X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=fc87a9686df8ee10eca0cf2d1d47e2e947b7c211;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=b9d544c8739eb31a13796c57de3532fd5e4e8c15;hpb=9355a2b6f0e6b0192ceef9fa31b11a9233b298ab;p=jalview.git

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index b9d544c..fc87a96 100644
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -217,8 +217,8 @@ public class surfacing {
     final static private String                                     INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                                     INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                                     SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private String                                     PRG_VERSION                                                                   = "2.501";
-    final static private String                                     PRG_DATE                                                                      = "170327";
+    final static private String                                     PRG_VERSION                                                                   = "2.503";
+    final static private String                                     PRG_DATE                                                                      = "170518";
     final static private String                                     E_MAIL                                                                        = "phyloxml@gmail.com";
     final static private String                                     WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
     final static private boolean                                    IGNORE_DUFS_DEFAULT                                                           = true;
@@ -1776,9 +1776,11 @@ public class surfacing {
         ForesterUtil
                 .programMessage( PRG_NAME,
                                  "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
+        final int LEVEL = 0;
         try {
             MinimalDomainomeCalculator.calc( false,
                                              intrees[ 0 ],
+                                             LEVEL,
                                              protein_lists_per_species,
                                              SEPARATOR_FOR_DA,
                                              -1,
@@ -1791,6 +1793,7 @@ public class surfacing {
         try {
             MinimalDomainomeCalculator.calc( true,
                                              intrees[ 0 ],
+                                             LEVEL,
                                              protein_lists_per_species,
                                              SEPARATOR_FOR_DA,
                                              -1,
@@ -2312,7 +2315,7 @@ public class surfacing {
                 .println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" );
         System.out.println();
         System.out
-        .println("[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
+                .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
         System.out.println();
     }
 }