X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=afaedb8fe27add58671b07d3df66b8f72d339b76;hb=37fd8c26efada7832b61e5af5c0d56baa69608c3;hp=9efe17e4e4f9bcbcaba4aff8fd8c39a6712eda4a;hpb=0af39ffc83a804e0f3f0d7618fcdc9e5073c0a0b;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 9efe17e..afaedb8 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -71,6 +71,8 @@ public class AppletJmol extends EmbmenuFrame implements
   MenuItem turn = new MenuItem("Turn Propensity");
 
   MenuItem buried = new MenuItem("Buried Index");
+  
+  MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
 
   MenuItem user = new MenuItem("User Defined Colours");
 
@@ -132,7 +134,7 @@ public class AppletJmol extends EmbmenuFrame implements
           AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
-    jmb = new AppletJmolBinding(this, new PDBEntry[]
+    jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
     { pdbentry }, new SequenceI[][]
     { seq }, new String[][]
     { chains }, protocol);
@@ -157,12 +159,12 @@ public class AppletJmol extends EmbmenuFrame implements
     }
 
     String alreadyMapped = StructureSelectionManager
-            .getStructureSelectionManager().alreadyMappedToFile(
+            .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile(
                     pdbentry.getId());
     MCview.PDBfile reader = null;
     if (alreadyMapped != null)
     {
-      reader = StructureSelectionManager.getStructureSelectionManager()
+      reader = StructureSelectionManager.getStructureSelectionManager(ap.av.applet)
               .setMapping(seq, chains, pdbentry.getFile(), protocol);
       // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
       // FOR NOW, LETS JUST OPEN A NEW WINDOW
@@ -180,14 +182,15 @@ public class AppletJmol extends EmbmenuFrame implements
     hydro.addActionListener(this);
     chain.addActionListener(this);
     seqColour.addItemListener(this);
+    jmolColour.addItemListener(this);
     zappo.addActionListener(this);
     taylor.addActionListener(this);
     helix.addActionListener(this);
     strand.addActionListener(this);
     turn.addActionListener(this);
     buried.addActionListener(this);
+    purinepyrimidine.addActionListener(this);
     user.addActionListener(this);
-    jmolColour.addActionListener(this);
     
     jmolHelp.addActionListener(this);
 
@@ -201,6 +204,7 @@ public class AppletJmol extends EmbmenuFrame implements
     coloursMenu.add(strand);
     coloursMenu.add(turn);
     coloursMenu.add(buried);
+    coloursMenu.add(purinepyrimidine);
     coloursMenu.add(user);
     coloursMenu.add(jmolColour);
     helpMenu.add(jmolHelp);
@@ -383,8 +387,7 @@ public class AppletJmol extends EmbmenuFrame implements
       {
         for (int s = 0; s < jmb.pdbentry.length; s++)
         {
-          sb.append(StructureSelectionManager
-                  .getStructureSelectionManager().printMapping(
+          sb.append(jmb.printMapping(
                           jmb.pdbentry[s].getFile()));
           sb.append("\n");
         }
@@ -445,6 +448,10 @@ public class AppletJmol extends EmbmenuFrame implements
       setEnabled(buried);
       jmb.setJalviewColourScheme(new BuriedColourScheme());
     }
+    else if(evt.getSource() == purinepyrimidine)
+    {
+   	jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+    }
     else if (evt.getSource() == user)
     {
       setEnabled(user);