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

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index c7319e0..fc87a96 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -217,9 +217,9 @@ 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                                     E_MAIL                                                                        = "czmasek@burnham.org";
+    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;
     final static private boolean                                    IGNORE_COMBINATION_WITH_SAME_DEFAULLT                                         = false;
@@ -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,
@@ -2212,7 +2215,7 @@ public class surfacing {
         ForesterUtil.programMessage( PRG_NAME, surfacing.WWW );
         ForesterUtil
                 .programMessage( PRG_NAME,
-                                 "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs ../../genome_locations.txt]" );
+                                 "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
         ForesterUtil.programMessage( PRG_NAME, "OK" );
         System.out.println();
     }
@@ -2308,5 +2311,11 @@ public class surfacing {
         System.out
                 .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
         System.out.println();
+        System.out
+                .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]" );
+        System.out.println();
     }
 }