X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=b81c344197456608c24f594a9927e2e5336dd54d;hb=13ab52271b76b41ece153044b30316c23c4386a2;hp=cbfbbc46d093ef649f92adc13795d9117e358c37;hpb=28c13a67af0d57c53de532d0d50add7ab83f7d42;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index cbfbbc4..b81c344 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,61 +1,91 @@
+/*
+ * 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 javax.swing.JOptionPane;
-
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
 
 /**
- * GUI related routines for associating PDB files with sequences
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
+ * 
  * @author JimP
- *
+ * 
  */
 public class AssociatePdbFileWithSeq
 {
 
-/**
- * assocate the given PDB file with 
- * @param choice
- * @param sequence
- */
-  public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt)
+  private AssociatePdbFileWithSeq()
+  {
+    // inaccessible
+  }
+
+  /**
+   * Associate the given PDB file name or URL with a sequence. Do not map
+   * mouse-over events.
+   * 
+   * @param fileName
+   *          or URL
+   * @param type
+   *          will be DataType.FILE or DataType.URL
+   * @param sequence
+   *          to associate
+   * @param prompt
+   *          true if the user should be asked what to do if the specified file
+   *          does not seem to contain PDB information (StructureChooser only)
+   * @return null if file is not found
+   */
+  public static PDBEntry associatePdbWithSeq(String fileName,
+          DataSourceType type, SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
-    try
+    StructureFile pdbfile = null;
+    pdbfile = Desktop.getInstance().getStructureSelectionManager()
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, fileName, type);
+    if (pdbfile == null)
     {
-      MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-              protocol);
-
-      if (pdbfile.id == null)
-      {
-        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);
-      }
-      else
-      {
-        entry.setId(pdbfile.id);
-      }
-    } catch (java.io.IOException ex)
+      // stacktrace already thrown so just return
+      return null;
+    }
+    String id = pdbfile.getId();
+    if (id == null && (id = (prompt
+            ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
+                    MessageManager
+                            .getString("label.couldnt_find_pdb_id_in_file"),
+                    MessageManager.getString("label.no_pdb_id_in_file"),
+                    JvOptionPane.QUESTION_MESSAGE)
+            : null)) == null)
     {
-      ex.printStackTrace();
+      return null;
     }
-
-    entry.setFile(choice);
+    entry.setId(id);
+    entry.setType(PDBEntry.Type.FILE);
+    entry.setFile(fileName);
     sequence.getDatasetSequence().addPDBId(entry);
+    Desktop.getInstance().getStructureSelectionManager()
+            .registerPDBEntry(entry);
     return entry;
   }
-
 }