+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// 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
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// 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
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.sdi;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Event;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
-
-/*
- * Implements our algorithm for speciation - duplication inference (SDI). <p>
- * The initialization is accomplished by: </p> <ul> <li>method
- * "linkExtNodesOfG()" of class SDI: setting the links for the external nodes of
- * the gene tree <li>"preorderReID(int)" from class Phylogeny: numbering of
- * nodes of the species tree in preorder <li>the optional stripping of the
- * species tree is accomplished by method "stripTree(Phylogeny,Phylogeny)" of
- * class Phylogeny </ul> <p> The recursion part is accomplished by this class'
- * method "geneTreePostOrderTraversal(PhylogenyNode)". <p> Requires JDK 1.5 or
- * greater.
- *
- * @see SDI#linkNodesOfG()
- *
- * @see Phylogeny#preorderReID(int)
- *
- * @see
- * PhylogenyMethods#taxonomyBasedDeletionOfExternalNodes(Phylogeny,Phylogeny)
- *
- * @see #geneTreePostOrderTraversal(PhylogenyNode)
- *
- * @author Christian M. Zmasek
- */
-public final class GSDIold extends SDI {
-
- private final HashMap<PhylogenyNode, Integer> _transversal_counts;
- private final boolean _most_parsimonious_duplication_model;
- private final boolean _strip_gene_tree;
- private final boolean _strip_species_tree;
- private int _speciation_or_duplication_events_sum;
- private int _speciations_sum;
- private final List<PhylogenyNode> _stripped_gene_tree_nodes;
- private final List<PhylogenyNode> _stripped_species_tree_nodes;
- private final Set<PhylogenyNode> _mapped_species_tree_nodes;
-
- /**
- * Constructor which sets the gene tree and the species tree to be compared.
- * species_tree is the species tree to which the gene tree gene_tree will be
- * compared to - with method "infer(boolean)". Both Trees must be completely
- * binary and rooted. The actual inference is accomplished with method
- * "infer(boolean)". The mapping cost L can then be calculated with method
- * "computeMappingCost()".
- * <p>
- *
- * @see #infer(boolean)
- * @see SDI#computeMappingCostL()
- * @param gene_tree
- * reference to a rooted gene tree to which assign duplication vs
- * speciation, must have species names in the species name fields
- * for all external nodes
- * @param species_tree
- * reference to a rooted binary species tree which might get
- * stripped in the process, must have species names in the
- * species name fields for all external nodes
- *
- * @param most_parsimonious_duplication_model
- * set to true to assign nodes as speciations which would
- * otherwise be assiged as unknown because of polytomies in the
- * species tree.
- * @throws SdiException
- *
- */
- public GSDIold( final Phylogeny gene_tree,
- final Phylogeny species_tree,
- final boolean most_parsimonious_duplication_model,
- final boolean strip_gene_tree,
- final boolean strip_species_tree ) throws SdiException {
- super( gene_tree, species_tree );
- _speciation_or_duplication_events_sum = 0;
- _speciations_sum = 0;
- _most_parsimonious_duplication_model = most_parsimonious_duplication_model;
- _transversal_counts = new HashMap<PhylogenyNode, Integer>();
- _duplications_sum = 0;
- _strip_gene_tree = strip_gene_tree;
- _strip_species_tree = strip_species_tree;
- _stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
- _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
- _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
- getSpeciesTree().preOrderReId();
- linkNodesOfG();
- //geneTreePostOrderTraversal( getGeneTree().getRoot(), null );
- geneTreePostOrderTraversal2();
- }
-
- GSDIold( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean most_parsimonious_duplication_model )
- throws SdiException {
- this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
- }
-
- // s is the node on the species tree g maps to.
- private final void determineEvent( final PhylogenyNode s, final PhylogenyNode g ) {
- Event event = null;
- // Determine how many children map to same node as parent.
- int sum_g_childs_mapping_to_s = 0;
- for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode c = g.getChildNode( i );
- if ( c.getLink() == s ) {
- ++sum_g_childs_mapping_to_s;
- }
- }
- // Determine the sum of traversals.
- int traversals_sum = 0;
- int max_traversals = 0;
- PhylogenyNode max_traversals_node = null;
- if ( !s.isExternal() ) {
- for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode current_node = s.getChildNode( i );
- final int traversals = getTraversalCount( current_node );
- traversals_sum += traversals;
- if ( traversals > max_traversals ) {
- max_traversals = traversals;
- max_traversals_node = current_node;
- }
- }
- }
- // System.out.println( " sum=" + traversals_sum );
- // System.out.println( " max=" + max_traversals );
- // System.out.println( " m=" + sum_g_childs_mapping_to_s );
- if ( sum_g_childs_mapping_to_s > 0 ) {
- if ( traversals_sum == 2 ) {
- event = createDuplicationEvent();
- System.out.print( g.toString() );
- System.out.println( " : ==2" );
- // _transversal_counts.clear();
- }
- else if ( traversals_sum > 2 ) {
- if ( max_traversals <= 1 ) {
- if ( _most_parsimonious_duplication_model ) {
- event = createSpeciationEvent();
- }
- else {
- event = createSingleSpeciationOrDuplicationEvent();
- }
- }
- else {
- event = createDuplicationEvent();
- // normalizeTcounts( s );
- //System.out.println( g.toString() );
- _transversal_counts.put( max_traversals_node, 1 );
- // _transversal_counts.clear();
- }
- }
- else {
- event = createDuplicationEvent();
- // _transversal_counts.clear();
- }
- //normalizeTcounts( s );
- }
- else {
- event = createSpeciationEvent();
- }
- g.getNodeData().setEvent( event );
- }
-
- // private final void determineEvent2( final PhylogenyNode s, final PhylogenyNode g ) {
- // Event event = null;
- // // Determine how many children map to same node as parent.
- // int sum_g_childs_mapping_to_s = 0;
- // for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
- // final PhylogenyNode c = g.getChildNode( i );
- // if ( c.getLink() == s ) {
- // ++sum_g_childs_mapping_to_s;
- // }
- // }
- // // Determine the sum of traversals.
- // int traversals_sum = 0;
- // int max_traversals = 0;
- // PhylogenyNode max_traversals_node = null;
- // if ( !s.isExternal() ) {
- // for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- // final PhylogenyNode current_node = s.getChildNode( i );
- // final int traversals = getTraversalCount( current_node );
- // traversals_sum += traversals;
- // if ( traversals > max_traversals ) {
- // max_traversals = traversals;
- // max_traversals_node = current_node;
- // }
- // }
- // }
- // // System.out.println( " sum=" + traversals_sum );
- // // System.out.println( " max=" + max_traversals );
- // // System.out.println( " m=" + sum_g_childs_mapping_to_s );
- // if ( s.getNumberOfDescendants() == 2 ) {
- // if ( sum_g_childs_mapping_to_s == 0 ) {
- // event = createSpeciationEvent();
- // }
- // else {
- // event = createDuplicationEvent();
- // }
- // }
- // else {
- // if ( sum_g_childs_mapping_to_s == 2 ) {
- // event = createDuplicationEvent();
- // }
- // else if ( sum_g_childs_mapping_to_s == 1 ) {
- // event = createSingleSpeciationOrDuplicationEvent();
- // }
- // else {
- // event = createSpeciationEvent();
- // }
- // }
- // g.getNodeData().setEvent( event );
- // }
- final void geneTreePostOrderTraversal2() {
- PhylogenyNode g = null;
- for( PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
- g = it.next();
- if ( !g.isExternal() ) {
- for( PhylogenyNodeIterator itw = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
- PhylogenyNode gg = it.next();
- gg.setLink( null );
- }
- try {
- linkNodesOfG();
- }
- catch ( SdiException e ) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- _transversal_counts.clear();
- final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
- for( int i = 0; i < linked_nodes.length; ++i ) {
- if ( g.getChildNode( i ).getLink() == null ) {
- System.out.println( "link is null for " + g.getChildNode( i ) );
- System.exit( -1 );
- }
- linked_nodes[ i ] = g.getChildNode( i ).getLink();
- }
- final int[] min_max = obtainMinMaxIdIndices( linked_nodes );
- int min_i = min_max[ 0 ];
- int max_i = min_max[ 1 ];
- // initTransversalCounts();
- while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
- increaseTraversalCount( linked_nodes[ max_i ] );
- // if ( linked_nodes[ max_i ].isExternal() ) {
- // System.out.println( "i am ext!" );
- // PhylogenyNode n = linked_nodes[ max_i ];
- // while ( !n.isRoot() ) {
- // _transversal_counts.put( n, 0 );
- // n = n.getParent();
- // }
- // }
- linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
- final int[] min_max_ = obtainMinMaxIdIndices( linked_nodes );
- min_i = min_max_[ 0 ];
- max_i = min_max_[ 1 ];
- }
- final PhylogenyNode s = linked_nodes[ max_i ];
- g.setLink( s );
- // Determines whether dup. or spec.
