X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fanalysis%2FAncestralTaxonomyInference.java;h=11d678d323ea2bc092f05866a6a4d5807db861e6;hb=e22f363c7273fc888ef911ad1f20d520a6bf030e;hp=6b036ef2d1ae6fd6767f5758021074a053ff43fe;hpb=01586b5c6a1d65eeb20e144b5f858b9742079471;p=jalview.git

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 6b036ef..11d678d 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -20,7 +20,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.analysis;
 
@@ -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" );
             }
@@ -135,6 +124,7 @@ public final class AncestralTaxonomyInference {
         if ( last_common_lineage.isEmpty() ) {
             boolean saw_viruses = false;
             boolean saw_cellular_organism = false;
+            boolean saw_x = false;
             for( final String[] lineage : lineages ) {
                 if ( lineage.length > 0 ) {
                     if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.VIRUSES ) ) {
@@ -143,14 +133,17 @@ public final class AncestralTaxonomyInference {
                     else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.CELLULAR_ORGANISMS ) ) {
                         saw_cellular_organism = true;
                     }
-                    if ( saw_cellular_organism && saw_viruses ) {
+                    else if ( lineage[ 0 ].equalsIgnoreCase( UniProtTaxonomy.X ) ) {
+                        saw_x = true;
+                    }
+                    if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
                         break;
                     }
                 }
             }
-            if ( saw_cellular_organism && saw_viruses ) {
-                last_common_lineage.add( UniProtTaxonomy.CELLULAR_ORGANISMS );
-                last_common = UniProtTaxonomy.CELLULAR_ORGANISMS;
+            if ( ( saw_cellular_organism && saw_viruses ) || saw_x ) {
+                last_common_lineage.add( UniProtTaxonomy.X );
+                last_common = UniProtTaxonomy.X;
             }
             else {
                 String msg = "no common lineage for:\n";