X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FTestGSDI.java;h=045eebb2d671a6f6039b3589ab312e695f05c181;hb=d55628ea76bcf138e44e6aee3d0e953dec1c2360;hp=b26e800070f6fe68bb97eecdbdcd4ee968dde726;hpb=14f8357072fabd3b089bbe8c5eee7ce2a5be2c6e;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index b26e800..045eebb 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -27,19 +27,22 @@ 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 com.itextpdf.text.pdf.ArabicLigaturizer; +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 ); @@ -47,7 +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() { @@ -885,18 +888,9 @@ public final class TestGSDI { 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; } @@ -939,6 +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 ); @@ -1204,7 +1210,6 @@ 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_0p = TestGSDI.createPhylogeny( g2_0_ ); g2_0.setRooted( true ); @@ -1212,6 +1217,176 @@ public final class TestGSDI { 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 );