in progress

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" );
                         }

diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java
index 6ff9c10..71246dd 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterConstants.java
+++ b/forester/java/src/org/forester/util/ForesterConstants.java
@@ -27,7 +27,7 @@ package org.forester.util;
 
 public final class ForesterConstants {
 
-    public final static String  FORESTER_VERSION            = "1.007";
+    public final static String  FORESTER_VERSION            = "1.007+";
     public final static String  FORESTER_DATE               = "121130";
     public final static String  PHYLO_XML_VERSION           = "1.10";
     public final static String  PHYLO_XML_LOCATION          = "http://www.phyloxml.org";

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index 5c1cc73..b56a633 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -121,20 +121,16 @@ public final class SequenceDbWsTools {
                                                                          final int max_taxonomies_return )
             throws IOException {
         // Hack!  Craniata? .. 
-        // if ( sn.equals( "Drosophila" ) ) {
-        //     return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS );
-        // }
-        /* else*/if ( sn.equals( "Xenopus" ) ) {
+        if ( sn.equals( "Drosophila" ) ) {
+            return uniProtTaxonomyToList( UniProtTaxonomy.DROSOPHILA_GENUS );
+        }
+        else if ( sn.equals( "Xenopus" ) ) {
             return uniProtTaxonomyToList( UniProtTaxonomy.XENOPUS_GENUS );
         }
         // else if ( sn.equals( "Nucleariidae and Fonticula group" ) ) {
         //     return hack( UniProtTaxonomy.NUCLEARIIDAE_AND_FONTICULA );
         // }
         final List<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
-        System.out.println( "SN=" + sn );
-        for( final String string : result ) {
-            System.out.println( "|" + string );
-        }
         if ( result.size() > 0 ) {
             return parseUniProtTaxonomy( result );
         }

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
index 145569d..0884a6f 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java
@@ -45,8 +45,9 @@ public final class UniProtTaxonomy {
     public final static String          CELLULAR_ORGANISMS       = "cellular organisms";
     public final static String          VIRUSES                  = "Viruses";
     public final static UniProtTaxonomy DROSOPHILA_GENUS         = new UniProtTaxonomy( new String[] {
-            CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota", "Neoptera",
-            "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae", "Drosophila" },
+            CELLULAR_ORGANISMS, EUKARYOTA, "Metazoa", "Ecdysozoa", "Arthropoda", "Hexapoda", "Insecta", "Pterygota",
+            "Neoptera", "Endopterygota", "Diptera", "Brachycera", "Muscomorpha", "Ephydroidea", "Drosophilidae",
+            "Drosophila"                                                               },
                                                                                         "",
                                                                                         "fruit flies",
                                                                                         "Drosophila",
@@ -72,8 +73,6 @@ public final class UniProtTaxonomy {
                                                                                         "species",
                                                                                         "283909" );
 
-    // public final static UniProtTaxonomy NUCLEARIIDAE_AND_FONTICULA = new UniProtTaxonomy( new String[] {
-    //         CELLULAR_ORGANISMS, EUKARYOTA, "Nucleariidae and Fonticula group" }, "", "", "", "", "", "1001604" );
     public UniProtTaxonomy( final String line ) {
         final String[] items = line.split( "\t" );
         if ( items.length < 5 ) {