import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
-import jalview.ws.ebi.EBIFetchClient;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import java.io.File;
-import java.io.FileReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import java.io.Reader;
import java.net.URL;
+import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Vector;
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- EBIFetchClient ebi = new EBIFetchClient();
- // uniprotxml parameter required since december 2007
- // uniprotkb dbname changed introduced december 2008
- File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- ".xml");
- Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
+
+ String downloadstring = "http://www.uniprot.org/uniprot/" + queries
+ + ".xml";
+ URL url = null;
+ URLConnection urlconn = null;
+
+ url = new URL(downloadstring);
+ urlconn = url.openConnection();
+ InputStream istr = urlconn.getInputStream();
+ Vector<UniprotEntry> entries = getUniprotEntries(
+ new InputStreamReader(istr, "UTF-8"));
if (entries != null)
{
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> seqs = new ArrayList<>();
for (UniprotEntry entry : entries)
{
seqs.add(uniprotEntryToSequenceI(entry));
return al;
} catch (Exception e)
{
- stopQuery();
throw (e);
+ } finally
+ {
+ stopQuery();
}
}
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
String id = getUniprotEntryId(entry);
- SequenceI sequence = new Sequence(id, entry.getUniprotSequence()
- .getContent());
+ SequenceI sequence = new Sequence(id,
+ entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+ ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
dbRefs.add(dbRef);
}
- Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+ Vector<PDBEntry> onlyPdbEntries = new Vector<>();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
- dbr = new DBRefEntry(DBRefSource.ENSEMBL, DBRefSource.UNIPROT
- + ":" + dbVersion, cdsId.trim());
+ dbr = new DBRefEntry(DBRefSource.ENSEMBL,
+ DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
dbRefs.add(dbr);
}
}
-
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
- for (SequenceFeature sf : entry.getFeature())
+ for (UniprotFeature uf : entry.getFeature())
{
- sf.setFeatureGroup("Uniprot");
- sequence.addSequenceFeature(sf);
+ SequenceFeature copy = new SequenceFeature(uf.getType(),
+ uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+ copy.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(copy);
}
}
for (DBRefEntry dbr : dbRefs)
/**
*
* @param entry
- * UniportEntry
+ * UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
- // name.append("UniProt/Swiss-Prot");
- // use 'canonicalised' name for optimal id matching
- name.append(DBRefSource.UNIPROT);
- for (String accessionId : entry.getAccession())
- {
- name.append(BAR_DELIMITER);
- name.append(accessionId);
- }
for (String n : entry.getName())
{
- name.append(BAR_DELIMITER);
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
name.append(n);
}
return name.toString();