From 4e57c7dc6990ca5d36f8df6fdbd9c7917da87623 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Sun, 22 Apr 2012 06:33:35 +0000 Subject: [PATCH 1/1] some fixes --- forester/java/src/org/forester/application/surfacing.java | 4 ++-- forester/java/src/org/forester/surfacing/SurfacingUtil.java | 7 ++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 62c6981..ee93bbc 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -234,8 +234,8 @@ public class surfacing { final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; final static private String SEQ_EXTRACT_OPTION = "prot_extract"; final static private char SEPARATOR_FOR_INPUT_VALUES = '#'; - final static private String PRG_VERSION = "2.210"; - final static private String PRG_DATE = "2012.02.21"; + final static private String PRG_VERSION = "2.230"; + final static private String PRG_DATE = "2012.04.21"; final static private String E_MAIL = "czmasek@burnham.org"; final static private String WWW = "www.phylosoft.org/forester/applications/surfacing"; final static private boolean IGNORE_DUFS_DEFAULT = true; diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 9118dd4..24823a4 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -105,11 +105,12 @@ public final class SurfacingUtil { } }; public final static Pattern PATTERN_SP_STYLE_TAXONOMY = Pattern.compile( "^[A-Z0-9]{3,5}$" ); + private static final boolean USE_LAST = true; private SurfacingUtil() { // Hidden constructor. } - + public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome, final SortedSet binary_domain_combinations ) { final SortedMap all_cd = genome.getAllCombinableDomainsIds(); @@ -673,7 +674,7 @@ public final class SurfacingUtil { randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony; } else { - domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( true ); + domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST ); } SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER ); @@ -847,7 +848,7 @@ public final class SurfacingUtil { local_phylogeny_copy = phylogeny.copy(); String randomization = "no"; - secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( true ); + secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST ); -- 1.7.10.2