X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FTestGSDI.java;h=7b4b17e48c385086109d3a74a1d2a5ad6857c5a6;hb=fbb7c0a322111e5221773fed19591da29296efb5;hp=adf98338c8a565bb2c3f7b808ea8907336fb81be;hpb=01675e2c50b60d08b848dbafa52d42743318d270;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index adf9833..7b4b17e 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -21,30 +21,41 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; import java.io.IOException; -import org.forester.archaeopteryx.Archaeopteryx; +import org.forester.development.DevelopmentTools; import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.util.ParserUtils; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.data.Event; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.sdi.SDIutil.TaxonomyComparisonBase; +import org.forester.util.ForesterUtil; public final class TestGSDI { - private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { - final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ]; - p.setRooted( true ); - return p; - } + private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() + + "test_data" + ForesterUtil.getFileSeparator(); - private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { - return PhylogenyMethods.getInstance().obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); + public static void main( final String[] args ) { + if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) { + System.out.println( "binary failed" ); + } + if ( !TestGSDI.testGSDI_general() ) { + System.out.println( "general failed" ); + } + if ( !TestGSDI.testGSDIR_general() ) { + System.out.println( "general re-rooting failed" ); + } + else { + System.out.println( "OK" ); + } } public static boolean test() { @@ -54,11 +65,41 @@ public final class TestGSDI { if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) { return false; } + if ( !TestGSDI.testGSDIR_general() ) { + return false; + } return true; } + private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { + final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ]; + p.setRooted( true ); + return p; + } + + private final static Event getEvent( final Phylogeny p, final String n1, final String n2 ) { + return PhylogenyMethods.calculateLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); + } + private static boolean testGSDI_against_binary_gene_tree() { try { + final PhylogenyFactory factory0 = ParserBasedPhylogenyFactory.getInstance(); + final String s0 = "([&&NHX:S=1]);"; + final String gene_0_str = "([&&NHX:S=1],[&&NHX:S=1]);"; + final Phylogeny s_0 = factory0.create( s0, new NHXParser() )[ 0 ]; + final Phylogeny gene_0 = factory0.create( gene_0_str, new NHXParser() )[ 0 ]; + s_0.setRooted( true ); + gene_0.setRooted( true ); + final GSDI sdi0 = new GSDI( gene_0, s_0, false, false, false ); + if ( sdi0.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( sdi0.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi0.getSpeciationsSum() != 0 ) { + return false; + } final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final String multi_species_2_str = "(((((([&&NHX:S=1],[&&NHX:S=2])," + "([&&NHX:S=3],[&&NHX:S=4],[&&NHX:S=5]))," @@ -74,7 +115,7 @@ public final class TestGSDI { final Phylogeny gene_2_1 = factory.create( gene_2_1_str, new NHXParser() )[ 0 ]; multi_species_2.setRooted( true ); gene_2_1.setRooted( true ); - final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false ); + final GSDI sdi = new GSDI( gene_2_1, multi_species_2, false, false, false ); if ( sdi.getSpeciationOrDuplicationEventsSum() != 0 ) { return false; } @@ -91,7 +132,6 @@ public final class TestGSDI { private static boolean testGSDI_general() { try { - final PhylogenyMethods pm = PhylogenyMethods.getInstance(); final String s2_ = "((" + "([&&NHX:S=a1],[&&NHX:S=a2],[&&NHX:S=a3],[&&NHX:S=a4])," + "([&&NHX:S=b1],[&&NHX:S=b2],[&&NHX:S=b3],[&&NHX:S=b4])," + "([&&NHX:S=c1],[&&NHX:S=c2],[&&NHX:S=c3],[&&NHX:S=c4])," @@ -116,95 +156,114 @@ public final class TestGSDI { s1.setRooted( true ); final Phylogeny g1 = TestGSDI .createPhylogeny( "((((B[&&NHX:S=B],A1[&&NHX:S=A1]),C[&&NHX:S=C]),A2[&&NHX:S=A2]),D[&&NHX:S=D])" ); - final GSDI sdi1 = new GSDI( g1, s1, false ); + final GSDI sdi1 = new GSDI( g1, s1, false, false, false ); + // Archaeopteryx.createApplication( g1 ); + // Archaeopteryx.createApplication( s1 ); if ( sdi1.getDuplicationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent() + if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; } - if ( !( pm.obtainLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isDuplication() ) ) { + if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent() + .isDuplication() ) ) { return false; } - if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2 = TestGSDI .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" ); - final GSDI sdi2 = new GSDI( g2, s1, false ); + final GSDI sdi2 = new GSDI( g2, s1, false, false, false ); if ( sdi2.getDuplicationsSum() != 0 ) { return false; } - if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent() + if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; } - if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g3 = TestGSDI .