import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import javax.swing.JOptionPane;
-
/**
* GUI related routines for associating PDB files with sequences
*
{
/**
- * assocate the given PDB file with
+ * Associates the given file as a PDB structure for the given sequence.
*
* @param choice
+ * @param file
* @param sequence
+ * @param prompt
+ * @param ssmp
+ * @param forViewer
+ * @return
*/
public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
SequenceI sequence, boolean prompt,
- StructureSelectionManagerProvider ssmp)
+ StructureSelectionManagerProvider ssmp, boolean forViewer)
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[] { sequence }, null, choice,
- file);
+ .setMapping(forViewer, new SequenceI[]
+ { sequence }, null, choice, file);
if (pdbfile == null)
{
// stacktrace already thrown so just return
if (prompt)
{
- reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
MessageManager
.getString("label.couldnt_find_pdb_id_in_file"),
MessageManager.getString("label.no_pdb_id_in_file"),
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.QUESTION_MESSAGE);
}
if (reply == null)
{