only recalc group conservation after last sequence operated on in a bulk add/remove...

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index bd86275..e942b88 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
@@ -723,10 +724,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
             // just transfer the file name from the first sequence's first
             // PDBEntry
             file = new File(((PDBEntry) pdbseq
-                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).toURI().getPath().substring(1);
+                    .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath();
             jmb.pdbentry[pi].setFile(file);
             
-            files.append(" \"" + file + "\"");
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
           else
           {
@@ -749,7 +750,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
           }
           if (file != null)
           {
-            files.append(" \"" + file + "\"");
+            files.append(" \"" + Platform.escapeString(file) + "\"");
           }
         }
       }
@@ -1044,7 +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);