// 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));
+ "xml");
+ Vector<UniprotEntry> entries = getUniprotEntries(
+ new FileReader(file));
if (entries != null)
{
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();
if ("EMBL".equals(pdb.getType()))
{
// look for a CDS reference and add it, too.
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ String cdsId = (String) pdb.getProperty("protein sequence ID");
if (cdsId != null && cdsId.trim().length() > 0)
{
// remove version
* <property type="gene ID" value="ENSG00000158828"/>
* </dbReference>
*/
- String cdsId = (String) pdb.getProperty()
- .get("protein sequence ID");
+ 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);
}