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" ); - final GSDI sdi3 = new GSDI( g3, s1, false ); + final GSDI sdi3 = new GSDI( g3, s1, false, false, false ); if ( sdi3.getDuplicationsSum() != 0 ) { return false; } - if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent() + if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; } - if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g4 = TestGSDI .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" ); - final GSDI sdi4 = new GSDI( g4, s1, false ); + final GSDI sdi4 = new GSDI( g4, s1, false, false, false ); if ( sdi4.getDuplicationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) { + if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent() + .isDuplication() ) { return false; } - if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g5 = TestGSDI .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" ); - final GSDI sdi5 = new GSDI( g5, s1, false ); + final GSDI sdi5 = new GSDI( g5, s1, false, false, false ); if ( sdi5.getDuplicationsSum() != 3 ) { return false; } - if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) { + if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent() + .isDuplication() ) { return false; } - if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) { + if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent() + .isDuplication() ) { return false; } - if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) { + if ( !PhylogenyMethods.calculateLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent() + .isDuplication() ) { return false; } - if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2])," @@ -215,7 +274,7 @@ public final class TestGSDI { final Phylogeny gene7_2 = TestGSDI .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); gene7_2.setRooted( true ); - final GSDI sdi7_2 = new GSDI( gene7_2, species7, false ); + final GSDI sdi7_2 = new GSDI( gene7_2, species7, false, false, false ); if ( sdi7_2.getDuplicationsSum() != 1 ) { return false; } @@ -247,7 +306,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" ); - final GSDI sdi2_0 = new GSDI( g2_0, s2, false ); + final GSDI sdi2_0 = new GSDI( g2_0, s2, false, false, false ); if ( sdi2_0.getDuplicationsSum() != 0 ) { return false; } @@ -257,11 +316,12 @@ public final class TestGSDI { if ( sdi2_0.getSpeciationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" ); - final GSDI sdi2_1 = new GSDI( g2_1, s2, false ); + final GSDI sdi2_1 = new GSDI( g2_1, s2, false, false, false ); if ( sdi2_1.getDuplicationsSum() != 0 ) { return false; } @@ -271,11 +331,12 @@ public final class TestGSDI { if ( sdi2_1.getSpeciationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" ); - final GSDI sdi2_2 = new GSDI( g2_2, s2, false ); + final GSDI sdi2_2 = new GSDI( g2_2, s2, false, false, false ); if ( sdi2_2.getDuplicationsSum() != 0 ) { return false; } @@ -285,11 +346,12 @@ public final class TestGSDI { if ( sdi2_2.getSpeciationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" ); - final GSDI sdi2_3 = new GSDI( g2_3, s2, false ); + final GSDI sdi2_3 = new GSDI( g2_3, s2, false, false, false ); if ( sdi2_3.getDuplicationsSum() != 1 ) { return false; } @@ -299,11 +361,12 @@ public final class TestGSDI { if ( sdi2_3.getSpeciationsSum() != 0 ) { return false; } - if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) { + if ( !PhylogenyMethods.calculateLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData() + .getEvent().isDuplication() ) { return false; } final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" ); - final GSDI sdi2_4 = new GSDI( g2_4, s2, false ); + final GSDI sdi2_4 = new GSDI( g2_4, s2, false, false, false ); if ( sdi2_4.getDuplicationsSum() != 0 ) { return false; } @@ -313,14 +376,16 @@ public final class TestGSDI { if ( sdi2_4.getSpeciationsSum() != 2 ) { return false; } - if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" ); - final GSDI sdi2_5 = new GSDI( g2_5, s2, false ); + final GSDI sdi2_5 = new GSDI( g2_5, s2, false, false, false ); if ( sdi2_5.getDuplicationsSum() != 0 ) { return false; } @@ -330,14 +395,16 @@ public final class TestGSDI { if ( sdi2_5.getSpeciationsSum() != 2 ) { return false; } - if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" ); - final GSDI sdi2_6 = new GSDI( g2_6, s2, false ); + final GSDI sdi2_6 = new GSDI( g2_6, s2, false, false, false ); if ( sdi2_6.getDuplicationsSum() != 0 ) { return false; } @@ -347,14 +414,16 @@ public final class TestGSDI { if ( sdi2_6.getSpeciationsSum() != 2 ) { return false; } - if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" ); - final GSDI sdi2_7 = new GSDI( g2_7, s2, false ); + final GSDI sdi2_7 = new GSDI( g2_7, s2, false, false, false ); if ( sdi2_7.getDuplicationsSum() != 0 ) { return false; } @@ -364,15 +433,16 @@ public final class TestGSDI { if ( sdi2_7.getSpeciationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } - if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent() + if ( !PhylogenyMethods.calculateLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; } final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" ); - final GSDI sdi2_8 = new GSDI( g2_8, s2, false ); + final GSDI sdi2_8 = new GSDI( g2_8, s2, false, false, false ); if ( sdi2_8.getDuplicationsSum() != 0 ) { return false; } @@ -382,15 +452,16 @@ public final class TestGSDI { if ( sdi2_8.getSpeciationsSum() != 1 ) { return false; } - if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent() + if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent() .isSpeciationOrDuplication() ) { return false; } - if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) { + if ( !PhylogenyMethods.calculateLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent() + .isSpeciation() ) { return false; } final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" ); - final GSDI sdi2_9 = new GSDI( g2_9, s2, false ); + final GSDI sdi2_9 = new GSDI( g2_9, s2, false, false, false ); if ( sdi2_9.getDuplicationsSum() != 0 ) { return false; } @@ -407,7 +478,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" ); - final GSDI sdi2_10 = new GSDI( g2_10, s2, false ); + final GSDI sdi2_10 = new GSDI( g2_10, s2, false, false, false ); if ( sdi2_10.getDuplicationsSum() != 0 ) { return false; } @@ -424,7 +495,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" ); - final GSDI sdi2_11 = new GSDI( g2_11, s2, false ); + final GSDI sdi2_11 = new GSDI( g2_11, s2, false, false, false ); if ( sdi2_11.getDuplicationsSum() != 0 ) { return false; } @@ -441,7 +512,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" ); - final GSDI sdi2_12 = new GSDI( g2_12, s2, false ); + final GSDI sdi2_12 = new GSDI( g2_12, s2, false, false, false ); if ( sdi2_12.getDuplicationsSum() != 0 ) { return false; } @@ -458,7 +529,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" ); - final GSDI sdi2_13 = new GSDI( g2_13, s2, false ); + final GSDI sdi2_13 = new GSDI( g2_13, s2, false, false, false ); if ( sdi2_13.getDuplicationsSum() != 0 ) { return false; } @@ -475,7 +546,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" ); - final GSDI sdi2_14 = new GSDI( g2_14, s2, false ); + final GSDI sdi2_14 = new GSDI( g2_14, s2, false, false, false ); if ( sdi2_14.getDuplicationsSum() != 1 ) { return false; } @@ -492,7 +563,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" ); - final GSDI sdi2_15 = new GSDI( g2_15, s2, false ); + final GSDI sdi2_15 = new GSDI( g2_15, s2, false, false, false ); if ( sdi2_15.getDuplicationsSum() != 1 ) { return false; } @@ -509,7 +580,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" ); - final GSDI sdi2_16 = new GSDI( g2_16, s2, false ); + final GSDI sdi2_16 = new GSDI( g2_16, s2, false, false, false ); if ( sdi2_16.getDuplicationsSum() != 1 ) { return false; } @@ -526,7 +597,7 @@ public final class TestGSDI { return false; } final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" ); - final GSDI sdi2_17 = new GSDI( g2_17, s2, false ); + final GSDI sdi2_17 = new GSDI( g2_17, s2, false, false, false ); if ( sdi2_17.getDuplicationsSum() != 1 ) { return false; } @@ -544,7 +615,7 @@ public final class TestGSDI { } final Phylogeny g2_18 = TestGSDI .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" ); - final GSDI sdi2_18 = new GSDI( g2_18, s2, false ); + final GSDI sdi2_18 = new GSDI( g2_18, s2, false, false, false ); if ( sdi2_18.getDuplicationsSum() != 3 ) { return false; } @@ -565,7 +636,7 @@ public final class TestGSDI { } final Phylogeny g2_19 = TestGSDI .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" ); - final GSDI sdi2_19 = new GSDI( g2_19, s2, false ); + final GSDI sdi2_19 = new GSDI( g2_19, s2, false, false, false ); if ( sdi2_19.getDuplicationsSum() != 1 ) { return false; } @@ -586,7 +657,7 @@ public final class TestGSDI { } final Phylogeny g2_20 = TestGSDI .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" ); - final GSDI sdi2_20 = new GSDI( g2_20, s2, false ); + final GSDI sdi2_20 = new GSDI( g2_20, s2, false, false, false ); if ( sdi2_20.getDuplicationsSum() != 1 ) { return false; } @@ -607,7 +678,7 @@ public final class TestGSDI { } final Phylogeny g2_21 = TestGSDI .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" ); - final GSDI sdi2_21 = new GSDI( g2_21, s2, false ); + final GSDI sdi2_21 = new GSDI( g2_21, s2, false, false, false ); if ( sdi2_21.getDuplicationsSum() != 1 ) { return false; } @@ -628,9 +699,9 @@ public final class TestGSDI { } final Phylogeny g2_22 = TestGSDI .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],n4[&&NHX:S=n4]))" ); - final GSDI sdi2_22 = new GSDI( g2_22, s2, false ); - Archaeopteryx.createApplication( g2_22 ); - Archaeopteryx.createApplication( s2 ); + final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false ); + //Archaeopteryx.createApplication( g2_22 ); + //Archaeopteryx.createApplication( s2 ); if ( sdi2_22.getDuplicationsSum() != 0 ) { return false; } @@ -649,574 +720,736 @@ public final class TestGSDI { if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) { return false; } - // final Phylogeny g2_23 = TestGSDI - // .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" ); - // final GSDI sdi2_23 = new GSDI( g2_23, s2, false ); - // if ( sdi2_23.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_23.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_24 = TestGSDI - // .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" ); - // final GSDI sdi2_24 = new GSDI( g2_24, s2, false ); - // if ( sdi2_24.