+/*
+ * 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.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
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
+ *
* @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)
+ /**
+ * assocate the given PDB file with
+ *
+ * @param choice
+ * @param sequence
+ */
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
- try
+ StructureFile pdbfile = null;
+ pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .setMapping(false, new SequenceI[] { sequence }, null, choice,
+ file);
+ if (pdbfile == null)
{
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
- protocol);
+ // stacktrace already thrown so just return
+ return null;
+ }
+ if (pdbfile.getId() == 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 = JvOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.couldnt_find_pdb_id_in_file"),
+ MessageManager.getString("label.no_pdb_id_in_file"),
+ JvOptionPane.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.getId());
}
+ entry.setType(PDBEntry.Type.FILE);
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ if (pdbfile != null)
+ {
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .registerPDBEntry(entry);
+ }
return entry;
}
-
}