X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolViewer.java;h=52c253d34a8117b1950fe4260c2e8dcfd170e8e4;hb=efee78d45ceeb879d98fedd399a71d84a5ecd5f8;hp=3b6ea99087b972b43bffcb456c790b466299f26e;hpb=57fd11364c284318be3cae3ded0df30a36ee0d98;p=jalview.git

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 3b6ea99..52c253d 100644
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import java.awt.event.ActionEvent;
@@ -50,9 +70,7 @@ public class PymolViewer extends StructureViewerBase
           AlignmentPanel ap)
   {
     this();
-    openNewPymol(ap, new PDBEntry[] { pdb },
-            new SequenceI[][]
-            { seqs });
+    openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs });
   }
 
   public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs,
@@ -161,11 +179,12 @@ public class PymolViewer extends StructureViewerBase
   public void run()
   {
     // todo pull up much of this
-  
+
     StringBuilder errormsgs = new StringBuilder(128);
     List<PDBEntry> filePDB = new ArrayList<>();
     List<Integer> filePDBpos = new ArrayList<>();
-    String[] curfiles = binding.getStructureFiles(); // files currently in viewer
+    String[] curfiles = binding.getStructureFiles(); // files currently in
+                                                     // viewer
     for (int pi = 0; pi < binding.getPdbCount(); pi++)
     {
       String file = null;
@@ -186,8 +205,7 @@ public class PymolViewer extends StructureViewerBase
         /*
          * got file already
          */
-        file = new File(thePdbEntry.getFile()).getAbsoluteFile()
-                .getPath();
+        file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath();
         // todo - skip if already loaded in PyMOL
       }
       if (file != null)
@@ -196,7 +214,7 @@ public class PymolViewer extends StructureViewerBase
         filePDBpos.add(Integer.valueOf(pi));
       }
     }
-        
+
     if (!filePDB.isEmpty())
     {
       /*
@@ -215,6 +233,14 @@ public class PymolViewer extends StructureViewerBase
           return;
         }
       }
+      if (!binding.isViewerRunning())
+      {
+        // nothing to do
+        // TODO: ensure we tidy up JAL-3619
+
+        return;
+      }
+
       int num = -1;
       for (PDBEntry pe : filePDB)
       {
@@ -244,16 +270,23 @@ public class PymolViewer extends StructureViewerBase
               stopProgressBar("", startTime);
             }
 
-            StructureFile pdb = binding.getSsm().setMapping(
-                    binding.getSequence()[pos], binding.getChains()[pos],
-                    pe.getFile(), protocol,
-                    getProgressIndicator());
+            StructureFile pdb = null;
+            if (pe.hasStructureFile())
+            {
+              pdb = pe.getStructureFile();
+              Console.debug("(Re)Using StructureFile " + pdb.getId());
+            }
+            else
+            {
+              pdb = binding.getSsm().setMapping(binding.getSequence()[pos],
+                      binding.getChains()[pos], pe.getFile(), protocol,
+                      getProgressIndicator());
+            }
             binding.stashFoundChains(pdb, pe.getFile());
           } catch (Exception ex)
           {
-            Console.error(
-                    "Couldn't open " + pe.getFile() + " in Chimera viewer!",
-                    ex);
+            Console.error("Couldn't open " + pe.getFile() + " in "
+                    + getViewerName() + "!", ex);
           } finally
           {
             // Cache.debug("File locations are " + files);
@@ -326,8 +359,7 @@ public class PymolViewer extends StructureViewerBase
       boolean opened = binding.openSession(pymolSessionFile);
       if (!opened)
       {
-        Console.error(
-                "An error occurred opening PyMOL session file "
+        Console.error("An error occurred opening PyMOL session file "
                 + pymolSessionFile);
       }
     }
@@ -351,7 +383,9 @@ public class PymolViewer extends StructureViewerBase
   {
     return "PyMOL";
   }
+
   JMenuItem writeFeatures = null;
+
   @Override
   protected void initMenus()
   {
@@ -362,8 +396,8 @@ public class PymolViewer extends StructureViewerBase
 
     writeFeatures = new JMenuItem(
             MessageManager.getString("label.create_viewer_attributes"));
-    writeFeatures.setToolTipText(MessageManager
-            .getString("label.create_viewer_attributes_tip"));
+    writeFeatures.setToolTipText(
+            MessageManager.getString("label.create_viewer_attributes_tip"));
     writeFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -374,7 +408,7 @@ public class PymolViewer extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
   }
-  
+
   @Override
   protected void buildActionMenu()
   {
@@ -385,8 +419,8 @@ public class PymolViewer extends StructureViewerBase
   protected void sendFeaturesToPymol()
   {
     int count = binding.sendFeaturesToViewer(getAlignmentPanel());
-    statusBar.setText(
-            MessageManager.formatMessage("label.attributes_set", count, getViewerName())); 
+    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+            count, getViewerName()));
   }
 
 }