// uniprotxml parameter required since december 2007
// uniprotkb dbname changed introduced december 2008
File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- null);
+ null, ".xml");
Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
if (entries != null)
StringBuilder desc = new StringBuilder(32);
if (entry.getProtein() != null && entry.getProtein().getName() != null)
{
+ boolean first = true;
for (String nm : entry.getProtein().getName())
{
- desc.append(nm).append(" ");
+ if (!first)
+ {
+ desc.append(" ");
+ }
+ first = false;
+ desc.append(nm);
}
}
return desc.toString();
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
- name.append("UniProt/Swiss-Prot");
+ // 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);