X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;fp=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=705102ad5c357a85cc3d036f36ea08244ac2c978;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=6aba7b6a6b4e31bca8cd4ed4639fe475378c8610;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 6aba7b6..705102a 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.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.util.ArrayList;
@@ -77,8 +97,7 @@ public class PymolBindingModel extends AAStructureBindingModel
     {
       // todo promote to StructureCommandsI.showLabel()
       String modelId = getModelIdForFile(atom.getPdbFile());
-      sb.append(String.format(" %s//%s/%d/*", modelId,
-              atom.getChain(),
+      sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
               atom.getPdbResNum()));
     }
     String labelSpec = sb.toString();
@@ -121,7 +140,7 @@ public class PymolBindingModel extends AAStructureBindingModel
   @Override
   public boolean isViewerRunning()
   {
-    return pymolManager.isPymolLaunched();
+    return pymolManager != null && pymolManager.isPymolLaunched();
   }
 
   @Override
@@ -161,20 +180,21 @@ public class PymolBindingModel extends AAStructureBindingModel
      * a second parameter sets the pdbid as the loaded PyMOL object name
      */
     String pdbId = pe.getId();
-    try {
-      String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+    try
+    {
+      String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
       pdbId = safePDBId.replace('%', '_');
       pdbId = pdbId.replace("-", "__");
       char fc = pdbId.charAt(0);
       // put an 's' before any numerics
-      if (fc>='0' && fc<='9')
+      if (fc >= '0' && fc <= '9')
       {
-        pdbId = 's'+pdbId;
+        pdbId = 's' + pdbId;
       }
-//      pdbId.replace('-', 0)
+      // pdbId.replace('-', 0)
     } catch (Exception x)
     {
-      Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
+      Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
     }
     cmd.addParameter(pdbId);