JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index fe0aedf..1f540da 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,18 +20,15 @@
  */
 package jalview.gui;
 
-import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
- * GUI related routines for associating PDB files with sequences
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
  * 
  * @author JimP
  * 
@@ -39,58 +36,56 @@ import javax.swing.JOptionPane;
 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, DataSourceType file,
-          SequenceI sequence, boolean prompt,
-          StructureSelectionManagerProvider ssmp)
+  public static PDBEntry associatePdbWithSeq(String fileName,
+          DataSourceType type, SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
-    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+    pdbfile = Desktop.getStructureSelectionManager()
             .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, file);
+            { sequence }, null, fileName, type);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.getId() == null)
-    {
-      String reply = null;
-
-      if (prompt)
-      {
-        reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
-                MessageManager
-                        .getString("label.couldnt_find_pdb_id_in_file"),
-                MessageManager.getString("label.no_pdb_id_in_file"),
-                JvOptionPane.QUESTION_MESSAGE);
-      }
-      if (reply == null)
-      {
-        return null;
-      }
-
-      entry.setId(reply);
-    }
-    else
+    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)
     {
-      entry.setId(pdbfile.getId());
+      return null;
     }
+    entry.setId(id);
     entry.setType(PDBEntry.Type.FILE);
-
-    if (pdbfile != null)
-    {
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
-      StructureSelectionManager.getStructureSelectionManager(ssmp)
-              .registerPDBEntry(entry);
-    }
+    entry.setFile(fileName);
+    sequence.getDatasetSequence().addPDBId(entry);
+    Desktop.getInstance().getStructureSelectionManager()
+            .registerPDBEntry(entry);
     return entry;
   }
 }