X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=802b1d42e68f091388a6a83f15d076229e9b3bd9;hb=e22f363c7273fc888ef911ad1f20d520a6bf030e;hp=394c4f662fb1a4c5fcaf0546939a573bc36631ae;hpb=bfef347dd10a29b0e95d4a7ca87e997e443f45c4;p=jalview.git

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 394c4f6..802b1d4 100644
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -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 {
@@ -2061,7 +2061,8 @@ 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 ) {