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_24.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_25 = TestGSDI - // .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" ); - // final GSDI sdi2_25 = new GSDI( g2_25, s2, false ); - // if ( sdi2_25.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_25.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_26 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" ); - // final GSDI sdi2_26 = new GSDI( g2_26, s2, false ); - // if ( sdi2_26.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) { - // return false; - // } - // if ( sdi2_26.getSpeciationsSum() != 3 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) { - // return false; - // } - // final Phylogeny g2_27 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" ); - // final GSDI sdi2_27 = new GSDI( g2_27, s2, false ); - // if ( sdi2_27.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_27.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_28 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" ); - // final GSDI sdi2_28 = new GSDI( g2_28, s2, false ); - // if ( sdi2_28.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_28.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) { - // return false; - // } - // final Phylogeny g2_29 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" ); - // final GSDI sdi2_29 = new GSDI( g2_29, s2, false ); - // if ( sdi2_29.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) { - // return false; - // } - // if ( sdi2_29.getSpeciationsSum() != 1 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_30 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" ); - // final GSDI sdi2_30 = new GSDI( g2_30, s2, false ); - // if ( sdi2_30.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_30.getSpeciationsSum() != 1 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) { - // return false; - // } - // final Phylogeny g2_31 = TestGSDI - // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" ); - // final GSDI sdi2_31 = new GSDI( g2_31, s2, false ); - // if ( sdi2_31.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_31.getSpeciationsSum() != 1 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) { - // return false; - // } - // final Phylogeny g2_32 = TestGSDI - // .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); - // final GSDI sdi2_32 = new GSDI( g2_32, s2, false ); - // if ( sdi2_32.getDuplicationsSum() != 0 ) { - // return false; - // } - // if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) { - // return false; - // } - // if ( sdi2_32.getSpeciationsSum() != 3 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) { - // return false; - // } - // //- - // final Phylogeny g2_33_d = TestGSDI - // .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" ); - // final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false ); - // Archaeopteryx.createApplication( g2_33_d ); - // // Archaeopteryx.createApplication( s2 ); - // //- - // final Phylogeny g2_33 = TestGSDI - // .createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); - // final GSDI sdi2_33 = new GSDI( g2_33, s2, false ); - // Archaeopteryx.createApplication( g2_33 ); - // // Archaeopteryx.createApplication( s2 ); - // if ( sdi2_33.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) { - // return false; - // } - // if ( sdi2_33.getSpeciationsSum() != 3 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_34 = TestGSDI - // .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" ); - // final GSDI sdi2_34 = new GSDI( g2_34, s2, false ); - // if ( sdi2_34.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_34.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_35 = TestGSDI - // .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" ); - // final GSDI sdi2_35 = new GSDI( g2_35, s2, false ); - // if ( sdi2_35.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_35.getSpeciationsSum() != 3 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) { - // return false; - // } - // final Phylogeny g2_36 = TestGSDI - // .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" ); - // final GSDI sdi2_36 = new GSDI( g2_36, s2, false ); - // if ( sdi2_36.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_36.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_37 = TestGSDI - // .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" ); - // final GSDI sdi2_37 = new GSDI( g2_37, s2, false ); - // if ( sdi2_37.getDuplicationsSum() != 1 ) { - // return false; - // } - // if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_37.getSpeciationsSum() != 2 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) { - // return false; - // } - // final Phylogeny g2_38 = TestGSDI - // .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" ); - // final GSDI sdi2_38 = new GSDI( g2_38, s2, false ); - // if ( sdi2_38.getDuplicationsSum() != 5 ) { - // return false; - // } - // if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) { - // return false; - // } - // if ( sdi2_38.getSpeciationsSum() != 0 ) { - // return false; - // } - // final Phylogeny g2_100 = TestGSDI - // .