From c23f28e21e50f93f6e695bdc86247f2700c35869 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Jul 2006 12:58:26 +0000
Subject: [PATCH] Prepare for launchFullApplication

---
 src/jalview/appletgui/AlignFrame.java |   78 ++++++++++++++++++++++++++++-----
 1 file changed, 68 insertions(+), 10 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index a68c797..93f48ee 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -59,6 +59,8 @@ public class AlignFrame extends Frame implements ActionListener,
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
 
+    seqLimits.setState(viewport.showJVSuffix);
+
     if(applet!=null)
     {
       String param = applet.getParameter("sortBy");
@@ -198,7 +200,7 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_C:
-        if (viewport.cursorMode)
+        if (viewport.cursorMode && !evt.isControlDown())
         {
           alignPanel.seqPanel.setCursorColumn();
         }
@@ -371,6 +373,8 @@ public void itemStateChanged(ItemEvent evt)
       inputText_actionPerformed();
     else if(evt.getSource()==loadTree)
       loadTree_actionPerformed();
+    else if(evt.getSource()==loadApplication)
+      launchFullApplication();
     else if(evt.getSource()==closeMenuItem)
       closeMenuItem_actionPerformed();
     else if(evt.getSource()==copy)
@@ -501,6 +505,63 @@ public void itemStateChanged(ItemEvent evt)
                                                       viewport.showJVSuffix));
   }
 
+  void launchFullApplication()
+  {
+    StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?");
+
+    url.append("open="+
+               appendProtocol( applet.getParameter("file") ) );
+
+    if(applet.getParameter("features")!=null)
+    {
+      url.append( "&features=" );
+      url.append( appendProtocol( applet.getParameter("features") ) );
+    }
+
+    if(applet.getParameter("defaultColour")!=null)
+    {
+      url.append("&colour=" +
+                 removeWhiteSpace(applet.getParameter("defaultColour"))
+          );
+    }
+
+    if(applet.getParameter("userDefinedColour")!=null)
+    {
+      url.append( "&colour=" +
+                 removeWhiteSpace( applet.getParameter("userDefinedColour") )
+         );
+    }
+
+    showURL(url.toString(), "FULL_APP");
+  }
+
+
+  String removeWhiteSpace(String colour)
+  {
+    StringBuffer sb = new StringBuffer();
+    for (int i = 0; i < colour.length(); i++)
+    {
+      if (Character.isWhitespace(colour.charAt(i)))
+        sb.append("%20");
+      else
+        sb.append(colour.charAt(i));
+    }
+
+    return sb.toString();
+  }
+
+
+  String appendProtocol(String url)
+  {
+    try{
+       new URL(url);
+    }catch(java.net.MalformedURLException ex)
+    {
+      url = applet.getCodeBase()+url;
+    }
+    return url;
+  }
+
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.components.remove(viewport.alignment);
@@ -1463,12 +1524,7 @@ public void itemStateChanged(ItemEvent evt)
 
   public void removeRedundancyMenuItem_actionPerformed()
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
-    Frame frame = new Frame();
-    frame.add(sp);
-    jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
-                                     400, 120);
-
+     new RedundancyPanel(alignPanel);
   }
 
   public void pairwiseAlignmentMenuItem_actionPerformed()
@@ -1583,8 +1639,6 @@ public void itemStateChanged(ItemEvent evt)
 
   void loadTree_actionPerformed()
   {
-    TreePanel tp = null;
-
       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
       cap.setText("Paste your Newick tree file here.");
       cap.treeImport = true;
@@ -1706,6 +1760,7 @@ public void itemStateChanged(ItemEvent evt)
     {
       try
       {
+        System.out.println("Show url: "+url);
         applet.getAppletContext().showDocument(new java.net.URL(url),
                                                target);
       }
@@ -1722,6 +1777,7 @@ public void itemStateChanged(ItemEvent evt)
 
     protected MenuBar alignFrameMenuBar = new MenuBar();
     protected Menu fileMenu = new Menu("File");
+    protected MenuItem loadApplication = new MenuItem("View in Full Application");
     protected MenuItem loadTree = new MenuItem("Load Associated Tree");
     protected MenuItem closeMenuItem = new MenuItem("Close");
     protected Menu editMenu = new Menu("Edit");
@@ -1832,6 +1888,7 @@ public void itemStateChanged(ItemEvent evt)
         outputTextboxMenu.add(item);
       }
         closeMenuItem.addActionListener(this);
+        loadApplication.addActionListener(this);
 
         loadTree.addActionListener(this);
         selectAllSequenceMenuItem.addActionListener(this);
@@ -1997,6 +2054,7 @@ public void itemStateChanged(ItemEvent evt)
         alignFrameMenuBar.add(helpMenu);
         fileMenu.add(inputText);
         fileMenu.add(outputTextboxMenu);
+       // fileMenu.add(loadApplication);
         fileMenu.addSeparator();
         fileMenu.add(loadTree);
         fileMenu.add(closeMenuItem);
@@ -2127,7 +2185,7 @@ public void itemStateChanged(ItemEvent evt)
 
    // setVisible(false);
     fileMenu.remove(closeMenuItem);
-    fileMenu.remove(2); // Seperator
+    fileMenu.remove(3); // Seperator
 
     applet.setLayout(new BorderLayout());
     applet.add(embeddedMenu, BorderLayout.NORTH);
-- 
1.7.10.2