work for rrm project (ComPhy 2012 Moscow)

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

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 6999f8b..5a6a32a 100644 (file)
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -35,13 +35,13 @@ 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.seqdb.UniProtTaxonomy;
 
 public final class AncestralTaxonomyInference {
 
     public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
             AncestralTaxonomyInferenceException {
-        TaxonomyDataObtainer.clearCachesIfTooLarge();
+        TaxonomyDataManager.clearCachesIfTooLarge();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( !node.isExternal() ) {
@@ -61,12 +61,12 @@ public final class AncestralTaxonomyInference {
         int shortest_lin_length = Integer.MAX_VALUE;
         for( final PhylogenyNode desc : descs ) {
             if ( desc.getNodeData().isHasTaxonomy()
-                    && ( TaxonomyDataObtainer.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
+                    && ( TaxonomyDataManager.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
                             .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                final UniProtTaxonomy up_tax = TaxonomyDataObtainer.obtainUniProtTaxonomy( desc.getNodeData()
+                final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
                         .getTaxonomy(), null, null );
                 if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
                     String desc_str = "";
@@ -103,17 +103,6 @@ public final class AncestralTaxonomyInference {
                 else {
                     node = "[" + desc.getId() + "]";
                 }
-                //   final List<PhylogenyNode> e = desc.getAllExternalDescendants();
-                //TODO remove me!
-                //                System.out.println();
-                //                int x = 0;
-                //                for( final PhylogenyNode object : e ) {
-                //                    System.out.println( x + ":" );
-                //                    System.out.println( object.getName() + "  " );
-                //                    x++;
-                //                }
-                //                System.out.println();
-                //
                 throw new AncestralTaxonomyInferenceException( "node " + node
                         + " has no or inappropriate taxonomic information" );
             }
@@ -169,7 +158,7 @@ public final class AncestralTaxonomyInference {
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
         tax.setScientificName( last_common );
-        final UniProtTaxonomy up_tax = TaxonomyDataObtainer.obtainUniProtTaxonomyFromLineage( last_common_lineage );
+        final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {