X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FTestGSDI.java;h=045eebb2d671a6f6039b3589ab312e695f05c181;hb=fffc26ac5f8cf4eaa5faea6a7e369b94d381d859;hp=6cf3c72f275919c8af3316ad3477dc9f8389b0a6;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index 6cf3c72..045eebb 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -5,7 +5,7 @@ // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved -// +// // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either @@ -15,7 +15,7 @@ // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. -// +// // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA @@ -29,14 +29,20 @@ import java.io.IOException; 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.SDI.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(); + private final static Phylogeny createPhylogeny( final String nhx ) throws IOException { final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ]; p.setRooted( true ); @@ -44,7 +50,7 @@ public final class TestGSDI { } 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(); + return PhylogenyMethods.obtainLCA( p.getNode( n1 ), p.getNode( n2 ) ).getNodeData().getEvent(); } public static boolean test() { @@ -92,12 +98,33 @@ 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])," + + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),(" + + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4])," + + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4])," + + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4])," + + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),(" + + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4])," + + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4])," + + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4])," + + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),(" + + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4])," + + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4])," + + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4])," + + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])" + + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])"; + final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ]; + s2.setRooted( true ); final String s1_ = "((([&&NHX:S=A2],[&&NHX:S=A1]),[&&NHX:S=B],[&&NHX:S=C]),[&&NHX:S=D])"; final Phylogeny s1 = ParserBasedPhylogenyFactory.getInstance().create( s1_, new NHXParser() )[ 0 ]; 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 ); + // Archaeopteryx.createApplication( g1 ); + // Archaeopteryx.createApplication( s1 ); if ( sdi1.getDuplicationsSum() != 1 ) { return false; } @@ -227,25 +254,6 @@ public final class TestGSDI { if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) { return false; } - 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])," - + "([&&NHX:S=d1],[&&NHX:S=d2],[&&NHX:S=d3],[&&NHX:S=d4])),(" - + "([&&NHX:S=e1],[&&NHX:S=e2],[&&NHX:S=e3],[&&NHX:S=e4])," - + "([&&NHX:S=f1],[&&NHX:S=f2],[&&NHX:S=f3],[&&NHX:S=f4])," - + "([&&NHX:S=g1],[&&NHX:S=g2],[&&NHX:S=g3],[&&NHX:S=g4])," - + "([&&NHX:S=h1],[&&NHX:S=h2],[&&NHX:S=h3],[&&NHX:S=h4])),(" - + "([&&NHX:S=i1],[&&NHX:S=i2],[&&NHX:S=i3],[&&NHX:S=i4])," - + "([&&NHX:S=j1],[&&NHX:S=j2],[&&NHX:S=j3],[&&NHX:S=j4])," - + "([&&NHX:S=k1],[&&NHX:S=k2],[&&NHX:S=k3],[&&NHX:S=k4])," - + "([&&NHX:S=l1],[&&NHX:S=l2],[&&NHX:S=l3],[&&NHX:S=l4])),(" - + "([&&NHX:S=m1],[&&NHX:S=m2],[&&NHX:S=m3],[&&NHX:S=m4])," - + "([&&NHX:S=n1],[&&NHX:S=n2],[&&NHX:S=n3],[&&NHX:S=n4])," - + "([&&NHX:S=o1],[&&NHX:S=o2],[&&NHX:S=o3],[&&NHX:S=o4])," - + "([&&NHX:S=p1],[&&NHX:S=p2],[&&NHX:S=p3],[&&NHX:S=p4])" - + "),[&&NHX:S=x],[&&NHX:S=y],[&&NHX:S=z])"; - final Phylogeny s2 = ParserBasedPhylogenyFactory.getInstance().create( s2_, new NHXParser() )[ 0 ]; - s2.setRooted( true ); final Phylogeny g2_0 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],m3[&&NHX:S=m3])" ); final GSDI sdi2_0 = new GSDI( g2_0, s2, false ); if ( sdi2_0.getDuplicationsSum() != 0 ) { @@ -629,6 +637,8 @@ 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 ); if ( sdi2_22.getDuplicationsSum() != 0 ) { return false; } @@ -923,6 +933,18 @@ public final class TestGSDI { 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 ); + 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 ); @@ -1188,23 +1210,183 @@ public final class TestGSDI { 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 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 ); + 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 ); @@ -1212,4 +1394,23 @@ 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" ); + } + else { + System.out.println( "general OK" ); + } + // boolean success = test(); + // if ( success ) { + // System.out.println( "OK" ); + // } + // else { + // System.out.println( "failed" ); + // } + } }