X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing_hmmpfam.java;h=476640b450e48760d3fe5372f3af3a04948e2f00;hb=5c10c6e6d65f086e4a021d358314f377bb97342d;hp=eeeb5bb99eb2aa49e118c0e17d760523423a4477;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/application/surfacing_hmmpfam.java b/forester/java/src/org/forester/application/surfacing_hmmpfam.java
index eeeb5bb..476640b 100644
--- 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,
@@ -2017,7 +2019,6 @@ public class surfacing_hmmpfam {
                                              true,
                                              surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
                                              surfacing_hmmpfam.PRG_NAME,
-                                             display_histograms,
                                              out_dir,
                                              write_pwc_files );
             String matrix_output_file = new String( output_file.toString() );