X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAssociatePdbFileWithSeq.java;h=1f540dacfd159fa9c3ba05f4feb3709f315ef743;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=ce75821a3535dea439bf1dcef203e730aea0e8f1;hpb=e248608bb20e000c17ddc79390d9c1f1f0470e4f;p=jalview.git

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index ce75821..1f540da 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,15 @@
  */
 package jalview.gui;
 
-import javax.swing.JOptionPane;
 import jalview.datamodel.PDBEntry;
 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
  * 
@@ -34,53 +36,56 @@ import jalview.util.MessageManager;
 public class AssociatePdbFileWithSeq
 {
 
+  private AssociatePdbFileWithSeq()
+  {
+    // inaccessible
+  }
+
   /**
-   * assocate the given PDB file with
+   * Associate the given PDB file name or URL with a sequence. Do not map
+   * mouse-over events.
    * 
-   * @param choice
+   * @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 PDBEntry associatePdbWithSeq(String choice, String protocol,
-          SequenceI sequence, boolean prompt)
+  public static PDBEntry associatePdbWithSeq(String fileName,
+          DataSourceType type, SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
-    MCview.PDBfile pdbfile = null;
-    try
+    StructureFile pdbfile = null;
+    pdbfile = Desktop.getStructureSelectionManager()
+            .setMapping(false, new SequenceI[]
+            { sequence }, null, fileName, type);
+    if (pdbfile == null)
     {
-      // TODO JAL-674 extract secondary structure and transfer it to associated
-      // sequence
-      pdbfile = new MCview.PDBfile(false, false, choice, protocol);
-      if (pdbfile.id == null)
-      {
-        String reply = null;
-
-        if (prompt)
-        {
-          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);
-        }
-        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;
   }
 }