- determineEvent( s, g );
- }
- }
- }
-
- final void geneTreePostOrderTraversal() {
- PhylogenyNode prev;
- PhylogenyNode g = null;
- for( PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
- prev = g;
- g = it.next();
- if ( !g.isExternal() ) {
- final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
- for( int i = 0; i < linked_nodes.length; ++i ) {
- if ( g.getChildNode( i ).getLink() == null ) {
- System.out.println( "link is null for " + g.getChildNode( i ) );
- System.exit( -1 );
- }
- linked_nodes[ i ] = g.getChildNode( i ).getLink();
- }
- final int[] min_max = obtainMinMaxIdIndices( linked_nodes );
- int min_i = min_max[ 0 ];
- int max_i = min_max[ 1 ];
- // initTransversalCounts();
- while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
- increaseTraversalCount( linked_nodes[ max_i ] );
- // if ( linked_nodes[ max_i ].isExternal() ) {
- // System.out.println( "i am ext!" );
- // PhylogenyNode n = linked_nodes[ max_i ];
- // while ( !n.isRoot() ) {
- // _transversal_counts.put( n, 0 );
- // n = n.getParent();
- // }
- // }
- linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
- final int[] min_max_ = obtainMinMaxIdIndices( linked_nodes );
- min_i = min_max_[ 0 ];
- max_i = min_max_[ 1 ];
- }
- final PhylogenyNode s = linked_nodes[ max_i ];
- g.setLink( s );
- // Determines whether dup. or spec.
- determineEvent( s, g );
- if ( false ) {
- System.out.println( "******" );
- _transversal_counts.clear();
- }
- }
- }
- }
-
- /**
- * Traverses the subtree of PhylogenyNode g in postorder, calculating the
- * mapping function M, and determines which nodes represent speciation
- * events and which ones duplication events.
- * <p>
- * Preconditions: Mapping M for external nodes must have been calculated and
- * the species tree must be labeled in preorder.
- * <p>
- *
- * @param g
- * starting node of a gene tree - normally the root
- */
- final void geneTreePostOrderTraversal( final PhylogenyNode g ) {
- if ( !g.isExternal() ) {
- for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
- geneTreePostOrderTraversal( g.getChildNode( i ) );
- }
- final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
- for( int i = 0; i < linked_nodes.length; ++i ) {
- if ( g.getChildNode( i ).getLink() == null ) {
- System.out.println( "link is null for " + g.getChildNode( i ) );
- System.exit( -1 );
- }
- linked_nodes[ i ] = g.getChildNode( i ).getLink();
- }
- final int[] min_max = obtainMinMaxIdIndices( linked_nodes );
- int min_i = min_max[ 0 ];
- int max_i = min_max[ 1 ];
- // initTransversalCounts();
- while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
- increaseTraversalCount( linked_nodes[ max_i ] );
- // if ( linked_nodes[ max_i ].isExternal() ) {
- // System.out.println( "i am ext!" );
- // PhylogenyNode n = linked_nodes[ max_i ];
- // while ( !n.isRoot() ) {
- // _transversal_counts.put( n, 0 );
- // n = n.getParent();
- // }
- // }
- linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
- final int[] min_max_ = obtainMinMaxIdIndices( linked_nodes );
- min_i = min_max_[ 0 ];
- max_i = min_max_[ 1 ];
- }
- final PhylogenyNode s = linked_nodes[ max_i ];
- g.setLink( s );
- // Determines whether dup. or spec.