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" ); - // final GSDI sdi2_100 = new GSDI( g2_100, s2, false ); - // if ( sdi2_100.getDuplicationsSum() != 4 ) { - // return false; - // } - // if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) { - // return false; - // } - // if ( sdi2_100.getSpeciationsSum() != 4 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) { - // return false; - // } - // final Phylogeny g2_101 = TestGSDI - // .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" ); - // final GSDI sdi2_101 = new GSDI( g2_101, s2, false ); - // if ( sdi2_101.getDuplicationsSum() != 2 ) { - // return false; - // } - // if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) { - // return false; - // } - // if ( sdi2_101.getSpeciationsSum() != 5 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) { - // return false; - // } - // final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 ); - // DevelopmentTools.numberSpeciesInOrder( s_7_4 ); - // final Phylogeny g_7_4_1 = TestGSDI - // .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((" - // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5])," - // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11])," - // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17])," - // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23])," - // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29])," - // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35])," - // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41])," - // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47])," - // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53])," - // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59])," - // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" ); - // final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false ); - // if ( sdi7_4_1.getDuplicationsSum() != 54 ) { - // return false; - // } - // if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) { - // return false; - // } - // if ( sdi7_4_1.getSpeciationsSum() != 4 ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) { - // return false; - // } - // final Phylogeny g_7_4_2 = TestGSDI - // .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((" - // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5])," - // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11])," - // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17])," - // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23])," - // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29])," - // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35])," - // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41])," - // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47])," - // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53])," - // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59])," - // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])," - // + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" ); - // final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false ); - // if ( sdi7_4_2.getDuplicationsSum() != 58 ) { - // return false; - // } - // if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) { - // return false; - // } - // if ( sdi7_4_2.getSpeciationsSum() != 5 ) { - // return false; - // } - //--------------------- - // final String g2_0_ = - // "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))"; - // final Phylogeny g2_0 = factory.create( g2_0_, new NHXParser() )[ - // 0 ]; - // g2_0.setRooted( true ); - // final GSDI sdi2_0 = new GSDI( g2_0, s2, false ); - // if ( sdi2_0.getDuplicationsSum() != 0 ) { - // return false; - // } - // final String g2_1_= ""; - // final Phylogeny g2_1 = factory.create( g2_1_, new NHXParser() )[ - // 0 ]; - // g2_1.setRooted( true ); - // final GSDI sdi2_1 = new GSDI( g2_1, s2, false ); - // if ( sdi2_1.getDuplicationsSum() != 0 ) { - // return false; - // } + final Phylogeny g2_23 = TestGSDI + .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" ); + final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false ); + if ( sdi2_23.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_23.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_24 = TestGSDI + .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" ); + final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false ); + if ( sdi2_24.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_24.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_25 = TestGSDI + .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" ); + final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false ); + if ( sdi2_25.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_25.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_26 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" ); + final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false ); + if ( sdi2_26.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( sdi2_26.getSpeciationsSum() != 3 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) { + return false; + } + final Phylogeny g2_27 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" ); + final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false ); + if ( sdi2_27.