inprogress

[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 394c4f6..89ce71c 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -215,8 +215,8 @@ 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                                                                   = "2.403";
-    final static private String                                     PRG_DATE                                                                      = "131127";
+    final static private String                                     PRG_VERSION                                                                   = "2.404";
+    final static private String                                     PRG_DATE                                                                      = "140319";
     final static private String                                     E_MAIL                                                                        = "czmasek@burnham.org";
     final static private String                                     WWW                                                                           = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
     final static private boolean                                    IGNORE_DUFS_DEFAULT                                                           = true;
@@ -379,9 +379,9 @@ public class surfacing {
         if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
             output_binary_domain_combinationsfor_graph_analysis = true;
         }
-        final boolean output_binary_domain_combinationsfor_counts = false;
+        boolean output_binary_domain_combinationsfor_counts = false;
         if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) {
-            output_binary_domain_combinationsfor_graph_analysis = true;
+            output_binary_domain_combinationsfor_counts = true;
         }
         if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) {
             try {
@@ -1817,7 +1817,8 @@ public class surfacing {
         final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
                                                                                      sort_by_species_count_first,
                                                                                      number_of_genomes == 2,
-                                                                                     CALC_SIMILARITY_SCORES );
+                                                                                     CALC_SIMILARITY_SCORES,
+                                                                                     true );
         switch ( scoring ) {
             case COMBINATIONS:
                 pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
@@ -2061,7 +2062,8 @@ public class surfacing {
             SurfacingUtil.writeProteinListsForAllSpecies( out_dir,
                                                           protein_lists_per_species,
                                                           gwcd_list,
-                                                          output_list_of_all_proteins_per_domain_e_value_max );
+                                                          output_list_of_all_proteins_per_domain_e_value_max,
+                                                          positive_filter_file != null ? filter : null );
         }
         gwcd_list = null;
         if ( all_bin_domain_combinations_gained_fitch != null ) {
@@ -2194,16 +2196,9 @@ public class surfacing {
         System.out.println( DA_ANALYSIS_OPTION + ": to perform DA analysis" );
         System.out.println( PERFORM_DOMAIN_LENGTH_ANALYSIS_OPTION + ": to perform domain length analysis" );
         System.out.println();
-        System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
-                + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
-                + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o "
-                + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
         System.out.println();
-        System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
-                + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
-                + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
-                + "-dc_sort=dom -ignore_with_self -no_singles -ie=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
-                + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
+        System.out
+                .println( "Example: surfacing -p2g=pfam2go_130621.txt -obo=gene_onotology_130621.obo -species_tree=tol_156.xml -last -detail=punctilious -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();
     }
 }