- determineEvent( s, g );
- }
- }
-
- private final Event createDuplicationEvent() {
- final Event event = Event.createSingleDuplicationEvent();
- ++_duplications_sum;
- return event;
- }
-
- private final Event createSingleSpeciationOrDuplicationEvent() {
- final Event event = Event.createSingleSpeciationOrDuplicationEvent();
- ++_speciation_or_duplication_events_sum;
- return event;
- }
-
- private final Event createSpeciationEvent() {
- final Event event = Event.createSingleSpeciationEvent();
- ++_speciations_sum;
- return event;
- }
-
- public final int getSpeciationOrDuplicationEventsSum() {
- return _speciation_or_duplication_events_sum;
- }
-
- public final int getSpeciationsSum() {
- return _speciations_sum;
- }
-
- private final int getTraversalCount( final PhylogenyNode node ) {
- if ( _transversal_counts.containsKey( node ) ) {
- return _transversal_counts.get( node );
- }
- return 0;
- }
-
- private final void increaseTraversalCount( final PhylogenyNode node ) {
- if ( _transversal_counts.containsKey( node ) ) {
- _transversal_counts.put( node, _transversal_counts.get( node ) + 1 );
- }
- else {
- _transversal_counts.put( node, 1 );
- }
- // System.out.println( "count for node " + node.getID() + " is now "
- // + getTraversalCount( node ) );
- }
-
- private void normalizeTcounts( final PhylogenyNode s ) {
- // int min_traversals = Integer.MAX_VALUE;
- // for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- // final PhylogenyNode current_node = s.getChildNode( i );
- // final int traversals = getTraversalCount( current_node );
- // if ( traversals < min_traversals ) {
- // min_traversals = traversals;
- // }
- // }
- for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode current_node = s.getChildNode( i );
- // _transversal_counts.put( current_node, getTraversalCount( current_node ) - min_traversals );
- if ( getTraversalCount( current_node ) > 1 ) {
- _transversal_counts.put( current_node, 1 );
- }
- }
- }
-
- /**
- * This allows for linking of internal nodes of the species tree (as opposed
- * to just external nodes, as in the method it overrides.
- * @throws SdiException
- *
- */
- @Override
- // final void linkNodesOfG() {
- // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = createTaxonomyToNodeMap();
- // if ( _strip_gene_tree ) {
- // stripGeneTree( speciestree_ext_nodes );
- // if ( ( _gene_tree == null ) || ( _gene_tree.getNumberOfExternalNodes() < 2 ) ) {
- // throw new IllegalArgumentException( "species tree does not contain any"
- // + " nodes matching species in the gene tree" );
- // }
- // }
- // // Retrieve the reference to the PhylogenyNode with a matching species.
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- // }
- // final PhylogenyNode s = speciestree_ext_nodes.get( g.getNodeData().getTaxonomy() );
- // if ( s == null ) {
- // throw new IllegalArgumentException( "species " + g.getNodeData().getTaxonomy()
- // + " not present in species tree" );
- // }
- // g.setLink( s );
- // }
- // }
- final void linkNodesOfG() throws SdiException {
- final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
- final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
- final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
- // System.out.println( "comp base is: " + tax_comp_base );
- // Stringyfied taxonomy is the key, node is the value.
- for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode s = iter.next();
- species_tree_ext_nodes.add( s );
- final String tax_str = taxonomyToString( s, tax_comp_base );
- if ( !ForesterUtil.isEmpty( tax_str ) ) {
- if ( species_to_node_map.containsKey( tax_str ) ) {
- throw new SdiException( "taxonomy \"" + s + "\" is not unique in species tree" );
- }
- species_to_node_map.put( tax_str, s );
- }
- }
- // Retrieve the reference to the node with a matching stringyfied taxonomy.
