Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff5df66..142e7fc 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;
@@ -49,6 +50,7 @@ import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
 
 /**
  * Main class for Jalview Application <br>
@@ -91,12 +93,23 @@ 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");
-    }
+    // 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());
+    // System.out
+    // .println("--------------------------------------------> in here");
+    // } catch (UnsupportedLookAndFeelException e)
+    // {
+    // // TODO Auto-generated catch block
+    // e.printStackTrace();
+    // }
+    // }
 
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
@@ -172,6 +185,21 @@ 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)
     {
@@ -397,6 +425,10 @@ public class Jalview
         {
           af.getViewport().setSortByTree(true);
         }
+        if (aparser.contains("no-annotation"))
+        {
+          af.getViewport().setShowAnnotation(false);
+        }
         if (aparser.contains("nosortbytree"))
         {
           af.getViewport().setSortByTree(false);
@@ -484,6 +516,14 @@ 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);
@@ -615,6 +655,8 @@ 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"