in progress

[jalview.git] / forester / java / src / org / forester / application / surfacing_hmmpfam.java

diff --git a/forester/java/src/org/forester/application/surfacing_hmmpfam.java b/forester/java/src/org/forester/application/surfacing_hmmpfam.java
index 8a1a107..476640b 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing_hmmpfam.java
+++ b/forester/java/src/org/forester/application/surfacing_hmmpfam.java
@@ -52,6 +52,7 @@ import org.forester.go.OBOparser;
 import org.forester.go.PfamToGoMapping;
 import org.forester.go.PfamToGoParser;
 import org.forester.io.parsers.HmmPfamOutputParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
@@ -495,7 +496,7 @@ public class surfacing_hmmpfam {
             }
             try {
                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
-                        .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+                        .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
                 if ( p_array.length < 1 ) {
                     ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
                             + "] does not contain any phylogeny in phyloXML format" );
@@ -1973,6 +1974,7 @@ public class surfacing_hmmpfam {
                     .writeDomainSimilaritiesToFile( html_desc,
                                                     new StringBuilder( number_of_genomes + " genomes" ),
                                                     writer,
+                                                    null,
                                                     similarities,
                                                     number_of_genomes == 2,
                                                     species_order,