X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPairwiseGenomeComparator.java;h=a3b0e668cf8f42f86431e5f9dccf93db19c31452;hb=4aaa7b9109d4a4d7ed9c2f6cbba7c960a81a9ed0;hp=e9ee8b3d4864eb0d8507ff56473c496a5be65c80;hpb=f47d5c382bc4e329ff6977ebcc46b75b57ffc901;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index e9ee8b3..a3b0e66 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -43,6 +43,7 @@ import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
+import org.forester.phylogeny.Phylogeny;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.util.DescriptiveStatistics;
@@ -51,10 +52,9 @@ import org.forester.util.ForesterUtil;
 public class PairwiseGenomeComparator {
 
     private List<DistanceMatrix> _domain_distance_scores_means;
-    private List<DistanceMatrix> _shared_domains_based_distances;
     private List<DistanceMatrix> _shared_binary_combinations_based_distances;
+    private List<DistanceMatrix> _shared_domains_based_distances;
 
-    //private List<HistogramData>  _histogram_datas;
     public PairwiseGenomeComparator() {
         init();
     }
@@ -63,9 +63,6 @@ public class PairwiseGenomeComparator {
         return _domain_distance_scores_means;
     }
 
-    //public List<HistogramData> getHistogramDatas() {
-    //    return _histogram_datas;
-    //}
     public List<DistanceMatrix> getSharedBinaryCombinationsBasedDistances() {
         return _shared_binary_combinations_based_distances;
     }
@@ -74,20 +71,13 @@ public class PairwiseGenomeComparator {
         return _shared_domains_based_distances;
     }
 
-    private void init() {
-        //_histogram_datas = new ArrayList<HistogramData>();
-        _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
-        _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
-        _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
-    }
-
     public void performPairwiseComparisons( final StringBuilder html_desc,
                                             final boolean sort_by_species_count_first,
                                             final Detailedness detailedness,
                                             final boolean ignore_domains_without_combs_in_all_spec,
                                             final boolean ignore_domains_specific_to_one_species,
                                             final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
-                                            final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+                                            final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                             final DomainSimilarity.DomainSimilarityScoring scoring,
                                             final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                             final Map<GoId, GoTerm> go_id_to_term_map,
@@ -102,7 +92,9 @@ public class PairwiseGenomeComparator {
                                             final String command_line_prg_name,
                                             final File out_dir,
                                             final boolean write_pairwise_comparisons,
-                                            final Map<String, Integer> tax_code_to_id_map ) {
+                                            final Map<String, Integer> tax_code_to_id_map,
+                                            final boolean calc_similarity_scores,
+                                            final Phylogeny phy ) {
         init();
         final BasicSymmetricalDistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
         final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
@@ -146,7 +138,8 @@ public class PairwiseGenomeComparator {
                 }
                 final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
                                                                                              sort_by_species_count_first,
-                                                                                             true );
+                                                                                             true,
+                                                                                             calc_similarity_scores );
                 final SortedSet<DomainSimilarity> similarities = calc
                         .calculateSimilarities( pw_calc,
                                                 genome_pair,
@@ -203,39 +196,30 @@ public class PairwiseGenomeComparator {
                         }
                         break;
                 }
-                DescriptiveStatistics pw_stats = null;
                 if ( write_pairwise_comparisons ) {
                     try {
                         final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? pairwise_similarities_output_file_str
                                 : out_dir + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
-                        pw_stats = SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
-                                                                                new StringBuilder( species_i + "-"
-                                                                                        + species_j ),
-                                                                                writer,
-                                                                                null,
-                                                                                similarities,
-                                                                                true,
-                                                                                null,
-                                                                                domain_similarity_print_option,
-                                                                                scoring,
-                                                                                false,
-                                                                                tax_code_to_id_map,
-                                                                                false );
+                        SurfacingUtil.writeDomainSimilaritiesToFile( html_desc,
+                                                                     new StringBuilder( species_i + "-" + species_j ),
+                                                                     null,
+                                                                     writer,
+                                                                     null,
+                                                                     similarities,
+                                                                     true,
+                                                                     null,
+                                                                     domain_similarity_print_option,
+                                                                     scoring,
+                                                                     false,
+                                                                     tax_code_to_id_map,
+                                                                     phy,
+                                                                     null );
                     }
                     catch ( final IOException e ) {
                         ForesterUtil.fatalError( command_line_prg_name, "Failed to write similarites to: \""
                                 + pairwise_similarities_output_file_str + "\" [" + e.getMessage() + "]" );
                     }
                 }
-                if ( pw_stats != null ) {
-                    if ( pw_stats.getMin() >= pw_stats.getMax() ) {
-                        ForesterUtil
-                                .printWarningMessage( command_line_prg_name, "for [" + species_i + "-" + species_j
-                                        + "] score minimum is [" + pw_stats.getMin() + "] while score maximum is ["
-                                        + pw_stats.getMax()
-                                        + "], possibly indicating that a genome is compared to itself" );
-                    }
-                }
             }
         }
         getDomainDistanceScoresMeans().add( domain_distance_scores_means );
@@ -309,6 +293,12 @@ public class PairwiseGenomeComparator {
         }
     }
 
+    private void init() {
+        _domain_distance_scores_means = new ArrayList<DistanceMatrix>();
+        _shared_domains_based_distances = new ArrayList<DistanceMatrix>();
+        _shared_binary_combinations_based_distances = new ArrayList<DistanceMatrix>();
+    }
+
     static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
         String[] all_domain_ids_array;
         final SortedSet<String> all_domain_ids = new TreeSet<String>();