From 1472d0ec482c8642dab9336b17041e6e398acb78 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 27 Nov 2013 21:18:16 +0000
Subject: [PATCH] inprogress

---
 .../src/org/forester/application/surfacing.java     |    7 ++++---
 .../src/org/forester/surfacing/SurfacingUtil.java   |   19 +++++++++++++++----
 2 files changed, 19 insertions(+), 7 deletions(-)

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 ) {
diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 1433d70..e646ba4 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -1886,9 +1886,16 @@ public final class SurfacingUtil {
         catch ( final IOException e ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
         }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
-                + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
-                + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        if ( input_file_properties[ i ].length == 3 ) {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+                    + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        }
+        else {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+                    + dc_outfile_dot + "\"" );
+        }
     }
 
     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
@@ -2511,12 +2518,16 @@ public final class SurfacingUtil {
     public static void writeProteinListsForAllSpecies( final File output_dir,
                                                        final SortedMap<Species, List<Protein>> protein_lists_per_species,
                                                        final List<GenomeWideCombinableDomains> gwcd_list,
-                                                       final double domain_e_cutoff ) {
+                                                       final double domain_e_cutoff,
+                                                       final Set<String> pos_filter_doms ) {
         final SortedSet<String> all_domains = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
             all_domains.addAll( gwcd.getAllDomainIds() );
         }
         for( final String domain : all_domains ) {
+            if ( !ForesterUtil.isEmpty( pos_filter_doms ) && !pos_filter_doms.contains( domain ) ) {
+                continue;
+            }
             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
             checkForOutputFileWriteability( out );
             try {
-- 
1.7.10.2