From 6a60c733dc23235562e32583e68284efa5d29ac9 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:19:24 +0000
Subject: [PATCH] Allow loading from Zip files

---
 src/jalview/bin/JalviewLite.java |   38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 858c391..199a843 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -94,9 +94,7 @@ public class JalviewLite extends Applet
            && getParameter("embedded").equalsIgnoreCase("true"))
         {
           embedded = true;
-          LoadingThread loader = new LoadingThread(file,
-                            AppletFormatAdapter.URL,
-                            applet);
+          LoadingThread loader = new LoadingThread(file, applet);
           loader.start();
         }
         else if (file != null)
@@ -108,7 +106,6 @@ public class JalviewLite extends Applet
                     public void actionPerformed(ActionEvent e)
                     {
                         LoadingThread loader = new LoadingThread(file,
-                            AppletFormatAdapter.URL,
                             applet);
                         loader.start();
                       }
@@ -141,7 +138,7 @@ public class JalviewLite extends Applet
      }
       if ( (sequences != null) && (sequences.length > 0))
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
+        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
         af.statusBar.setText("Successfully loaded file " + args[0]);
       }
     }
@@ -262,15 +259,16 @@ public class JalviewLite extends Applet
         JalviewLite applet;
 
         public LoadingThread(String _file,
-                             String _protocol,
                              JalviewLite _applet)
         {
             file = _file;
             if(inArchive(file))
               protocol = AppletFormatAdapter.CLASSLOADER;
             else
-              protocol = _protocol;
-
+            {
+              file = addProtocol(file);
+              protocol = AppletFormatAdapter.URL;
+            }
             format = new jalview.io.IdentifyFile().Identify(file, protocol);
             applet = _applet;
         }
@@ -288,13 +286,12 @@ public class JalviewLite extends Applet
             if ((sequences != null) && (sequences.length > 0))
             {
               currentAlignFrame = new AlignFrame(new Alignment(sequences),
-                                                 applet, file);
+                                                 applet,
+                                                 file,
+                                                 embedded);
 
               initialAlignFrame = currentAlignFrame;
 
-              if (embedded)
-                currentAlignFrame.setEmbedded();
-
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
 
@@ -317,12 +314,7 @@ public class JalviewLite extends Applet
 
                     if (fin.getTree() != null)
                     {
-                      TreePanel tp = null;
-                      tp = new TreePanel(currentAlignFrame.viewport,
-                                         currentAlignFrame.viewport.getAlignment().getSequences(),
-                                         fin, "FromFile", treeFile);
-                      addFrame(tp, treeFile, 600, 500);
-                      currentAlignFrame.addTreeMenuItem(tp, treeFile);
+                      currentAlignFrame.loadTree(fin, treeFile);
                     }
                   }
                   catch (Exception ex)
@@ -391,7 +383,15 @@ public class JalviewLite extends Applet
          */
         boolean inArchive(String file)
         {
-          return ( getClass().getResourceAsStream("/" + file) != null );
+          //This might throw a security exception in certain browsers
+          //Netscape Communicator for instance.
+          try{
+            return (getClass().getResourceAsStream("/" + file) != null);
+          }catch(Exception ex)
+          {
+            System.out.println("Exception checking resources: "+file+" "+ex);
+            return false;
+          }
         }
 
         String addProtocol(String file)
-- 
1.7.10.2