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[jalview.git] / forester / java / src / org / forester / sdi / SDIutil.java

diff --git a/forester/java/src/org/forester/sdi/SDIutil.java b/forester/java/src/org/forester/sdi/SDIutil.java
index 5526618..4e12ae6 100644 (file)
--- 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;
@@ -70,8 +72,8 @@ 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 )
-            throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
+                                                    final TAXONOMY_EXTRACTION taxonomy_extraction_in_nhx_trees )
+                                                            throws FileNotFoundException, PhyloXmlDataFormatException, IOException, SDIException {
         Phylogeny species_tree;
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
         final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
@@ -85,15 +87,21 @@ 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 );
             switch ( comp_base ) {
                 case SCIENTIFIC_NAME:
                     PhylogenyMethods
-                            .transferNodeNameToField( species_tree,
-                                                      PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
-                                                      true );
+                    .transferNodeNameToField( species_tree,
+                                              PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+                                              true );
                     break;
                 case CODE:
                     PhylogenyMethods.transferNodeNameToField( species_tree,