import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
* @param choice
* @param sequence
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol,
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
SequenceI sequence, boolean prompt,
StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
StructureFile pdbfile = null;
pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[] { sequence }, null, choice,
- protocol);
+ .setMapping(false, 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)
{