X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=e942b88d9f1a93807891429d49ecf47209356a6a;hb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;hp=e500240773a4f728a2ba30040dad8ffe03fc8a22;hpb=77ab7d6694e27575261ab58c098eee76e68c2228;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e500240..e942b88 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.
  * 
@@ -35,6 +35,7 @@ import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.Platform;
 
 public class AppJmol extends GStructureViewer implements Runnable,
         SequenceStructureBinding, ViewSetProvider
@@ -321,7 +322,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
     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);
@@ -335,24 +335,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     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)
-    {
-      initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
-    }
-*/
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -736,9 +723,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
-                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
-            files.append(" \"" + file + "\"");
+            file = new File(((PDBEntry) pdbseq
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath();
+            jmb.pdbentry[pi].setFile(file);
+            
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
           else
           {
@@ -761,7 +750,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
           }
           if (file != null)
           {
-            files.append(" \"" + file + "\"");
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
         }
       }
@@ -1056,7 +1045,12 @@ 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);