X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=ea425d0b228e8e1273f35b1f1d308adf7b3be1fd;hb=f174f7c02a8357a4a35c6254739c98fafcca757a;hp=55d60a2760f2fc63a2b98f508170c5101e0a4c32;hpb=4e41b9392ea7ed42b864a324cdb154ca51a2a09b;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 55d60a2..ea425d0 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -88,6 +88,20 @@ public class JalviewLite extends Applet
 
         file = getParameter("file");
 
+        if(file==null)
+        {
+          //Maybe the sequences are added as parameters
+          StringBuffer data = new StringBuffer("PASTE");
+          int i=1;
+          while( (file=getParameter("sequence"+i))!=null)
+          {
+            data.append(file.toString()+"\n");
+            i++;
+          }
+          if(data.length()>5)
+            file = data.toString();
+        }
+
         final JalviewLite applet = this;
         if(getParameter("embedded")!=null
            && getParameter("embedded").equalsIgnoreCase("true"))
@@ -261,7 +275,12 @@ public class JalviewLite extends Applet
                              JalviewLite _applet)
         {
             file = _file;
-            if(inArchive(file))
+            if(file.startsWith("PASTE"))
+            {
+              file = file.substring(5);
+              protocol = AppletFormatAdapter.PASTE;
+            }
+            else if(inArchive(file))
               protocol = AppletFormatAdapter.CLASSLOADER;
             else
             {
@@ -289,13 +308,18 @@ public class JalviewLite extends Applet
                                                  file,
                                                  embedded);
 
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 
               initialAlignFrame = currentAlignFrame;
 
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
 
-                String treeFile = applet.getParameter("treeFile");
+                String treeFile = applet.getParameter("tree");
+                if(treeFile==null)
+                  treeFile = applet.getParameter("treeFile");
+
                 if (treeFile != null)
                 {
                   try
@@ -329,12 +353,13 @@ public class JalviewLite extends Applet
                 if( !inArchive(param) )
                   param = addProtocol( param );
 
-                currentAlignFrame.parseFeaturesFile(param);
+                currentAlignFrame.parseFeaturesFile(param, protocol);
               }
 
               param = getParameter("showFeatureSettings");
               if(param !=null && param.equalsIgnoreCase("true"))
               {
+                currentAlignFrame.viewport.showSequenceFeatures(true);
                 currentAlignFrame.featureSettings_actionPerformed();
               }
 
@@ -344,7 +369,7 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);