X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FTestGSDI.java;h=7b4b17e48c385086109d3a74a1d2a5ad6857c5a6;hb=e35f4cbe193b2c61036498e5f3aa7e2deea9c448;hp=ed1e4d13573596953af5bb2b06f301021fb1814c;hpb=da91573ed6cc107d27b2a18ec31c88a1447a4e80;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java
index ed1e4d1..7b4b17e 100644
--- a/forester/java/src/org/forester/sdi/TestGSDI.java
+++ b/forester/java/src/org/forester/sdi/TestGSDI.java
@@ -41,7 +41,7 @@ import org.forester.util.ForesterUtil;
 public final class TestGSDI {
 
     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
-                                                          + "test_data" + ForesterUtil.getFileSeparator();
+            + "test_data" + ForesterUtil.getFileSeparator();
 
     public static void main( final String[] args ) {
         if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) {
@@ -1283,7 +1283,7 @@ public final class TestGSDI {
             //--
             final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ];
             final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gene_tree_tax_code_4.xml" )[ 0 ];
+                                                                                 + "gene_tree_tax_code_4.xml" )[ 0 ];
             final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true );
             if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
                 return false;
@@ -1296,7 +1296,7 @@ public final class TestGSDI {
             }
             //--
             final Phylogeny gsdi_test_gene_tree_sn_wnt = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
+                                                                                      + "gsdi_test_gene_tree_sn_wnt.xml" )[ 0 ];
             gsdi_test_gene_tree_sn_wnt.setRooted( true );
             final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true );
             if ( a.getDuplicationsSum() != 33 ) {
@@ -1319,7 +1319,7 @@ public final class TestGSDI {
             }
             //--
             final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gsdi_test_species_tree_sn.xml" )[ 0 ];
+                                                                                         + "gsdi_test_species_tree_sn.xml" )[ 0 ];
             final GSDI b = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(),
                                      gsdi_test_species_tree_sn_xml.copy(),
                                      false,
@@ -1386,9 +1386,9 @@ public final class TestGSDI {
             }
             //--
             final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
+                                                                                         + "gsdi_test_gene_tree_codes.xml" )[ 0 ];
             final Phylogeny gsdi_test_species_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gsdi_test_species_tree_codes.xml" )[ 0 ];
+                                                                                            + "gsdi_test_species_tree_codes.xml" )[ 0 ];
             final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(),
                                      gsdi_test_species_tree_codes_xml.copy(),
                                      false,
@@ -1420,7 +1420,7 @@ public final class TestGSDI {
             }
             //--
             final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA
-                    + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
+                                                                                      + "gsdi_test_gene_tree_sn.xml" )[ 0 ];
             final GSDI e = new GSDI( gsdi_test_gene_tree_sn_xml.copy(),
                                      gsdi_test_species_tree_sn_xml.copy(),
                                      false,
@@ -1467,7 +1467,7 @@ public final class TestGSDI {
             final Phylogeny gene_0 = factory0.create( gene_0_str, new NHXParser() )[ 0 ];
             s_0.setRooted( true );
             gene_0.setRooted( true );
-            final GSDIR sdi0 = new GSDIR( gene_0, s_0, true, true );
+            final GSDIR sdi0 = new GSDIR( gene_0, s_0, true, true, true );
             if ( sdi0.getSpeciationsSum() != 0 ) {
                 return false;
             }
@@ -1482,7 +1482,7 @@ public final class TestGSDI {
             final Phylogeny gene_00 = factory00.create( gene_00_str, new NHXParser() )[ 0 ];
             s_00.setRooted( true );
             gene_00.setRooted( true );
-            final GSDIR sdi00 = new GSDIR( gene_00, s_00, true, true );
+            final GSDIR sdi00 = new GSDIR( gene_00, s_00, true, true, true );
             if ( sdi00.getSpeciationsSum() != 0 ) {
                 return false;
             }
@@ -1495,25 +1495,25 @@ public final class TestGSDI {
             s1.setRooted( true );
             final Phylogeny g1 = TestGSDI
                     .createPhylogeny( "(HUMAN[&&NHX:S=HUMAN],(RAT[&&NHX:S=RAT],(CAEEL[&&NHX:T=:S=CAEEL],YEAST[&&NHX:S=YEAST])))" );
-            final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false );
+            final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false, true );
             if ( sdi1.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
             final Phylogeny g2 = TestGSDI
                     .createPhylogeny( "(((HUMAN[&&NHX:S=HUMAN],RAT[&&NHX:S=RAT]),CAEEL[&&NHX:T=:S=CAEEL]),YEAST[&&NHX:S=YEAST])" );
-            final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false );
+            final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false, true );
             if ( sdi2.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
             final Phylogeny g3 = TestGSDI
                     .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" );
-            final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false );
+            final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false, true );
             if ( sdi3.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
             final Phylogeny g4 = TestGSDI
                     .createPhylogeny( "(((((MOUSE[&&NHX:S=MOUSE],[&&NHX:S=RAT]),[&&NHX:S=HUMAN]),([&&NHX:S=ARATH],[&&NHX:S=YEAST])),[&&NHX:S=CAEEL]),[&&NHX:S=CAEBR])" );
-            final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false );
+            final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false, true );
             if ( sdi4.getMinDuplicationsSum() != 0 ) {
                 return false;
             }
@@ -1522,7 +1522,7 @@ public final class TestGSDI {
             final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2str, new NHXParser() )[ 0 ];
             s2.setRooted( true );
             final Phylogeny g5 = TestGSDI.createPhylogeny( s2str );
-            final GSDIR sdi5 = new GSDIR( g5, s2, false, false );
+            final GSDIR sdi5 = new GSDIR( g5, s2, false, false, true );
             if ( sdi5.getMinDuplicationsSum() != 0 ) {
                 System.out.println( sdi5.getMinDuplicationsSum() );
                 return false;