phylotastic hackathon at NESCENT 120608

[jalview.git] / forester / java / src / org / forester / analysis / TaxonomyDataManager.java

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 674c9c6..8f9dcc4 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -38,6 +38,7 @@ import javax.swing.JOptionPane;
 
 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;
@@ -46,8 +47,8 @@ import org.forester.phylogeny.data.Identifier;
 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 {
 
@@ -175,19 +176,19 @@ 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 ) {
@@ -521,7 +522,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final String getBaseUrl() {
-        return UniProtWsTools.BASE_URL;
+        return AncestralTaxonomyInferrer.getBaseUrl();
     }
 
     @Override