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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
394c4f6
..
802b1d4
100644
(file)
--- 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;
}
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 ) ) {
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 {
}
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,
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 ) {
}
gwcd_list = null;
if ( all_bin_domain_combinations_gained_fitch != null ) {