+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
public static final String FEATURE_RES_NUM = "RESNUM";
- private static String currentDefaultFomart = DBRefSource.PDB;
-
/*
* (non-Javadoc)
*
stopQuery();
return null;
}
- String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
- : ".xml";
+ String ext = StructureImportSettings.getDefaultStructureFileFormat()
+ .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+ StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
+ ext)
.getAbsolutePath();
stopQuery();
if (file == null)
pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFomart());
+ StructureImportSettings.getDefaultStructureFileFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
|| chid.trim().equals(chain.trim()) || (chain
.trim().length() == 0 && chid.equals("_")))))
{
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
+ "|" + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
@Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
@Override
return 0;
}
- public static String getCurrentDefaultFomart()
- {
- return currentDefaultFomart;
- }
-
- public static void setCurrentDefaultFomart(String currentDefaultFomart)
- {
- Pdb.currentDefaultFomart = currentDefaultFomart;
- }
/**
* Returns a descriptor for suitable feature display settings with