import org.forester.util.TaxonomyUtil;
import org.forester.ws.seqdb.SequenceDbWsTools;
import org.forester.ws.seqdb.UniProtTaxonomy;
-import org.forester.archaeopteryx.*;
public final class TaxonomyDataManager extends RunnableProcess {
CODE, SN, CN, ID, LIN;
}
private static final int MAX_CACHE_SIZE = 100000;
- private static final int MAX_TAXONOMIES_TO_RETURN = 10;
+ private static final int MAX_TAXONOMIES_TO_RETURN = 2000;
private static final HashMap<String, UniProtTaxonomy> _sn_up_cache_map = new HashMap<String, UniProtTaxonomy>();
private static final HashMap<String, UniProtTaxonomy> _lineage_up_cache_map = new HashMap<String, UniProtTaxonomy>();
private static final HashMap<String, UniProtTaxonomy> _code_up_cache_map = new HashMap<String, UniProtTaxonomy>();
}
private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
- if ( query.indexOf( "XX" ) == 3 && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
+ if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
-
}
-
return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
}