- for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode g = iter.next();
- if ( !g.getNodeData().isHasTaxonomy() ) {
- if ( _strip_gene_tree ) {
- _stripped_gene_tree_nodes.add( g );
- }
- else {
- throw new SdiException( "gene tree node \"" + g + "\" has no taxonomic data" );
- }
- }
- else {
- final String tax_str = taxonomyToString( g, tax_comp_base );
- if ( ForesterUtil.isEmpty( tax_str ) ) {
- if ( _strip_gene_tree ) {
- _stripped_gene_tree_nodes.add( g );
- }
- else {
- throw new SdiException( "gene tree node \"" + g + "\" has no appropriate taxonomic data" );
- }
- }
- else {
- final PhylogenyNode s = species_to_node_map.get( tax_str );
- if ( s == null ) {
- if ( _strip_gene_tree ) {
- _stripped_gene_tree_nodes.add( g );
- }
- else {
- throw new SdiException( "taxonomy \"" + g.getNodeData().getTaxonomy()
- + "\" not present in species tree" );
- }
- }
- else {
- g.setLink( s );
- _mapped_species_tree_nodes.add( s );
- // System.out.println( "setting link of " + g + " to " + s );
- }
- }
- }
- } // for loop
- if ( _strip_gene_tree ) {
- for( final PhylogenyNode g : _stripped_gene_tree_nodes ) {
- _gene_tree.deleteSubtree( g, true );
- }
- }
- if ( _strip_species_tree ) {
- for( final PhylogenyNode s : species_tree_ext_nodes ) {
- if ( !_mapped_species_tree_nodes.contains( s ) ) {
- _species_tree.deleteSubtree( s, true );
- }
- }
- }
- }
-
- public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
- return _mapped_species_tree_nodes;
- }
-
- // final private HashMap<Taxonomy, PhylogenyNode> createTaxonomyToNodeMap() {
- // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = new HashMap<Taxonomy, PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _species_tree.iteratorLevelOrder(); iter.hasNext(); ) {
- // final PhylogenyNode n = iter.next();
- // if ( n.getNodeData().isHasTaxonomy() ) {
- // if ( speciestree_ext_nodes.containsKey( n.getNodeData().getTaxonomy() ) ) {
- // throw new IllegalArgumentException( "taxonomy [" + n.getNodeData().getTaxonomy()
- // + "] is not unique in species phylogeny" );
- // }
- // speciestree_ext_nodes.put( n.getNodeData().getTaxonomy(), n );
- // }
- // }
- // return speciestree_ext_nodes;
- // }
- // private final void stripGeneTree( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- // }
- // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // }
- // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- // _gene_tree.deleteSubtree( n, true );
- // }
- // }
- // private final void stripGeneTree2( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // else {
- // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // }
- // }
- // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- // _gene_tree.deleteSubtree( n, true );
- // }
- // }
- public static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree ) {
- int with_id_count = 0;
- int with_code_count = 0;
- int with_sn_count = 0;
- int max = 0;
- for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- final PhylogenyNode g = iter.next();
- if ( g.getNodeData().isHasTaxonomy() ) {
- final Taxonomy tax = g.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
- if ( ++with_id_count > max ) {
- max = with_id_count;
- }
- }
- if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- if ( ++with_code_count > max ) {
- max = with_code_count;
- }
- }
- if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- if ( ++with_sn_count > max ) {
- max = with_sn_count;
- }
- }
- }
- }
- if ( max == 0 ) {
- throw new IllegalArgumentException( "gene tree has no taxonomic data" );
- }
- else if ( max == 1 ) {
- throw new IllegalArgumentException( "gene tree has only one node with taxonomic data" );
- }
- else if ( max == with_sn_count ) {
- return SDI.TaxonomyComparisonBase.SCIENTIFIC_NAME;
- }
- else if ( max == with_id_count ) {
- return SDI.TaxonomyComparisonBase.ID;
- }
- else {
- return SDI.TaxonomyComparisonBase.CODE;
- }
- }
-
- public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
- return _stripped_gene_tree_nodes;
- }
-
- @Override
- public final String toString() {
- final StringBuffer sb = new StringBuffer();
- sb.append( "Most parsimonious duplication model: " + _most_parsimonious_duplication_model );
- sb.append( ForesterUtil.getLineSeparator() );
- sb.append( "Speciations sum : " + getSpeciationsSum() );
- sb.append( ForesterUtil.getLineSeparator() );
- sb.append( "Duplications sum : " + getDuplicationsSum() );
- sb.append( ForesterUtil.getLineSeparator() );
- if ( !_most_parsimonious_duplication_model ) {
- sb.append( "Speciation or duplications sum : " + getSpeciationOrDuplicationEventsSum() );
- sb.append( ForesterUtil.getLineSeparator() );
- }
- sb.append( "mapping cost L : " + computeMappingCostL() );
- return sb.toString();
- }
-
- static final int[] obtainMinMaxIdIndices( final PhylogenyNode[] linked_nodes ) {
- int max_i = 0;
- int min_i = 0;
- int max_i_id = -Integer.MAX_VALUE;
- int min_i_id = Integer.MAX_VALUE;
- for( int i = 0; i < linked_nodes.length; ++i ) {
- final int id_i = linked_nodes[ i ].getId();
- if ( id_i > max_i_id ) {
- max_i = i;
- max_i_id = linked_nodes[ max_i ].getId();
- }
- if ( id_i < min_i_id ) {
- min_i = i;
- min_i_id = linked_nodes[ min_i ].getId();
- }
- }
- return new int[] { min_i, max_i };
- }
- /**
- * Updates the mapping function M after the root of the gene tree has been
- * moved by one branch. It calculates M for the root of the gene tree and
- * one of its two children.
