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=54d52552f327178c34d0eb47d2d6680bcd5734ed;hpb=877d1e4a2f3e2a937197dc57253ba2cead14a4d6;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index 54d5255..7b4b17e 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -21,13 +21,12 @@ // 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; @@ -36,22 +35,27 @@ 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.SDI.TaxonomyComparisonBase; +import org.forester.sdi.SDIutil.TaxonomyComparisonBase; 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(); - 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(); + 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() { @@ -61,11 +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]))," @@ -81,7 +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; } @@ -122,7 +156,7 @@ 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 ) { @@ -146,7 +180,7 @@ public final class TestGSDI { } 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; } @@ -168,7 +202,7 @@ public final class TestGSDI { } 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; } @@ -190,7 +224,7 @@ public final class TestGSDI { } 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; } @@ -208,7 +242,7 @@ public final class TestGSDI { } 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; } @@ -240,7 +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; } @@ -272,7 +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; } @@ -287,7 +321,7 @@ public final class TestGSDI { 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; } @@ -302,7 +336,7 @@ public final class TestGSDI { 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; } @@ -317,7 +351,7 @@ public final class TestGSDI { 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; } @@ -332,7 +366,7 @@ public final class TestGSDI { 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; } @@ -351,7 +385,7 @@ public final class TestGSDI { 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; } @@ -370,7 +404,7 @@ public final class TestGSDI { 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; } @@ -389,7 +423,7 @@ public final class TestGSDI { 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; } @@ -408,7 +442,7 @@ public final class TestGSDI { 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; } @@ -427,7 +461,7 @@ public final class TestGSDI { 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; } @@ -444,7 +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; } @@ -461,7 +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; } @@ -478,7 +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; } @@ -495,7 +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; } @@ -512,7 +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; } @@ -529,7 +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; } @@ -546,7 +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; } @@ -563,7 +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; } @@ -581,7 +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; } @@ -602,7 +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; } @@ -623,7 +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; } @@ -644,7 +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; } @@ -665,7 +699,7 @@ 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 ); + final GSDI sdi2_22 = new GSDI( g2_22, s2, false, false, false ); //Archaeopteryx.createApplication( g2_22 ); //Archaeopteryx.createApplication( s2 ); if ( sdi2_22.getDuplicationsSum() != 0 ) { @@ -688,7 +722,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_23 = new GSDI( g2_23, s2, false, false, false ); if ( sdi2_23.getDuplicationsSum() != 0 ) { return false; } @@ -709,7 +743,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_24 = new GSDI( g2_24, s2, false, false, false ); if ( sdi2_24.getDuplicationsSum() != 0 ) { return false; } @@ -730,7 +764,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_25 = new GSDI( g2_25, s2, false, false, false ); if ( sdi2_25.getDuplicationsSum() != 0 ) { return false; } @@ -751,7 +785,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_26 = new GSDI( g2_26, s2, false, false, false ); if ( sdi2_26.getDuplicationsSum() != 0 ) { return false; } @@ -772,7 +806,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_27 = new GSDI( g2_27, s2, false, false, false ); if ( sdi2_27.getDuplicationsSum() != 0 ) { return false; } @@ -793,7 +827,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_28 = new GSDI( g2_28, s2, false, false, false ); if ( sdi2_28.getDuplicationsSum() != 0 ) { return false; } @@ -814,7 +848,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_29 = new GSDI( g2_29, s2, false, false, false ); if ( sdi2_29.getDuplicationsSum() != 0 ) { return false; } @@ -835,7 +869,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_30 = new GSDI( g2_30, s2, false, false, false ); if ( sdi2_30.getDuplicationsSum() != 1 ) { return false; } @@ -856,7 +890,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_31 = new GSDI( g2_31, s2, false, false, false ); if ( sdi2_31.getDuplicationsSum() != 1 ) { return false; } @@ -877,7 +911,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_32 = new GSDI( g2_32, s2, false, false, false ); if ( sdi2_32.getDuplicationsSum() != 0 ) { return false; } @@ -919,7 +953,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_33 = new