Merge branch 'features/JAL-1605_html-svg-export' into develop

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f80f341..50e3559 100755 (executable)
--- 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;
@@ -79,11 +80,6 @@ public class Jalview
   }
 
   /**
-   * Put protein=true for get a protein example
-   */
-  private static boolean protein = false;
-
-  /**
    * main class for Jalview application
    * 
    * @param args
@@ -402,6 +398,10 @@ public class Jalview
         {
           af.getViewport().setSortByTree(true);
         }
+        if (aparser.contains("no-annotation"))
+        {
+          af.getViewport().setShowAnnotation(false);
+        }
         if (aparser.contains("nosortbytree"))
         {
           af.getViewport().setSortByTree(false);
@@ -489,6 +489,14 @@ 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);
@@ -527,8 +535,7 @@ public class Jalview
     // ////////////////////
 
     if (!headless && file == null && vamsasImport == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
-            && protein == true)
+            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault(
               "STARTUP_FILE",
@@ -621,6 +628,8 @@ 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"
@@ -658,7 +667,7 @@ public class Jalview
               public void run()
               {
                 Cache.log
-                        .info("Initialising googletracker for usage stats.");
+                        .debug("Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
                 Cache.log.debug("Tracking enabled.");
               }
@@ -666,7 +675,7 @@ public class Jalview
             {
               public void run()
               {
-                Cache.log.info("Not enabling Google Tracking.");
+                Cache.log.debug("Not enabling Google Tracking.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);