- * <p>
- * To be used ONLY by method "SDIunrooted.fastInfer(Phylogeny,Phylogeny)".
- * <p>
- * (Last modfied: )
- *
- * @param prev_root_was_dup
- * true if the previous root was a duplication, false otherwise
- * @param prev_root_c1
- * child 1 of the previous root
- * @param prev_root_c2
- * child 2 of the previous root
- * @return number of duplications which have been assigned in gene tree
- */
- // int updateM( final boolean prev_root_was_dup,
- // final PhylogenyNode prev_root_c1, final PhylogenyNode prev_root_c2 ) {
- // final PhylogenyNode root = getGeneTree().getRoot();
- // if ( ( root.getChildNode1() == prev_root_c1 )
- // || ( root.getChildNode2() == prev_root_c1 ) ) {
- // calculateMforNode( prev_root_c1 );
- // }
- // else {
- // calculateMforNode( prev_root_c2 );
- // }
- // Event event = null;
- // if ( prev_root_was_dup ) {
- // event = Event.createSingleDuplicationEvent();
- // }
- // else {
- // event = Event.createSingleSpeciationEvent();
- // }
- // root.getPhylogenyNodeData().setEvent( event );
- // calculateMforNode( root );
- // return getDuplications();
- // } // updateM( boolean, PhylogenyNode, PhylogenyNode )
- // Helper method for updateM( boolean, PhylogenyNode, PhylogenyNode )
- // Calculates M for PhylogenyNode n, given that M for the two children
- // of n has been calculated.
- // (Last modified: 10/02/01)
- // private void calculateMforNode( final PhylogenyNode n ) {
- // if ( !n.isExternal() ) {
- // boolean was_duplication = n.isDuplication();
- // PhylogenyNode a = n.getChildNode1().getLink(), b = n
- // .getChildNode2().getLink();
- // while ( a != b ) {
- // if ( a.getID() > b.getID() ) {
- // a = a.getParent();
- // }
- // else {
- // b = b.getParent();
- // }
- // }
- // n.setLink( a );
- // Event event = null;
- // if ( ( a == n.getChildNode1().getLink() )
- // || ( a == n.getChildNode2().getLink() ) ) {
- // event = Event.createSingleDuplicationEvent();
- // if ( !was_duplication ) {
- // increaseDuplications();
- // }
- // }
- // else {
- // event = Event.createSingleSpeciationEvent();
- // if ( was_duplication ) {
- // decreaseDuplications();
- // }
- // }
- // n.getPhylogenyNodeData().setEvent( event );
- // }
- // } // calculateMforNode( PhylogenyNode )
-}
import java.io.IOException;
import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.development.DevelopmentTools;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
+import com.itextpdf.text.pdf.ArabicLigaturizer;
+
public final class TestGSDI {
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
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 );
+ // Archaeopteryx.createApplication( g1 );
+ // Archaeopteryx.createApplication( s1 );
if ( sdi1.getDuplicationsSum() != 1 ) {
return false;
}
if ( !pm.obtainLCA( g1.getNode( "D" ), g1.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
return false;
}
- // final Phylogeny g2 = TestGSDI
- // .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
- // final GSDI sdi2 = new GSDI( g2, s1, false );
- // if ( sdi2.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
- // .isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g3 = TestGSDI
- // .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
- // final GSDI sdi3 = new GSDI( g3, s1, false );
- // if ( sdi3.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
- // .isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g4 = TestGSDI
- // .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
- // final GSDI sdi4 = new GSDI( g4, s1, false );
- // if ( sdi4.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g5 = TestGSDI
- // .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
- // final GSDI sdi5 = new GSDI( g5, s1, false );
- // if ( sdi5.getDuplicationsSum() != 3 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
- // + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
- // + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
- // + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
- // + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
- // final Phylogeny gene7_2 = TestGSDI
- // .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
- // gene7_2.setRooted( true );
- // final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
- // if ( sdi7_2.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
- // return false;
- // }
- // 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 ) {
- // return false;
- // }
- // if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_0.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
- // final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
- // if ( sdi2_1.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_1.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
- // final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
- // if ( sdi2_2.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_2.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
- // final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
- // if ( sdi2_3.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_3.getSpeciationsSum() != 0 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
- // final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
- // if ( sdi2_4.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_4.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
- // final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
- // if ( sdi2_5.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_5.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
- // final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
- // if ( sdi2_6.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_6.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
- // final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
- // if ( sdi2_7.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_7.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
- // .isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
- // final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
- // if ( sdi2_8.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_8.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
- // .isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
- // final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
- // if ( sdi2_9.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_9.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
- // final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
- // if ( sdi2_10.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_10.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
- // final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
- // if ( sdi2_11.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_11.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
