X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=afaedb8fe27add58671b07d3df66b8f72d339b76;hb=37fd8c26efada7832b61e5af5c0d56baa69608c3;hp=42e6f56cfdfccf4378446f0de5ad2b5615f21efd;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 42e6f56..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.
  * 
@@ -52,6 +52,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
 
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+  
   MenuItem chain = new MenuItem("By Chain");
 
   MenuItem charge = new MenuItem("Charge & Cysteine");
@@ -69,6 +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");
 
@@ -83,6 +87,7 @@ public class AppletJmol extends EmbmenuFrame implements
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
+  ArrayList _aps = new ArrayList();
 
   String fileLoadingError;
 
@@ -129,7 +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);
@@ -154,12 +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
@@ -177,14 +182,16 @@ 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);
-
+    
     jmolHelp.addActionListener(this);
 
     coloursMenu.add(seqColour);
@@ -197,8 +204,9 @@ 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);
     this.setLayout(new BorderLayout());
 
@@ -379,8 +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");
         }
@@ -441,6 +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);
@@ -473,23 +484,29 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   /**
-   * tick or untick the seqColour menu entry depending upon if it was selected
+   * tick or untick the seqColour menu entry or jmoColour entry depending upon if it was selected
    * or not.
    * 
    * @param itm
    */
   private void setEnabled(MenuItem itm)
   {
+    jmolColour.setState(itm == jmolColour);
     seqColour.setState(itm == seqColour);
     jmb.setColourBySequence(itm == seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
+    if (evt.getSource() == jmolColour)
+    {
+      setEnabled(jmolColour);
+      jmb.setColourBySequence(false);
+    } else
     if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -517,7 +534,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -528,7 +545,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -632,4 +649,16 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     jmb.setJalviewColourScheme(ucs);
   }
+
+  public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+  {
+    for (int i=0;i<_aps.size();i++)
+    {
+      if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
+      {
+        return ((AlignmentPanel)_aps.get(i));
+      }
+    }
+    return ap;
+  }
 }