X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FSDIutil.java;h=077f81852bc97a376063db619750f845e1335d0f;hb=4f293d657212059c78fb7649e330842bfea5909a;hp=55266189b30dcbc589fd4752152bd7df8c4e72b5;hpb=99c1b5211c817dbe35a646589d9c4dbf508b8d50;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/SDIutil.java b/forester/java/src/org/forester/sdi/SDIutil.java
index 5526618..077f818 100644
--- a/forester/java/src/org/forester/sdi/SDIutil.java
+++ b/forester/java/src/org/forester/sdi/SDIutil.java
@@ -6,7 +6,9 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.io.parsers.util.ParserUtils;
@@ -70,7 +72,7 @@ public class SDIutil {
                                                     final File species_tree_file,
                                                     final boolean replace_undescores_in_nhx_trees,
                                                     final boolean ignore_quotes_in_nhx_trees,
-                                                    final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
+                                                    final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
             throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
         Phylogeny species_tree;
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
@@ -85,6 +87,12 @@ public class SDIutil {
                 nhx.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
                 nhx.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
             }
+            else if ( p instanceof NexusPhylogeniesParser ) {
+                final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
+                nex.setReplaceUnderscores( replace_undescores_in_nhx_trees );
+                nex.setIgnoreQuotes( ignore_quotes_in_nhx_trees );
+                nex.setTaxonomyExtraction( taxonomy_extraction_in_nhx_trees );
+            }
             species_tree = factory.create( species_tree_file, p )[ 0 ];
             species_tree.setRooted( true );
             final TaxonomyComparisonBase comp_base = determineTaxonomyComparisonBase( gene_tree );