X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FPairwiseGenomeComparator.java;h=ed4eae73769feba8241f994b8aff130554b6ab49;hb=d605114bdf420c6cb680b02bb10ea25f09db769c;hp=b23f82b9ec058b0bfc94a74210acb274fda9e4ab;hpb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index b23f82b..ed4eae7 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -96,9 +96,9 @@ public class PairwiseGenomeComparator {
                                             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 );
-        final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix domain_distance_scores_means = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+        final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
         if ( verbose ) {
             System.out.println();
             System.out.println( "Pairwise genome distances:" );
@@ -264,8 +264,8 @@ public class PairwiseGenomeComparator {
             final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
                                                                                   jacknife_ratio,
                                                                                   generator );
-            final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
-            final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
+            final DistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
             for( int i = 0; i < number_of_genomes; ++i ) {
                 final String species_i = species[ i ].getSpeciesId();
                 shared_domains_based_distances.setIdentifier( i, species_i );