From 60245f183dfaedf3b683e723682efd3cc26000c8 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 3 Jul 2013 20:43:22 +0000
Subject: [PATCH] inprogress

---
 forester/java/src/org/forester/application/surfacing.java          |    3 ++-
 .../java/src/org/forester/surfacing/DomainParsimonyCalculator.java |    4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index b3c1446..295844b 100644
--- 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
diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
index e2db537..4de0b35 100644
--- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
@@ -206,7 +206,7 @@ public final class DomainParsimonyCalculator {
         else {
             states = createMatrixOfBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList() );
         }
-        fitch.execute( getPhylogeny(), states );
+        fitch.execute( getPhylogeny(), states, true );
         setGainLossMatrix( fitch.getGainLossMatrix() );
         setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
         setCost( fitch.getCost() );
@@ -242,7 +242,7 @@ public final class DomainParsimonyCalculator {
         }
         final CharacterStateMatrix<BinaryStates> states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(),
                                                                                                                                   newmap );
-        fitch.execute( getPhylogeny(), states );
+        fitch.execute( getPhylogeny(), states, true );
         setGainLossMatrix( fitch.getGainLossMatrix() );
         setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() );
         setCost( fitch.getCost() );
-- 
1.7.10.2