JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index b81c344..fe0aedf 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,15 +20,18 @@
  */
 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. A single
- * static method.
+ * GUI related routines for associating PDB files with sequences
  * 
  * @author JimP
  * 
@@ -36,56 +39,58 @@ import jalview.util.MessageManager;
 public class AssociatePdbFileWithSeq
 {
 
-  private AssociatePdbFileWithSeq()
-  {
-    // inaccessible
-  }
-
   /**
-   * Associate the given PDB file name or URL with a sequence. Do not map
-   * mouse-over events.
+   * assocate the given PDB file with
    * 
-   * @param fileName
-   *          or URL
-   * @param type
-   *          will be DataType.FILE or DataType.URL
+   * @param choice
    * @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)
+  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+          SequenceI sequence, boolean prompt,
+          StructureSelectionManagerProvider ssmp)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
-    pdbfile = Desktop.getInstance().getStructureSelectionManager()
+    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[]
-            { sequence }, null, fileName, type);
+            { sequence }, null, choice, file);
     if (pdbfile == null)
     {
       // 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)
+    if (pdbfile.getId() == null)
     {
-      return 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
+    {
+      entry.setId(pdbfile.getId());
     }
-    entry.setId(id);
     entry.setType(PDBEntry.Type.FILE);
-    entry.setFile(fileName);
-    sequence.getDatasetSequence().addPDBId(entry);
-    Desktop.getInstance().getStructureSelectionManager()
-            .registerPDBEntry(entry);
+
+    if (pdbfile != null)
+    {
+      entry.setFile(choice);
+      sequence.getDatasetSequence().addPDBId(entry);
+      StructureSelectionManager.getStructureSelectionManager(ssmp)
+              .registerPDBEntry(entry);
+    }
     return entry;
   }
 }