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 b3c1446..fc98702 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -1625,7 +1625,7 @@ public class surfacing {
         if ( need_protein_lists_per_species ) {
             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
         }
-        final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
+        List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
         final SortedSet<String> all_domains_encountered = new TreeSet<String>();
         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
@@ -2276,6 +2276,7 @@ public class surfacing {
                                             gwcd_list,
                                             output_list_of_all_proteins_per_domain_e_value_max );
         }
+        gwcd_list = null;
         if ( all_bin_domain_combinations_gained_fitch != null ) {
             try {
                 executeFitchGainsAnalysis( new File( output_file
@@ -2521,7 +2522,7 @@ public class surfacing {
         System.out.println( surfacing.USE_LAST_IN_FITCH_OPTION + ": to use last in Fitch parsimony" );
         System.out.println( surfacing.WRITE_TO_NEXUS_OPTION + ": to output in Nexus format" );
         System.out.println( PERFORM_DC_REGAIN_PROTEINS_STATS_OPTION + ": to perform DC regain protein statistics" );
-        System.out.println( DA_ANALYSIS_OPTION + ": to DA analysis" );
+        System.out.println( DA_ANALYSIS_OPTION + ": to do DA 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"