From: cmzmasek@gmail.com Date: Wed, 3 Jul 2013 20:43:22 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=60245f183dfaedf3b683e723682efd3cc26000c8;p=jalview.git inprogress --- 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>(); } - final List gwcd_list = new ArrayList( number_of_genomes ); + List gwcd_list = new ArrayList( number_of_genomes ); final SortedSet all_domains_encountered = new TreeSet(); final SortedSet all_bin_domain_combinations_encountered = new TreeSet(); List 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 states = createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( getGenomeWideCombinableDomainsList(), newmap ); - fitch.execute( getPhylogeny(), states ); + fitch.execute( getPhylogeny(), states, true ); setGainLossMatrix( fitch.getGainLossMatrix() ); setBinaryInternalStatesMatrix( fitch.getInternalStatesMatrix() ); setCost( fitch.getCost() );