some fixes

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 62c6981..ee93bbc 100644 (file)
--- 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 (file)
--- 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<BinaryDomainCombination> binary_domain_combinations ) {
         final SortedMap<DomainId, CombinableDomains> 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 );