/*
 * 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 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. A single
 * static method.
 * 
 * @author JimP
 * 
 */
public class AssociatePdbFileWithSeq
{

  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();
    StructureFile pdbfile = null;
    pdbfile = Desktop.getStructureSelectionManager()
            .setMapping(false, new SequenceI[]
            { sequence }, null, fileName, type);
    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)
    {
      return null;
    }
    entry.setId(id);
    entry.setType(PDBEntry.Type.FILE);
    entry.setFile(fileName);
    sequence.getDatasetSequence().addPDBId(entry);
    Desktop.getStructureSelectionManager()
            .registerPDBEntry(entry);
    return entry;
  }
}