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_27.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_28 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" ); + final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false ); + if ( sdi2_28.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_28.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) { + return false; + } + final Phylogeny g2_29 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" ); + final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false ); + if ( sdi2_29.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) { + return false; + } + if ( sdi2_29.getSpeciationsSum() != 1 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_30 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" ); + final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false ); + if ( sdi2_30.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_30.getSpeciationsSum() != 1 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) { + return false; + } + final Phylogeny g2_31 = TestGSDI + .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" ); + final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false ); + if ( sdi2_31.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_31.getSpeciationsSum() != 1 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) { + return false; + } + final Phylogeny g2_32 = TestGSDI + .createPhylogeny( "((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); + final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false ); + if ( sdi2_32.getDuplicationsSum() != 0 ) { + return false; + } + if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) { + return false; + } + if ( sdi2_32.getSpeciationsSum() != 3 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_32, "a1", "z" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_33 = TestGSDI + .createPhylogeny( "(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1]),x[&&NHX:S=x]),p1[&&NHX:S=p1]),i1[&&NHX:S=i1]),k2[&&NHX:S=k2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" ); + final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false ); + if ( sdi2_33.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) { + return false; + } + if ( sdi2_33.getSpeciationsSum() != 3 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_33_d = TestGSDI + .createPhylogeny( "((((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?],(((((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2])[&&NHX:D=N],b1[&&NHX:S=b1])[&&NHX:D=N],c1[&&NHX:S=c1])[&&NHX:D=?],d1[&&NHX:S=d1])[&&NHX:D=?],x[&&NHX:S=x])[&&NHX:D=N],p1[&&NHX:S=p1])[&&NHX:D=?],i1[&&NHX:S=i1])[&&NHX:D=?],k2[&&NHX:S=k2])[&&NHX:D=Y],e1[&&NHX:S=e1])[&&NHX:D=Y],y[&&NHX:S=y])[&&NHX:D=Y],z[&&NHX:S=z])[&&NHX:D=?])" ); + final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false ); + if ( sdi2_33_d.getDuplicationsSum() != 3 ) { + return false; + } + if ( sdi2_33_d.getSpeciationOrDuplicationEventsSum() != 14 ) { + return false; + } + if ( sdi2_33_d.getSpeciationsSum() != 6 ) { + return false; + } + final Phylogeny g2_34 = TestGSDI + .createPhylogeny( "(((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4])" ); + final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false ); + if ( sdi2_34.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_34.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_35 = TestGSDI + .createPhylogeny( "((((n1_0[&&NHX:S=n1],n2_0[&&NHX:S=n2]),(n1_1[&&NHX:S=n1],n3_0[&&NHX:S=n3])),n4_0[&&NHX:S=n4]),a1_0[&&NHX:S=a1])" ); + final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false ); + if ( sdi2_35.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_35.getSpeciationsSum() != 3 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) { + return false; + } + final Phylogeny g2_36 = TestGSDI + .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" ); + final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false ); + if ( sdi2_36.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_36.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_37 = TestGSDI + .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" ); + final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false ); + if ( sdi2_37.getDuplicationsSum() != 1 ) { + return false; + } + if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_37.getSpeciationsSum() != 2 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) { + return false; + } + final Phylogeny g2_38 = TestGSDI + .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" ); + final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false ); + if ( sdi2_38.getDuplicationsSum() != 5 ) { + return false; + } + if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( sdi2_38.getSpeciationsSum() != 0 ) { + return false; + } + final Phylogeny g2_100 = TestGSDI + .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" ); + final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false ); + if ( sdi2_100.getDuplicationsSum() != 4 ) { + return false; + } + if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( sdi2_100.getSpeciationsSum() != 4 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) { + return false; + } + final Phylogeny g2_101 = TestGSDI + .