X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FTestSurfacing.java;h=c2b857c2a602d901bfc4437cf0242ae539aba570;hb=f47b5de663d2ca59a4d53587ea8d5cd20c594db2;hp=4ab0fb0a6e30b50ee63655c9a77925f2a927ff13;hpb=87d34f343d0262cd0c009c6f1da058a5a217bc64;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java
index 4ab0fb0..c2b857c 100644
--- a/forester/java/src/org/forester/surfacing/TestSurfacing.java
+++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java
@@ -327,7 +327,8 @@ public class TestSurfacing {
                                                                            new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                          false,
-                                                                                         false );
+                                                                                         false,
+                                                                                         true );
             final SortedSet<DomainSimilarity> sims = calc
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list,
@@ -477,7 +478,8 @@ public class TestSurfacing {
                                                                             new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc2 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                           false,
-                                                                                          false );
+                                                                                          false,
+                                                                                          true );
             final SortedSet<DomainSimilarity> sims2 = calc2
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list2,
@@ -564,7 +566,8 @@ public class TestSurfacing {
                                                                             new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc3 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                           false,
-                                                                                          false );
+                                                                                          false,
+                                                                                          true );
             final SortedSet<DomainSimilarity> sims3 = calc3
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list3,
@@ -575,7 +578,7 @@ public class TestSurfacing {
             if ( !sa3.getDomainId().equals( "A" ) ) {
                 return false;
             }
-            final SpeciesSpecificDomainSimilariyData ssdsd = sa3.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+            final SpeciesSpecificDcData ssdsd = sa3.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd.getCombinableDomainIdToCountsMap().size() != 4 ) {
                 return false;
             }
@@ -607,7 +610,8 @@ public class TestSurfacing {
                                                                             new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc4 = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                           true,
-                                                                                          false );
+                                                                                          false,
+                                                                                          true );
             final SortedSet<DomainSimilarity> sims4 = calc4
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list4,
@@ -618,7 +622,7 @@ public class TestSurfacing {
             if ( !sa4.getDomainId().equals( "A" ) ) {
                 return false;
             }
-            final SpeciesSpecificDomainSimilariyData ssdsd4 = sa4.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+            final SpeciesSpecificDcData ssdsd4 = sa4.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd4.getCombinableDomainIdToCountsMap().size() != 5 ) {
                 return false;
             }
@@ -726,7 +730,7 @@ public class TestSurfacing {
             if ( !sa5_d.getSpecies().last().equals( new BasicSpecies( "rabbit" ) ) ) {
                 return false;
             }
-            final SpeciesSpecificDomainSimilariyData ssdsd5 = sa5_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+            final SpeciesSpecificDcData ssdsd5 = sa5_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd5.getCombinableDomainIdToCountsMap().size() != 4 ) {
                 return false;
             }
@@ -861,7 +865,7 @@ public class TestSurfacing {
             if ( !sa6_d.getSpecies().last().equals( new BasicSpecies( "rabbit" ) ) ) {
                 return false;
             }
-            final SpeciesSpecificDomainSimilariyData ssdsd6 = sa6_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
+            final SpeciesSpecificDcData ssdsd6 = sa6_d.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd6.getCombinableDomainIdToCountsMap().size() != 5 ) {
                 return false;
             }
@@ -1038,7 +1042,8 @@ public class TestSurfacing {
                                                                            new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                          false,
-                                                                                         false );
+                                                                                         false,
+                                                                                         true );
             final SortedSet<DomainSimilarity> sims = calc
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list,
@@ -1146,7 +1151,8 @@ public class TestSurfacing {
                                                                            new BasicSpecies( "nemve" ) ) );
             final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID,
                                                                                          false,
-                                                                                         false );
+                                                                                         false,
+                                                                                         true );
             final SortedSet<DomainSimilarity> sims = calc
                     .calculateSimilarities( new CombinationsBasedPairwiseDomainSimilarityCalculator(),
                                             cdc_list,