+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
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 currentDefaultFormat = DBRefSource.PDB;
-
/*
* (non-Javadoc)
*
stopQuery();
return null;
}
- String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
+ String ext = StructureImportSettings.getCurrentDefaultFormat()
+ .equalsIgnoreCase("mmcif") ? ".cif"
: ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFormat().toLowerCase(), "raw", ext)
+ StructureImportSettings.getCurrentDefaultFormat().toLowerCase(),
+ ext)
.getAbsolutePath();
stopQuery();
if (file == null)
{
pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFormat());
+ jalview.io.DataSourceType.FILE,
+ StructureImportSettings.getCurrentDefaultFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
@Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
@Override
return 0;
}
- public static String getCurrentDefaultFormat()
- {
- return currentDefaultFormat;
- }
-
- public static void setCurrentDefaultFormat(String currentDefaultFomart)
- {
- Pdb.currentDefaultFormat = currentDefaultFomart;
- }
/**
* Returns a descriptor for suitable feature display settings with