JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 979a2e2..f67d6da 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,34 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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 javax.swing.JOptionPane;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import javax.swing.JOptionPane;
 
 /**
  * GUI related routines for associating PDB files with sequences
@@ -46,45 +44,51 @@ public class AssociatePdbFileWithSeq
    * @param sequence
    */
   public PDBEntry associatePdbWithSeq(String choice, String protocol,
-          SequenceI sequence, boolean prompt)
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
-    try
+    MCview.PDBfile pdbfile = null;
+    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+            .setMapping(false, new SequenceI[] { sequence }, null, choice,
+                    protocol);
+    if (pdbfile == null)
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
+      // stacktrace already thrown so just return
+      return null;
+    }
+    if (pdbfile.id == null)
+    {
+      String reply = null;
 
-      if (pdbfile.id == null)
+      if (prompt)
       {
-        String reply = null;
-
-        if (prompt)
-        {
-          reply = JOptionPane
-                  .showInternalInputDialog(
-                          Desktop.desktop,
-                          "Couldn't find a PDB id in the file supplied."
-                                  + "Please enter an Id to identify this structure.",
-                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
-        }
-        if (reply == null)
-        {
-          return null;
-        }
-
-        entry.setId(reply);
+        reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                MessageManager
+                        .getString("label.couldnt_find_pdb_id_in_file"),
+                MessageManager.getString("label.no_pdb_id_in_file"),
+                JOptionPane.QUESTION_MESSAGE);
       }
-      else
+      if (reply == null)
       {
-        entry.setId(pdbfile.id);
+        return null;
       }
 
-    } catch (java.io.IOException ex)
+      entry.setId(reply);
+    }
+    else
     {
-      ex.printStackTrace();
+      entry.setId(pdbfile.id);
     }
+    entry.setType(PDBEntry.Type.FILE);
 
-    entry.setFile(choice);
-    sequence.getDatasetSequence().addPDBId(entry);
+    if (pdbfile != null)
+    {
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+      StructureSelectionManager.getStructureSelectionManager(ssmp)
+              .registerPDBEntry(entry);
+    }
     return entry;
   }
 }