X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=955ad7be3313eea63ca8ba721b74107deaa4ff95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=fdf00c0fa867e603d542489166509c336dff9b3c;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fdf00c0..955ad7b 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.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.
  * 
@@ -26,6 +26,7 @@ import java.awt.event.*;
 import java.io.*;
 
 import jalview.jbgui.GStructureViewer;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
@@ -227,13 +228,20 @@ public class AppJmol extends GStructureViewer implements Runnable,
   }
   IProgressIndicator progressBar = null;
 
+  /**
+   * add a single PDB structure to a new or existing Jmol view
+   * @param pdbentry
+   * @param seq
+   * @param chains
+   * @param ap
+   */
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap)
+          final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
     // ////////////////////////////////
     // Is the pdb file already loaded?
-    String alreadyMapped = jmb.ssm.alreadyMappedToFile(
+    String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile(
                     pdbentry.getId());
 
     if (alreadyMapped != null)
@@ -246,7 +254,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
       if (option == JOptionPane.YES_OPTION)
       {
-        jmb.ssm.setMapping(seq, chains, alreadyMapped,
+        // TODO : Fix multiple seq to one chain issue here.
+        ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
                         AppletFormatAdapter.FILE);
         if (ap.seqPanel.seqCanvas.fr != null)
         {
@@ -262,7 +271,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           if (frames[i] instanceof AppJmol)
           {
-            AppJmol topJmol = ((AppJmol) frames[i]);
+            final AppJmol topJmol = ((AppJmol) frames[i]);
             // JBPNOTE: this looks like a binding routine, rather than a gui
             // routine
             for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
@@ -271,7 +280,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
               {
                 topJmol.jmb.addSequence(pe, seq);
                 topJmol.addAlignmentPanel(ap);
+                // add it to the set used for colouring
+                topJmol.useAlignmentPanelForColourbyseq(ap);
                 topJmol.buildJmolActionMenu();
+                ap.getStructureSelectionManager().sequenceColoursChanged(ap);
                 break;
               }
             }
@@ -306,27 +318,41 @@ public class AppJmol extends GStructureViewer implements Runnable,
       }
     }
     // /////////////////////////////////
-
-    jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
-    { pdbentry }, new SequenceI[][]
-    { seq }, null, null);
+    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+  }
+  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
+    boolean promptUser=pdbentrys.length==1;
+    progressBar = ap.alignFrame;
+    jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
+    if (pdbentrys.length>1)
+    {
+      alignAddedStructures=true;
+      useAlignmentPanelForSuperposition(ap);
+    }
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
-
-    if (pdbentry.getFile() != null)
-    {
-      initJmol("load \"" + pdbentry.getFile() + "\"");
-    }
-    else
+    worker=null;
+    String filelist="";
+//    for (PDBEntry pe: pdbentrys)
+//    {
+//      if (pe.getFile()==null)
+      {
+        addingStructures = false;
+        worker = new Thread(this);
+        worker.start();
+//        break;
+      }
+//      filelist+=" \""+pe.getFile()+"\"";
+              
+/*    }
+    if (worker==null)
     {
-      addingStructures = false;
-      worker = new Thread(this);
-      worker.start();
+      initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
     }
-
+*/
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -338,6 +364,17 @@ public class AppJmol extends GStructureViewer implements Runnable,
   }
 
   /**
+   * create a new Jmol containing several structures superimposed using the given alignPanel.
+   * @param ap
+   * @param pe
+   * @param seqs
+   */
+  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  {
+    openNewJmol(ap, pe, seqs);
+  }
+
+  /**
    * list of sequenceSet ids associated with the view
    */
   ArrayList<String> _aps = new ArrayList();
@@ -747,6 +784,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
               "Couldn't load file", JOptionPane.ERROR_MESSAGE);
 
     }
+    long lastnotify = jmb.getLoadNotifiesHandled();
     if (files.length() > 0)
     {
       if (!addingStructures)
@@ -772,7 +810,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
         cmd.append("\nloadingJalviewdata=null");
         final String command = cmd.toString();
         cmd = null;
-        long lastnotify = jmb.getLoadNotifiesHandled();
+        lastnotify = jmb.getLoadNotifiesHandled();
+        
         try
         {
           jmb.evalStateCommand(command);
@@ -786,37 +825,40 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           Cache.log.error("Couldn't add files to Jmol viewer!", ex);
         }
-        // need to wait around until script has finished
-        while (lastnotify >= jmb.getLoadNotifiesHandled())
-          ;
+      }
+    
+      // need to wait around until script has finished
+      while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+              : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
+      {
+        try
         {
-          try
-          {
-            Thread.sleep(35);
-          } catch (Exception e)
-          {
-          }
-        }
-        // refresh the sequence colours for the new structure(s)
-        for (AlignmentPanel ap : _colourwith)
+          Cache.log.debug("Waiting around for jmb notify.");
+          Thread.sleep(35);
+        } catch (Exception e)
         {
-          jmb.updateColours(ap);
         }
-        // do superposition if asked to
-        if (alignAddedStructures)
+      }
+      // refresh the sequence colours for the new structure(s)
+      for (AlignmentPanel ap : _colourwith)
+      {
+        jmb.updateColours(ap);
+      }
+      // do superposition if asked to
+      if (alignAddedStructures)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          public void run()
           {
-            public void run()
-            {
-              alignStructs_withAllAlignPanels();
-              // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
-            }
-          });
-          alignAddedStructures = false;
-        }
-        addingStructures = false;
+            alignStructs_withAllAlignPanels();
+            // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+          }
+        });
+        alignAddedStructures = false;
       }
+      addingStructures = false;
+
     }
     _started = false;
     worker = null;
@@ -1014,7 +1056,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
     buriedColour.setSelected(true);
     jmb.setJalviewColourScheme(new BuriedColourScheme());
   }
-
+  
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+    setJalviewColourScheme(new PurinePyrimidineColourScheme());
+  }
+  
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {
     userColour.setSelected(true);