in progress

[jalview.git] / forester / java / src / org / forester / surfacing / SurfacingUtil.java

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 9118dd4..c0b8b8f 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -71,6 +71,12 @@ import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.protein.BasicProtein;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.Domain;
+import org.forester.protein.DomainId;
+import org.forester.protein.Protein;
+import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
@@ -105,6 +111,7 @@ 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.
@@ -673,7 +680,7 @@ 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 );
@@ -840,18 +847,11 @@ public final class SurfacingUtil {
                           parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
-        
-        
         // FITCH DOMAIN COMBINATIONS
         // -------------------------
-         local_phylogeny_copy = phylogeny.copy();
-        String randomization = "no";
-       
-        secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( true );
-        
-      
-     
-      
+        local_phylogeny_copy = phylogeny.copy();
+        final String randomization = "no";
+        secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
@@ -866,9 +866,8 @@ public final class SurfacingUtil {
                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
-                + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" );
-   
-        
+                + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
+                + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt" );
     }
 
     public static void extractProteinNames( final List<Protein> proteins,
@@ -1161,7 +1160,7 @@ public final class SurfacingUtil {
                                                     final boolean remove_engulfed_domains,
                                                     final Protein protein ) {
         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
-                .getSpeciesId() );
+                .getSpeciesId(), protein.getLength() );
         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
         final List<Boolean> covered_positions = new ArrayList<Boolean>();
         for( final Domain domain : sorted ) {