+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
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;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
+import java.io.File;
import java.util.ArrayList;
import java.util.List;
stopQuery();
return null;
}
- String ext = StructureImportSettings.getDefaultStructureFileFormat()
- .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
+
+ /*
+ * ensure that an mmCIF format structure file is saved with extension.cif,
+ * because the Chimera "open" command recognises this extension
+ */
+ Type pdbFileFormat = StructureImportSettings
+ .getDefaultStructureFileFormat();
+ String ext = pdbFileFormat.getExtension();
+ String fetchFormat = pdbFileFormat.getFormat();
+
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile(
- "pdb:" + id,
- StructureImportSettings.getDefaultStructureFileFormat()
- .toLowerCase(), ext).getAbsolutePath();
+ File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
+ file = tmpFile.getAbsolutePath();
stopQuery();
if (file == null)
{
}
try
{
-
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
+ : FileFormat.MMCif;
pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- StructureImportSettings.getDefaultStructureFileFormat());
+ DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();