/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ * 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/>.
+ * 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 javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
SequenceI sequence, boolean prompt)
{
PDBEntry entry = new PDBEntry();
+ MCview.PDBfile pdbfile = null;
try
{
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
-
+ // 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);
+ 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)
{