From fdeeb42848df5648feab5acc978a44e667785a1e Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 26 Oct 2016 11:31:53 +0100
Subject: [PATCH] JAL-2284 basic support for exporting BioJS MSA viewer via
 CLI

---
 src/jalview/bin/Jalview.java        |   17 +++++++++++++++++
 src/jalview/gui/AlignFrame.java     |    2 +-
 src/jalview/io/BioJsHTMLOutput.java |   12 +++++++++---
 3 files changed, 27 insertions(+), 4 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 763b10b..164ba27 100755
--- 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"
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63620e5..80ee82d 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1347,7 +1347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
-    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+    bjs.exportJalviewAlignmentAsBioJsHtmlFile(null);
   }
 
   public void createImageMap(File file, String image)
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index f8fa1f5..817f75c 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -80,12 +80,15 @@ public class BioJsHTMLOutput
     }
   }
 
-  public void exportJalviewAlignmentAsBioJsHtmlFile()
+  public void exportJalviewAlignmentAsBioJsHtmlFile(String outputFile)
   {
-    String outputFile = null;
+    // String outputFile = null;
     try
     {
-      outputFile = getOutputFile();
+      if (outputFile == null)
+      {
+        outputFile = getOutputFile();
+      }
       AlignExportSettingI exportSettings = new AlignExportSettingI()
       {
         @Override
@@ -159,8 +162,11 @@ public class BioJsHTMLOutput
       new OOMWarning("Creating Image for " + outputFile, err);
     } catch (Exception e)
     {
+      if (pIndicator != null && !headless)
+      {
       pIndicator.setProgressBar(MessageManager.formatMessage(
               "info.error_creating_file", "HTML"), pSessionId);
+      }
       e.printStackTrace();
     }
   }
-- 
1.7.10.2