+
/*
* 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.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;
-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();
}
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
-
- private static String currentDefaultFormat = DBRefSource.PDB;
-
/*
* (non-Javadoc)
*
@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 = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".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,
- getCurrentDefaultFormat().toLowerCase(), "raw", ext)
- .getAbsolutePath();
+ File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
+ file = tmpFile.getAbsolutePath();
stopQuery();
if (file == null)
{
}
try
{
-
- pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFormat());
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
+ : FileFormat.MMCif;
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
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("_")))))
+ 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
/*
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[] { id,
- ((chain == null) ? "' '" : chain) }));
+ "exception.no_pdb_records_for_chain", new String[]
+ { id, ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file
}
/**
- * 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
* <ul>