import org.forester.archaeopteryx.MainFrameApplication;
import org.forester.archaeopteryx.TreePanel;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
import org.forester.archaeopteryx.tools.RunnableProcess;
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.SequenceDbWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
public final class TaxonomyDataManager extends RunnableProcess {
}
private final static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query ) throws IOException {
- return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
+ return SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
}
private final static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
- return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
+ return SequenceDbWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
}
private final static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
- return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
+ return SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
}
private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
- return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
+ return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
}
static final boolean isHasAppropriateId( final Taxonomy tax ) {
}
private final String getBaseUrl() {
- return UniProtWsTools.BASE_URL;
+ return AncestralTaxonomyInferrer.getBaseUrl();
}
@Override