*/
package jalview.gui;
-import javax.swing.JOptionPane;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+
/**
* GUI related routines for associating PDB files with sequences
*
* @param sequence
*/
public PDBEntry associatePdbWithSeq(String choice, String protocol,
- SequenceI sequence, boolean prompt)
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp)
{
PDBEntry entry = new PDBEntry();
MCview.PDBfile pdbfile = null;
- try
+ pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, choice, protocol);
+ if (pdbfile == null)
{
- // 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);
- }
- if (reply == null)
- {
- return null;
- }
+ // stacktrace already thrown so just return
+ return null;
+ }
+ if (pdbfile.id == null)
+ {
+ String reply = null;
- entry.setId(reply);
+ 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);
}
- else
+ if (reply == null)
{
- entry.setId(pdbfile.id);
+ return null;
}
- } catch (java.io.IOException ex)
+ entry.setId(reply);
+ }
+ else
{
- ex.printStackTrace();
+ entry.setId(pdbfile.id);
}
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ if (pdbfile != null)
+ {
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ StructureSelectionManager.getStructureSelectionManager(ssmp)
+ .registerPDBEntry(entry);
+ }
return entry;
}
}