import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
stopQuery();
return null;
}
- String ext = StructureImportSettings.getDefaultStructureFileFormat()
- .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
+ Type pdbFileFormat = StructureImportSettings
+ .getDefaultStructureFileFormat();
+ String ext = "." + pdbFileFormat.getExtension();
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id,
- StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
- ext)
+ file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
.getAbsolutePath();
stopQuery();
if (file == null)
}
try
{
-
+ // convert Type.PDB/MMCIF to FileFormat.PDB/MMCIF
+ // todo get rid of Type?
+ FileFormatI fileFormat = FileFormat.valueOf(pdbFileFormat.toString());
pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- StructureImportSettings.getDefaultStructureFileFormat());
+ DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();