+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*/
package jalview.ws.dbsources;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import com.stevesoft.pat.Regex;
*/
public class Pdb extends EbiFileRetrievedProxy
{
+ private static final String SEPARATOR = "|";
+ private static final String COLON = ":";
+ private static final int PDB_ID_LENGTH = 4;
+
+
public Pdb()
{
super();
@Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
- Vector result = new Vector();
String chain = null;
String id = null;
- if (queries.indexOf(":") > -1)
+ if (queries.indexOf(COLON) > -1)
{
- chain = queries.substring(queries.indexOf(":") + 1);
- id = queries.substring(0, queries.indexOf(":"));
+ chain = queries.substring(queries.indexOf(COLON) + 1);
+ id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
- if (queries.length() > 4 && chain == null)
+
+ /*
+ * extract chain code if it is appended to the id and we
+ * don't already have one
+ */
+ if (queries.length() > PDB_ID_LENGTH && chain == null)
{
- chain = queries.substring(4, 5);
- id = queries.substring(0, 4);
+ chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+ id = queries.substring(0, PDB_ID_LENGTH);
}
+
if (!isValidReference(id))
{
System.err.println("Ignoring invalid pdb query: '" + id + "'");
stopQuery();
return null;
}
+ String ext = StructureImportSettings.getDefaultStructureFileFormat()
+ .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ file = ebi.fetchDataAsFile("pdb:" + id,
+ StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
+ ext)
+ .getAbsolutePath();
stopQuery();
if (file == null)
{
{
pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE, "PDB");
+ jalview.io.AppletFormatAdapter.FILE,
+ StructureImportSettings.getDefaultStructureFileFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
chid = pid.getChainCode();
}
- ;
-
}
if (chain == null
|| (chid != null && (chid.equals(chain)
|| chid.trim().equals(chain.trim()) || (chain
.trim().length() == 0 && chid.equals("_")))))
{
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
- + "|" + pdbcs.getName());
+ // 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 + SEPARATOR + id
+ + SEPARATOR + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
@Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
@Override
{
return 0;
}
+
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}