X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=e184db7936bb9ed02579b74b30c8dbddea2d1b35;hb=e826e3b91cf0c0e00227f967c608e994861eca94;hp=bca50510d7308144a564c67b877179b1b2d1e934;hpb=da53a3eaf1e5c06ff6a2506b7b603086293a887e;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bca5051..e184db7 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,8 @@ package jalview.bin;
 
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.HtmlSvgOutput;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -44,11 +46,12 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
 
 /**
  * Main class for Jalview Application <br>
@@ -79,11 +82,6 @@ public class Jalview
   }
 
   /**
-   * Put protein=true for get a protein example
-   */
-  private static boolean protein = false;
-
-  /**
    * main class for Jalview application
    * 
    * @param args
@@ -96,12 +94,6 @@ public class Jalview
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
-    if (new Platform().isAMac())
-    {
-      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
-              "Jalview");
-      System.setProperty("apple.laf.useScreenMenuBar", "true");
-    }
 
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
@@ -177,6 +169,21 @@ public class Jalview
     } catch (Exception ex)
     {
     }
+    if (new Platform().isAMac())
+    {
+      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+              "Jalview");
+      System.setProperty("apple.laf.useScreenMenuBar", "true");
+      try
+      {
+        UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
+                .getLookAndFeel());
+      } catch (UnsupportedLookAndFeelException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+    }
 
     if (!headless)
     {
@@ -218,6 +225,9 @@ public class Jalview
       desktop.checkForNews();
     }
 
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(null, null);
+    bjs.updateBioJS();
+
     String file = null, protocol = null, format = null, data = null;
     jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
     Vector getFeatures = null; // vector of das source nicknames to fetch
@@ -402,6 +412,10 @@ 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 +503,14 @@ 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 +549,7 @@ 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 +642,8 @@ 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"
@@ -784,7 +807,7 @@ public class Jalview
        * = new Binding(); binding.setVariable("input", "world");
        * gse.run("hello.groovy", binding); </code>
        */
-      Class[] bspec;
+      Class<?>[] bspec;
       Object[] binding;
       int blen = ((jalviewContext[0] == null) ? 0 : 1)
               + ((jalviewContext[1] == null) ? 0 : 1);
@@ -794,7 +817,7 @@ public class Jalview
       binding = new Object[blen * 2];
       blen = 0;
       ClassLoader cl = null;
-      Map vbinding = new Hashtable();
+      Map<String, Object> vbinding = new HashMap<String, Object>();
       for (int jc = 0; jc < jalviewContext.length; jc++)
       {
         if (jalviewContext[jc] != null)
@@ -811,8 +834,8 @@ public class Jalview
           blen++;
         }
       }
-      Class gbindingc = cl.loadClass("groovy.lang.Binding");
-      Constructor gbcons;
+      Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
+      Constructor<?> gbcons;
       Object gbinding;
       try
       {
@@ -822,15 +845,15 @@ public class Jalview
       {
         // old style binding config - using series of string/object values to
         // setVariable.
-        gbcons = gbindingc.getConstructor(null);
-        gbinding = gbcons.newInstance(null);
+        gbcons = gbindingc.getConstructor();
+        gbinding = gbcons.newInstance();
         java.lang.reflect.Method setvar = gbindingc.getMethod(
                 "setVariable", bspec);
         setvar.invoke(gbinding, binding);
       }
-      ;
-      Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
-      Constructor gseccons = gsec.getConstructor(new Class[]
+
+      Class<?> gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+      Constructor<?> gseccons = gsec.getConstructor(new Class[]
       { URL[].class }); // String[].class });
       Object gse = gseccons.newInstance(new Object[]
       { new URL[]
@@ -930,7 +953,7 @@ public class Jalview
   private static FeatureFetcher startFeatureFetching(final Vector dasSources)
   {
     FeatureFetcher ff = new FeatureFetcher();
-    AlignFrame afs[] = Desktop.getAlignframes();
+    AlignFrame afs[] = Desktop.getAlignFrames();
     if (afs == null || afs.length == 0)
     {
       return null;