X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fphyloxml_converter.java;h=164bfeef1fc2d2f81a4ef8f1159ecebde56e43eb;hb=299c529fea070487998aee60ed7810af57f3a071;hp=8951e18bd38d80752984a6cf6db830fd19908aee;hpb=8161eb0ffe094f29eeefbb4e71eabcd0884c5e63;p=jalview.git

diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java
index 8951e18..164bfee 100644
--- a/forester/java/src/org/forester/application/phyloxml_converter.java
+++ b/forester/java/src/org/forester/application/phyloxml_converter.java
@@ -22,7 +22,7 @@
 // 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.application;
 
@@ -210,16 +210,17 @@ public class phyloxml_converter {
                         && ( field != PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
                     if ( extr_taxonomy_pf_only ) {
                         ( ( NHXParser ) parser )
-                                .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
                         replace_underscores = false;
                     }
                     else if ( extr_taxonomy ) {
-                        ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+                        ( ( NHXParser ) parser )
+                                .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
                         replace_underscores = false;
                     }
                 }
                 else {
-                    ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+                    ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
                 }
                 ( ( NHXParser ) parser ).setReplaceUnderscores( replace_underscores );
                 ( ( NHXParser ) parser ).setIgnoreQuotes( ignore_quotes );