- // final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
- // if ( sdi2_12.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_12.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
- // final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
- // if ( sdi2_13.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_13.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
- // final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
- // if ( sdi2_14.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_14.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
- // final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
- // if ( sdi2_15.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_15.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
- // final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
- // if ( sdi2_16.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_16.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
- // final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
- // if ( sdi2_17.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_17.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_18 = TestGSDI
- // .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
- // final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
- // if ( sdi2_18.getDuplicationsSum() != 3 ) {
- // return false;
- // }
- // if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_18.getSpeciationsSum() != 0 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_19 = TestGSDI
- // .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
- // final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
- // if ( sdi2_19.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_19.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_20 = TestGSDI
- // .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
- // final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
- // if ( sdi2_20.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_20.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_21 = TestGSDI
- // .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
- // final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
- // if ( sdi2_21.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_21.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
- // return false;
- // }
- // 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 ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_22.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_23 = TestGSDI
- // .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
- // final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
- // if ( sdi2_23.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_23.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_24 = TestGSDI
- // .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
- // final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
- // if ( sdi2_24.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_24.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_25 = TestGSDI
- // .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
- // final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
- // if ( sdi2_25.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_25.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_26 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
- // final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
- // if ( sdi2_26.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_26.getSpeciationsSum() != 3 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_27 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
- // final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
- // if ( sdi2_27.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_27.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_28 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
- // final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
- // if ( sdi2_28.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_28.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_29 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
- // final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
- // if ( sdi2_29.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
- // return false;
- // }
- // if ( sdi2_29.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_30 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
- // final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
- // if ( sdi2_30.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_30.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_31 = TestGSDI
- // .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
- // final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
- // if ( sdi2_31.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_31.getSpeciationsSum() != 1 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_32 = 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]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
- // final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
- // if ( sdi2_32.getDuplicationsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
- // return false;
- // }
- // if ( sdi2_32.getSpeciationsSum() != 3 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // 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;
- // }
- // if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
- // return false;
- // }
- // if ( sdi2_33.getSpeciationsSum() != 3 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
- // 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 ( sdi2_34.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_34.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_35 = 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]),a1_0[&&NHX:S=a1])" );
- // final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
- // if ( sdi2_35.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_35.getSpeciationsSum() != 3 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g2_36 = TestGSDI
- // .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
- // final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
- // if ( sdi2_36.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_36.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_37 = TestGSDI
- // .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
- // final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
- // if ( sdi2_37.getDuplicationsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_37.getSpeciationsSum() != 2 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_38 = TestGSDI
- // .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
- // final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
- // if ( sdi2_38.getDuplicationsSum() != 5 ) {
- // return false;
- // }
