-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.io.IdentifyFile;
+import jalview.util.MessageManager;
/**
* GUI related routines for associating PDB files with sequences
+ *
* @author JimP
- *
+ *
*/
public class AssociatePdbFileWithSeq
{
-/**
- * assocate the given PDB file with
- * @param choice
- * @param sequence
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
- * @throws ExceptionUnmatchedClosingParentheses
- */
- public PDBEntry associatePdbWithSeq(String choice, String protocol, SequenceI sequence, boolean prompt) throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ /**
+ * assocate the given PDB file with
+ *
+ * @param choice
+ * @param sequence
+ */
+ public PDBEntry associatePdbWithSeq(String choice, String protocol,
+ SequenceI sequence, boolean prompt)
{
PDBEntry entry = new PDBEntry();
try
{
-
- System.out.println("This is a annotation PDB");
-
-
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
- protocol);
+ MCview.PDBfile pdbfile = new MCview.PDBfile(choice, protocol);
if (pdbfile.id == null)
{
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 (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);
+ }
if (reply == null)
{
return null;
{
entry.setId(pdbfile.id);
}
-
+
} catch (java.io.IOException ex)
{
ex.printStackTrace();
entry.setFile(choice);
sequence.getDatasetSequence().addPDBId(entry);
return entry;
-
}
-
}