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=62ab0f85e0d86030186ed8d54f14ada50f7994b3;hpb=caebe5e946fc15f9042dc70cac985910c6205e3c;p=jalview.git diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index 62ab0f8..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]))," @@ -1249,7 +1283,7 @@ public final class TestGSDI { //-- final Phylogeny tol_143_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA + "tol_143.xml" )[ 0 ]; final Phylogeny gene_tree_tax_code_4_ = ParserUtils.readPhylogenies( PATH_TO_TEST_DATA - + "gene_tree_tax_code_4.xml" )[ 0 ]; + + "gene_tree_tax_code_4.xml" )[ 0 ]; final GSDI gsdi_143_4_1 = new GSDI( gene_tree_tax_code_4_.copy(), tol_143_.copy(), false, true, true ); if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) { return false; @@ -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, false ); + 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, false ); + 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, false ); + 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, false ); + 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" ); - // } - } }