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.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 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() {
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 );
- Archaeopteryx.createApplication( gsdi_143_4_1.getGeneTree() );
if ( gsdi_143_4_1.getDuplicationsSum() != 21 ) {
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 );
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