X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=d53ddc8802471a3614e15190c136ebef333a970c;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3bd21b57b8a747c10309e0dbe6f390276c3d7850;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 3bd21b5..d53ddc8 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,101 +1,93 @@
-/*******************************************************************************
- * 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
- *
+/*
+ * 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.
- *
+ * 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.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.IdentifyFile;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import javax.swing.JOptionPane;
 
 /**
  * GUI related routines for associating PDB files with sequences
+ * 
  * @author JimP
- *
+ * 
  */
 public class AssociatePdbFileWithSeq
 {
 
-/**
- * assocate the given PDB file with 
- * @param choice
- * @param sequence
- * @throws SAXException 
- * @throws ParserConfigurationException 
- * @throws ExceptionFileFormatOrSyntax 
- * @throws ExceptionLoadingFailed 
- * @throws ExceptionPermissionDenied 
- * @throws InterruptedException 
- * @throws ExceptionUnmatchedClosingParentheses 
- */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  /**
+   * assocate the given PDB file with
+   * 
+   * @param choice
+   * @param sequence
+   */
+  public PDBEntry associatePdbWithSeq(String choice, String protocol,
+          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)
     {
- 
-    		System.out.println("This is a annotation PDB");
-    	
-    	
-      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.setFile(choice);
-    sequence.getDatasetSequence().addPDBId(entry);
+    if (pdbfile != null)
+    {
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+      StructureSelectionManager.getStructureSelectionManager(ssmp)
+              .registerPDBEntry(entry);
+    }
     return entry;
-    
   }
-
 }