cleanup

[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 5bd7d7b..847a8db 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -178,7 +178,7 @@ public class surfacing {
     final static private String                                     NO_ENGULFING_OVERLAP_OPTION                                                   = "no_eo";
     final static private String                                     IGNORE_COMBINATION_WITH_SAME_OPTION                                           = "ignore_self_comb";
     final static private String                                     PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION                                       = "dc_regain_stats";
-    final static private String                                     DA_ANALYSIS_OPTION                                                            = "DA_analyis";
+    final static private String                                     DA_ANALYSIS_OPTION                                                            = "da_analyis";
     final static private String                                     USE_LAST_IN_FITCH_OPTION                                                      = "last";
     public final static String                                      PAIRWISE_DOMAIN_COMPARISONS_PREFIX                                            = "pwc_";
     final static private String                                     PAIRWISE_DOMAIN_COMPARISONS_OPTION                                            = "pwc";
@@ -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 ) {