From 9344c308a62c48e2ddedd12247edab74e581c2e7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 15 Sep 2005 09:09:17 +0000
Subject: [PATCH] Applet has main method, excutable

---
 src/jalview/appletgui/AlignFrame.java |   53 ++++++++++++++++++---------------
 src/jalview/appletgui/IdPanel.java    |   13 ++++----
 src/jalview/bin/JalviewLite.java      |   37 +++++++++++++++++++----
 3 files changed, 69 insertions(+), 34 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 14a341d..289e761 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -48,40 +48,43 @@ public class AlignFrame
     add(alignPanel);
     alignPanel.validate();
 
-    String treeFile = applet.getParameter("treeFile");
-    if (treeFile != null)
+    if(applet!=null)
     {
-      try
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
+        try
+        {
+          treeFile = treeFile;
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-        if (fin.getTree() != null)
+          if (fin.getTree() != null)
+          {
+            TreePanel tp = null;
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                               fin, "FromFile", applet.getCodeBase() + treeFile);
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+            addTreeMenuItem(tp, treeFile);
+          }
+        }
+        catch (Exception ex)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase() + treeFile);
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-          addTreeMenuItem(tp, treeFile);
+          ex.printStackTrace();
         }
       }
-      catch (Exception ex)
+
+      String param = applet.getParameter("sortBy");
+      if (param != null)
       {
-        ex.printStackTrace();
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
       }
     }
 
-    String param = applet.getParameter("sortBy");
-    if(param!=null)
-    {
-      if (param.equalsIgnoreCase("Id"))
-        sortIDMenuItem_actionPerformed(null);
-      else if (param.equalsIgnoreCase("Pairwise Identity"))
-        sortPairwiseMenuItem_actionPerformed(null);
-    }
-
     this.addWindowListener(new WindowAdapter()
     {
       public void windowClosing(WindowEvent e)
@@ -127,6 +130,8 @@ public class AlignFrame
   {
     PaintRefresher.components.remove(viewport.alignment);
     dispose();
+    if(PaintRefresher.components.size()==0 && applet==null)
+      System.exit(0);
   }
 
   Stack historyList = new Stack();
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index f3db9be..b6e6a2b 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -50,14 +50,17 @@ public class IdPanel
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
-    for(int i=1; i<10; i++)
+    if(parent.alignFrame.applet!=null)
     {
-      label = parent.alignFrame.applet.getParameter("linkLabel_"+i);
-      url = parent.alignFrame.applet.getParameter("linkURL_"+i);
+      for (int i = 1; i < 10; i++)
+      {
+        label = parent.alignFrame.applet.getParameter("linkLabel_" + i);
+        url = parent.alignFrame.applet.getParameter("linkURL_" + i);
 
-      if(label!=null && url!=null)
-        links.addElement(label+"|"+url);
+        if (label != null && url != null)
+          links.addElement(label + "|" + url);
 
+      }
     }
     if (links.size() < 1)
     {
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index b99d642..c9ec391 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -98,6 +98,26 @@ public class JalviewLite extends Applet
         }
     }
 
+    public static void main(String [] args)
+    {
+      if(args.length!=1)
+      {
+        System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+        System.exit(1);
+      }
+
+      String format = jalview.io.IdentifyFile.Identify(args[0],"File");
+      SequenceI[] sequences = FormatAdapter.readFile(args[0], "File", format);
+
+      if ( (sequences != null) && (sequences.length > 0))
+      {
+        AlignFrame af = new AlignFrame(new Alignment(sequences), null);
+        addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,
+                 AlignFrame.NEW_WINDOW_HEIGHT);
+        af.statusBar.setText("Successfully loaded file " + args[0]);
+      }
+    }
+
     /**
      * Displays the given URL in a new browser window
      *
@@ -111,14 +131,21 @@ public class JalviewLite extends Applet
 
       public static void showURL(String url, String target)
       {
-        try
+        if(applet==null)
         {
-          applet.getAppletContext().showDocument(new java.net.URL(url),
-                                                 target);
+          System.out.println("Not running as applet - no browser available.");
         }
-        catch (Exception ex)
+        else
         {
-          ex.printStackTrace();
+          try
+          {
+            applet.getAppletContext().showDocument(new java.net.URL(url),
+                target);
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
         }
       }
 
-- 
1.7.10.2