import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import javax.swing.JOptionPane;
-
/**
* GUI related routines for associating PDB files with sequences
*
* @param choice
* @param sequence
*/
- public PDBEntry associatePdbWithSeq(String choice, String protocol,
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
SequenceI sequence, boolean prompt,
StructureSelectionManagerProvider ssmp)
{
+ return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
+ TFType.DEFAULT, null, true);
+ }
+
+ public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
+ SequenceI sequence, boolean prompt,
+ StructureSelectionManagerProvider ssmp, TFType tft,
+ String paeFilename, boolean doXferSettings)
+ {
PDBEntry entry = new PDBEntry();
- StructureFile pdbfile = null;
- pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
- .setMapping(false, new SequenceI[] { sequence }, null, choice,
- protocol);
+ StructureFile pdbfile = StructureSelectionManager
+ .getStructureSelectionManager(ssmp)
+ .setMapping(false, new SequenceI[]
+ { sequence }, null, choice, file, tft, paeFilename,
+ doXferSettings);
if (pdbfile == null)
{
// stacktrace already thrown so just return
sequence.getDatasetSequence().addPDBId(entry);
StructureSelectionManager.getStructureSelectionManager(ssmp)
.registerPDBEntry(entry);
+ entry.setStructureFile(pdbfile);
}
+ if (tft != null)
+ entry.setProperty("TFType", tft.name());
+ if (paeFilename != null)
+ entry.setProperty("PAEFile", paeFilename);
return entry;
}
}