X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=09e87013484837b26038173afea1de51deac5861;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=199a843cb66245466bb2e7eea32288a72ef16f23;hpb=6a60c733dc23235562e32583e68284efa5d29ac9;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 199a843..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
@@ -28,7 +28,6 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import jalview.appletgui.TreePanel;
 
 
 /**
@@ -47,7 +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;
@@ -89,6 +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"))
@@ -262,7 +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
             {
@@ -290,12 +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
@@ -329,7 +353,14 @@ 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();
               }
 
              param = getParameter("annotations");
@@ -338,11 +369,38 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);
 
                currentAlignFrame.alignPanel.fontChanged();
+               currentAlignFrame.alignPanel.setScrollValues(0,0);
+
+             }
+
+             param = getParameter("jnetfile");
+             if (param != null)
+             {
+               try
+               {
+                 if (inArchive(param))
+                   protocol = AppletFormatAdapter.CLASSLOADER;
+                 else
+                 {
+                   protocol = AppletFormatAdapter.URL;
+                   param = addProtocol(param);
+                 }
+
+                 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                     param, protocol);
+                 new JnetAnnotationMaker().add_annotation(predictions,
+                     currentAlignFrame.viewport.getAlignment(),
+                     0,false); // do not add sequence profile from concise output
+                 currentAlignFrame.alignPanel.fontChanged();
+                 currentAlignFrame.alignPanel.setScrollValues(0, 0);
+               } catch (Exception ex) {
+                 ex.printStackTrace();
+               }
              }