// 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
// 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
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 );
}
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() {
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;
}
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 ) {
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;
}
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 );
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 );
}
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" );
+ // }
+ }
}
git://source.jalview.org / jalview.git / blobdiff