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" ); + final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false ); + if ( sdi2_101.getDuplicationsSum() != 2 ) { + return false; + } + if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( sdi2_101.getSpeciationsSum() != 5 ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) { + return false; + } + final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 ); + DevelopmentTools.numberSpeciesInOrder( s_7_4 ); + final Phylogeny g_7_4_1 = TestGSDI + .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((" + + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5])," + + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11])," + + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17])," + + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23])," + + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29])," + + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35])," + + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41])," + + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47])," + + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53])," + + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59])," + + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" ); + final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false, false, false ); + if ( sdi7_4_1.getDuplicationsSum() != 54 ) { + return false; + } + if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) { + return false; + } + if ( sdi7_4_1.getSpeciationsSum() != 4 ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) { + return false; + } + if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) { + return false; + } + final Phylogeny g_7_4_2 = TestGSDI + .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((" + + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5])," + + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11])," + + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17])," + + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23])," + + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29])," + + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35])," + + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41])," + + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47])," + + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53])," + + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59])," + + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])," + + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" ); + final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false, false, false ); + if ( sdi7_4_2.getDuplicationsSum() != 58 ) { + return false; + } + if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) { + return false; + } + if ( sdi7_4_2.getSpeciationsSum() != 5 ) { + return false; + } + final String g2_0_ = "(([&&NHX:S=a1],[&&NHX:S=a2]),([&&NHX:S=o2],[&&NHX:S=o4]))"; + final Phylogeny g2_0p = TestGSDI.createPhylogeny( g2_0_ ); + g2_0.setRooted( true ); + final GSDI sdi2_0p = new GSDI( g2_0p, s2, false, false, false ); + if ( sdi2_0p.getDuplicationsSum() != 0 ) { + return false; + } + //-- + 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 ]; + 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; + } + if ( gsdi_143_4_1.getSpeciationsSum() != 28 ) { + return false; + } + if ( gsdi_143_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) { + return false; + } + //-- + 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.setRooted( true ); + final GSDI a = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), tol_143_.copy(), false, true, true ); + if ( a.getDuplicationsSum() != 33 ) { + return false; + } + if ( a.getSpeciationsSum() != 31 ) { + return false; + } + if ( a.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( a.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + return false; + } + if ( a.getMappedExternalSpeciesTreeNodes().size() != 26 ) { + return false; + } + if ( a.getReMappedScientificNamesFromGeneTree().size() != 0 ) { + return false; + } + //-- + final Phylogeny gsdi_test_species_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + + "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, + true, + true ); + if ( b.getDuplicationsSum() != 8 ) { + return false; + } + if ( b.getSpeciationsSum() != 2 ) { + return false; + } + if ( b.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( b.