"rio" work

[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 50cd1cc..2bc654f 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -335,7 +335,6 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     .get( lineage.size() - 1 ) );
             if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
                 for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
-                    System.out.println( "up_taxonomy=" + up_taxonomy.getScientificName() );
                     boolean match = true;
                     I: for( int i = 0; i < lineage.size(); ++i ) {
                         if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {
@@ -345,6 +344,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     }
                     if ( match ) {
                         if ( up_tax != null ) {
+                            //TODO this is dead code?!
                             throw new AncestralTaxonomyInferenceException( "lineage \""
                                     + ForesterUtil.stringListToString( lineage, " > " ) + "\" is not unique" );
                         }