From 4aa1854d47a868ddd53a7eb8538ed11f2e36d9ff Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 17 Apr 2007 10:42:39 +0000
Subject: [PATCH] Applet remembers PDBEntries, can launch multiple structures
 from popupmenu

---
 src/jalview/appletgui/APopupMenu.java |   35 +++++++++++++++++++++++++++------
 src/jalview/appletgui/AppletJmol.java |    3 ++-
 src/jalview/bin/JalviewLite.java      |   16 ++++++++++-----
 3 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index ede493e..b281fcd 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -28,6 +28,7 @@ import jalview.analysis.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.io.AppletFormatAdapter;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -474,12 +475,34 @@ public class APopupMenu
 
   void addPDB()
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
-    cap.setText("Paste your PDB file here.");
-    cap.setPDBImport(seq);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+    if(seq.getPDBId()!=null)
+    {
+      PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
+
+      if ( ap.av.applet.jmolAvailable )
+       new jalview.appletgui.AppletJmol(entry,
+                                        new Sequence[]
+                                        {seq},
+                                        ap,
+                                        AppletFormatAdapter.URL);
+     else
+
+       new MCview.AppletPDBViewer(entry,
+                                  new Sequence[]
+                                  {seq},
+                                  ap,
+                                  AppletFormatAdapter.URL);
+
+    }
+    else
+    {
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+      cap.setText("Paste your PDB file here.");
+      cap.setPDBImport(seq);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+    }
   }
 
   private void jbInit()
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 2c2a979..b7e67c1 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -93,7 +93,8 @@ public class AppletJmol extends Frame
     {
        StructureSelectionManager.getStructureSelectionManager()
             .setMapping(seq, pdbentry.getFile(), protocol);
-        return;
+       //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
+       //FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
 
     renderPanel = new RenderPanel();
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index e01e0e8..ffdbb1b 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -150,7 +150,7 @@ public class JalviewLite
 
   boolean embedded = false;
 
-  public boolean jmolAvailable = true;
+  public boolean jmolAvailable = false;
 
   /**
    * init method for Jalview Applet
@@ -159,13 +159,15 @@ public class JalviewLite
   {
     try
     {
-      Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
-
-      jmolAvailable = true;
+      if (!System.getProperty("java.version").startsWith("1.1"))
+      {
+        Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+        jmolAvailable = true;
+      }
     }
     catch (java.lang.ClassNotFoundException ex)
     {
-      System.out.println("Jmol not found - Using MCview for structures");
+      System.out.println("Jmol not available - Using MCview for structures");
     }
 
     int r = 255;
@@ -549,6 +551,10 @@ public class JalviewLite
 
           pdb.setFile(param);
 
+          for(int i=0; i<seqs.length; i++)
+          {
+            ((Sequence)seqs[i]).addPDBId(pdb);
+          }
 
           if (jmolAvailable)
             new jalview.appletgui.AppletJmol(pdb,
-- 
1.7.10.2