GSDI( g2_33, s2, false, false, false ); if ( sdi2_33.getDuplicationsSum() != 1 ) { return false; } @@ -964,7 +998,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_33_d = new GSDI( g2_33_d, s2, false, false, false ); if ( sdi2_33_d.getDuplicationsSum() != 3 ) { return false; } @@ -976,7 +1010,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_34 = new GSDI( g2_34, s2, false, false, false ); if ( sdi2_34.getDuplicationsSum() != 1 ) { return false; } @@ -1000,7 +1034,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_35 = new GSDI( g2_35, s2, false, false, false ); if ( sdi2_35.getDuplicationsSum() != 1 ) { return false; } @@ -1027,7 +1061,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_36 = new GSDI( g2_36, s2, false, false, false ); if ( sdi2_36.getDuplicationsSum() != 1 ) { return false; } @@ -1051,7 +1085,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_37 = new GSDI( g2_37, s2, false, false, false ); if ( sdi2_37.getDuplicationsSum() != 1 ) { return false; } @@ -1075,7 +1109,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_38 = new GSDI( g2_38, s2, false, false, false ); if ( sdi2_38.getDuplicationsSum() != 5 ) { return false; } @@ -1087,7 +1121,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_100 = new GSDI( g2_100, s2, false, false, false ); if ( sdi2_100.getDuplicationsSum() != 4 ) { return false; } @@ -1123,7 +1157,7 @@ public final class TestGSDI { } 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 ); + final GSDI sdi2_101 = new GSDI( g2_101, s2, false, false, false ); if ( sdi2_101.getDuplicationsSum() != 2 ) { return false; } @@ -1172,7 +1206,7 @@ public final class TestGSDI { + "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 ); + 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; } @@ -1229,7 +1263,7 @@ public final class TestGSDI { + "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 ); + 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; } @@ -1242,14 +1276,14 @@ public final class TestGSDI { 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 ); + 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 ]; + + "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; @@ -1262,7 +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 ) { @@ -1285,7 +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, @@ -1352,9 +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, @@ -1386,7 +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, @@ -1426,63 +1460,73 @@ public final class TestGSDI { 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 ); - // Archaeopteryx.createApplication( s1.copy() ); 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, 1 ); + final GSDIR sdi1 = new GSDIR( g1.copy(), s1.copy(), false, false, true ); if ( sdi1.getMinDuplicationsSum() != 0 ) { return false; } - System.out.println( sdi1.getDuplicationsSumStats().getSummaryAsString() ); - // Archaeopteryx.createApplication( sdi1.getMinDuplicationsSumGeneTrees().get( 0 ) ); - // 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, 1 ); + final GSDIR sdi2 = new GSDIR( g2.copy(), s1.copy(), false, false, true ); if ( sdi2.getMinDuplicationsSum() != 0 ) { return false; } - System.out.println( sdi2.getDuplicationsSumStats().getSummaryAsString() ); - // Archaeopteryx.createApplication( sdi2.getMinDuplicationsSumGeneTrees().get( 0 ) ); - // final Phylogeny g3 = TestGSDI .createPhylogeny( "(RAT[&&NHX:S=RAT],HUMAN[&&NHX:S=HUMAN],(YEAST[&&NHX:S=YEAST],CAEEL[&&NHX:T=:S=CAEEL]))" ); - // Archaeopteryx.createApplication( g3 ); - final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, 1 ); + final GSDIR sdi3 = new GSDIR( g3.copy(), s1.copy(), false, false, true ); if ( sdi3.getMinDuplicationsSum() != 0 ) { return false; } - System.out.println( sdi3.getDuplicationsSumStats().getSummaryAsString() ); - // Archaeopteryx.createApplication( sdi3.getMinDuplicationsSumGeneTrees().get( 0 ) ); - // 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])" ); - Archaeopteryx.createApplication( g4 ); - final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, 1 ); + final GSDIR sdi4 = new GSDIR( g4.copy(), s1.copy(), false, false, true ); if ( sdi4.getMinDuplicationsSum() != 0 ) { return false; } - System.out.println( sdi4.getDuplicationsSumStats().getSummaryAsString() ); - Archaeopteryx.createApplication( sdi4.getMinDuplicationsSumGeneTrees().get( 0 ) ); - // if ( !PhylogenyMethods.calculateLCA( g1.getNode( "B" ), g1.getNode( "A1" ) ).getNodeData().getEvent() - // .isSpeciation() ) { - // return false; - // } - // if ( !PhylogenyMethods.calculateLCA( g1.getNode( "C" ), g1.getNode( "A1" ) ).getNodeData().getEvent() - // .isSpeciationOrDuplication() ) { - // return false; - // } - // if ( !( PhylogenyMethods.calculateLCA( g1.getNode( "A2" ), g1.getNode( "A1" ) ).getNodeData().getEvent() - // .isDuplication() ) ) { - // return false; - // } - // if ( !PhylogenyMethods.calculateLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent() - // .isSpeciation() ) { - // 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; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -1490,26 +1534,4 @@ 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" ); - } - 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" ); - } - // boolean success = test(); - // if ( success ) { - // System.out.println( "OK" ); - // } - // else { - // System.out.println( "failed" ); - // } - } }