654,22 @@ public class Jalview
             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);
@@ -789,6 +805,7 @@ 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"