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + return false; + } + if ( b.getMappedExternalSpeciesTreeNodes().size() != 2 ) { + return false; + } + if ( b.getReMappedScientificNamesFromGeneTree().size() != 0 ) { + return false; + } + if ( b.getStrippedExternalGeneTreeNodes().size() != 87 ) { + return false; + } + if ( b.getStrippedSpeciesTreeNodes().size() != 17 ) { + return false; + } + //-- + final Phylogeny gsdi_test_species_tree_sn_nh = TestGSDI + .createPhylogeny( "((((((('Homo sapiens','Mus musculus')Euarchontoglires,'Petromyzon marinus')Vertebrata,'Nematostella vectensis')'Bilateria Cnidaria',(('Mycosphaerella graminicola','Mycosphaerella pini')Mycosphaerella,'Saccharomyces cerevisiae')'Pezizomycotina Saccharomycetales')Opisthokonta,('Plasmodium chabaudi','Plasmodium falciparum','Plasmodium yoelii yoelii')Plasmodium)Eukaryota,'Pyrococcus horikoshii')Neomura,(('Kineococcus radiotolerans','Kocuria rhizophila','Streptomyces coelicolor','Thermobifida fusca','Microlunatus phosphovorus'),'Bacteroides thetaiotaomicron'))'cellular organisms';" ); + PhylogenyMethods.transferNodeNameToField( gsdi_test_species_tree_sn_nh, + PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME, + true ); + final GSDI c = new GSDI( gsdi_test_gene_tree_sn_wnt.copy(), + gsdi_test_species_tree_sn_nh.copy(), + false, + true, + true ); + if ( c.getDuplicationsSum() != 8 ) { + return false; + } + if ( c.getSpeciationsSum() != 2 ) { + return false; + } + if ( c.getSpeciationOrDuplicationEventsSum() != 0 ) { + return false; + } + if ( c.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + return false; + } + if ( c.getMappedExternalSpeciesTreeNodes().size() != 2 ) { + return false; + } + if ( c.getReMappedScientificNamesFromGeneTree().size() != 0 ) { + return false; + } + if ( c.getStrippedExternalGeneTreeNodes().size() != 87 ) { + return false; + } + if ( c.getStrippedSpeciesTreeNodes().size() != 15 ) { + return false; + } + //-- + final Phylogeny gsdi_test_gene_tree_codes_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + + "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 ]; + final GSDI d = new GSDI( gsdi_test_gene_tree_codes_xml.copy(), + gsdi_test_species_tree_codes_xml.copy(), + false, + true, + true ); + if ( d.getDuplicationsSum() != 21 ) { + return false; + } + if ( d.getSpeciationsSum() != 28 ) { + return false; + } + if ( d.getSpeciationOrDuplicationEventsSum() != 6 ) { + return false; + } + if ( d.getTaxCompBase() != TaxonomyComparisonBase.CODE ) { + return false; + } + if ( d.getMappedExternalSpeciesTreeNodes().size() != 17 ) { + return false; + } + if ( d.getReMappedScientificNamesFromGeneTree().size() != 0 ) { + return false; + } + if ( d.getStrippedExternalGeneTreeNodes().size() != 12 ) { + return false; + } + if ( d.getStrippedSpeciesTreeNodes().size() != 3 ) { + return false; + } + //-- + final Phylogeny gsdi_test_gene_tree_sn_xml = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + + "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, + true, + true ); + if ( e.getDuplicationsSum() != 7 ) { + return false; + } + if ( e.getSpeciationsSum() != 9 ) { + return false; + } + if ( e.getSpeciationOrDuplicationEventsSum() != 1 ) { + return false; + } + if ( e.getTaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) { + return false; + } + if ( e.getMappedExternalSpeciesTreeNodes().size() != 12 ) { + return false; + } + if ( e.getReMappedScientificNamesFromGeneTree().size() != 8 ) { + return false; + } + if ( e.getStrippedExternalGeneTreeNodes().size() != 3 ) { + return false; + } + if ( e.getStrippedSpeciesTreeNodes().size() != 7 ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -1225,19 +1458,80 @@ public final class TestGSDI { return true; } - public static void main( final String[] args ) { - if ( !TestGSDI.testGSDI_against_binary_gene_tree() ) { - System.out.println( "binary failed" ); + private static boolean testGSDIR_general() { + try { + final PhylogenyFactory factory0 = ParserBasedPhylogenyFactory.getInstance(); + final String s0 = "([&&NHX:S=1]);"; + final String gene_0_str = "([&&NHX:S=1],[&&NHX:S=1]);"; + final Phylogeny s_0 = factory0.create( s0, new NHXParser() )[ 0 ]; + 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, true ); + if ( sdi0.getSpeciationsSum() != 0 ) { + return false; + } + if ( sdi0.getMinDuplicationsSum() != 1 ) { + return false; + } + // + final PhylogenyFactory factory00 = ParserBasedPhylogenyFactory.getInstance(); + final String s00 = "[&&NHX:S=1];"; + final String gene_00_str = "([&&NHX:S=1],[&&NHX:S=1]);"; + final Phylogeny s_00 = factory00.create( s00, new NHXParser() )[ 0 ]; + 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, true ); + if ( sdi00.getSpeciationsSum() != 0 ) { + return false; + } + if ( sdi00.getMinDuplicationsSum() != 1 ) { + return false; + } + // + final String s1str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),[&&NHX:S=ARATH])"; + final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1str, new NHXParser() )[ 0 ]; + 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, 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, 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, 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, true ); + if ( sdi4.getMinDuplicationsSum() != 0 ) { + return false; + } + // + final String s2str = "(((([&&NHX:S=HUMAN],([&&NHX:S=MOUSE],[&&NHX:S=RAT])),([&&NHX:S=CAEEL],[&&NHX:S=CAEBR])),[&&NHX:S=YEAST]),([&&NHX:S=ARATH],[&&NHX:S=SOYBN]))"; + 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, true ); + if ( sdi5.getMinDuplicationsSum() != 0 ) { + System.out.println( sdi5.getMinDuplicationsSum() ); + return false; + } } - if ( !TestGSDI.testGSDI_general() ) { - System.out.println( "general failed" ); + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; } - // boolean success = test(); - // if ( success ) { - // System.out.println( "OK" ); - // } - // else { - // System.out.println( "failed" ); - // } + return true; } }