From afcdc36e5f65333f8ff9ca3229b6cffdb27edca7 Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 5 Dec 2014 14:58:00 +0000
Subject: [PATCH] JAL-1605 added command line support for html export option

---
 src/jalview/bin/Jalview.java      |   11 +++++++++++
 src/jalview/gui/AlignFrame.java   |    2 +-
 src/jalview/io/HtmlSvgOutput.java |   15 +++++++++++----
 3 files changed, 23 insertions(+), 5 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f80f341..e5a22e0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.io.HtmlSvgOutput;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -489,6 +490,14 @@ public class Jalview
             System.out.println("Creating SVG image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("html"))
+          {
+            File imageFile = new java.io.File(file);
+            imageName = imageFile.getName();
+            new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+            System.out.println("Creating HTML image: " + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new java.io.File(file), imageName);
@@ -621,6 +630,8 @@ public class Jalview
                     + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
                     + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                     + "-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"
                     + "-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 3180993..42460dc 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1230,7 +1230,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // new HTMLOutput(alignPanel,
     // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
     // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
-    new HtmlSvgOutput(alignPanel);
+    new HtmlSvgOutput(null, alignPanel);
   }
 
   public void createImageMap(File file, String image)
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 4643858..4793ac4 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -29,20 +29,26 @@ public class HtmlSvgOutput
 
   AnnotationPanel annotationPanel;
 
-  public HtmlSvgOutput(AlignmentPanel ap)
+  public HtmlSvgOutput(File file, AlignmentPanel ap)
   {
 
       this.av = ap.av;
       this.ap = ap;
       this.annotationPanel = ap.getAnnotationPanel();
-    generateHtmlSvgOutput();
+    generateHtmlSvgOutput(file);
   }
 
-  public void generateHtmlSvgOutput()
+  public void generateHtmlSvgOutput(File file)
   {
-    File file = null;
     try
     {
+      if (file == null /*
+                        * && !(System.getProperty("java.awt.headless") != null
+                        * && System
+                        * .getProperty("java.awt.headless").equals("true"))
+                        */)
+      {
+
       JalviewFileChooser chooser = getHTMLChooser();
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle(ap.alignFrame.getTitle());
@@ -55,6 +61,7 @@ public class HtmlSvgOutput
                 .getSelectedFile().getParent());
         file = chooser.getSelectedFile();
       }
+      }
 
       AlignmentDimension aDimension = ap.getAlignmentDimension();
       SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
-- 
1.7.10.2