X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=09e87013484837b26038173afea1de51deac5861;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=53d55f31c94da5007297e6f3b595acd71ba8b66b;hpb=fbf333095c96e42635e648d74bc029fed496895a;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 53d55f3..09e8701 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
@@ -46,7 +46,7 @@ public class JalviewLite extends Applet
 
     //The currentAlignFrame is static, it will change
     //if and when the user selects a new window
-    static AlignFrame currentAlignFrame;
+    public static AlignFrame currentAlignFrame;
 
     //This is the first frame to be displayed, and does not change
     AlignFrame initialAlignFrame;
@@ -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
             {
@@ -289,6 +308,8 @@ public class JalviewLite extends Applet
                                                  file,
                                                  embedded);
 
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 
               initialAlignFrame = currentAlignFrame;
 
@@ -297,7 +318,8 @@ public class JalviewLite extends Applet
 
                 String treeFile = applet.getParameter("tree");
                 if(treeFile==null)
-                  applet.getParameter("treeFile");
+                  treeFile = applet.getParameter("treeFile");
+
                 if (treeFile != null)
                 {
                   try
@@ -337,6 +359,7 @@ public class JalviewLite extends Applet
               param = getParameter("showFeatureSettings");
               if(param !=null && param.equalsIgnoreCase("true"))
               {
+                currentAlignFrame.viewport.showSequenceFeatures(true);
                 currentAlignFrame.featureSettings_actionPerformed();
               }