- // if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_38.getSpeciationsSum() != 0 ) {
- // return false;
- // }
- // final Phylogeny g2_100 = TestGSDI
- // .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
- // final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
- // if ( sdi2_100.getDuplicationsSum() != 4 ) {
- // return false;
- // }
- // if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
- // return false;
- // }
- // if ( sdi2_100.getSpeciationsSum() != 4 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny g2_101 = TestGSDI
- // .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
- // final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
- // if ( sdi2_101.getDuplicationsSum() != 2 ) {
- // return false;
- // }
- // if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
- // return false;
- // }
- // if ( sdi2_101.getSpeciationsSum() != 5 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
- // return false;
- // }
- // final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
- // DevelopmentTools.numberSpeciesInOrder( s_7_4 );
- // final Phylogeny g_7_4_1 = TestGSDI
- // .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
- // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
- // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
- // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
- // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
- // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
- // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
- // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
- // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
- // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
- // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
- // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
- // final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
- // if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
- // return false;
- // }
- // if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
- // return false;
- // }
- // if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
- // return false;
- // }
- // if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
- // return false;
- // }
- // final Phylogeny g_7_4_2 = TestGSDI
- // .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
- // + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
- // + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
- // + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
- // + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
- // + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
- // + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
- // + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
- // + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
- // + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
- // + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
- // + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
- // + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
- // final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
- // if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
- // return false;
- // }
- // if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
- // return 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 Phylogeny g2 = TestGSDI
+ .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),B[&&NHX:S=B]),C[&&NHX:S=C]),D[&&NHX:S=D])" );
+ final GSDI sdi2 = new GSDI( g2, s1, false );
+ if ( sdi2.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "B" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "C" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2.getNode( "A1" ), g2.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g3 = TestGSDI
+ .createPhylogeny( "((((A2[&&NHX:S=A2],A1[&&NHX:S=A1]),C[&&NHX:S=C]),B[&&NHX:S=B]),D[&&NHX:S=D])" );
+ final GSDI sdi3 = new GSDI( g3, s1, false );
+ if ( sdi3.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "A2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "C" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "B" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g3.getNode( "A1" ), g3.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g4 = TestGSDI
+ .createPhylogeny( "(((B[&&NHX:S=B],C1[&&NHX:S=C]),C2[&&NHX:S=C]),D[&&NHX:S=D])" );
+ final GSDI sdi4 = new GSDI( g4, s1, false );
+ if ( sdi4.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "C2" ) ).getNodeData().getEvent().isDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g4.getNode( "B" ), g4.getNode( "D" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g5 = TestGSDI
+ .createPhylogeny( "(((D1[&&NHX:S=D],A1[&&NHX:S=A1]),B[&&NHX:S=B]),((D2[&&NHX:S=D],D3[&&NHX:S=D]),C[&&NHX:S=C]))" );
+ final GSDI sdi5 = new GSDI( g5, s1, false );
+ if ( sdi5.getDuplicationsSum() != 3 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "A1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "B" ) ).getNodeData().getEvent().isDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g5.getNode( "D1" ), g5.getNode( "D2" ) ).getNodeData().getEvent().isDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g5.getNode( "D2" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g5.getNode( "C" ), g5.getNode( "D3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny species7 = TestGSDI.createPhylogeny( "(((((((([&&NHX:S=a1],[&&NHX:S=a2]),"
+ + "([&&NHX:S=b1],[&&NHX:S=b2])),[&&NHX:S=x]),(([&&NHX:S=m1],[&&NHX:S=m2]),"
+ + "([&&NHX:S=n1],[&&NHX:S=n2]))),(([&&NHX:S=i1],[&&NHX:S=i2]),"
+ + "([&&NHX:S=j1],[&&NHX:S=j2]))),(([&&NHX:S=e1],[&&NHX:S=e2]),"
+ + "([&&NHX:S=f1],[&&NHX:S=f2]))),[&&NHX:S=y]),[&&NHX:S=z])" );
+ final Phylogeny gene7_2 = TestGSDI
+ .createPhylogeny( "(((((((((a1[&&NHX:S=a1],a2[&&NHX:S=a2]),b1[&&NHX:S=b1]),x[&&NHX:S=x]),m1[&&NHX:S=m1]),i1[&&NHX:S=i1]),j2[&&NHX:S=j2]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+ gene7_2.setRooted( true );
+ final GSDI sdi7_2 = new GSDI( gene7_2, species7, false );
+ if ( sdi7_2.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "a2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "x" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "m1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "i1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "j2" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "y" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( gene7_2, "a1", "z" ).isSpeciation() ) {
+ return false;
+ }
+ 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 ) {
+ return false;
+ }
+ if ( sdi2_0.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_0.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_0.getNode( "m1" ), g2_0.getNode( "m3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_1 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],h2[&&NHX:S=h2])" );
+ final GSDI sdi2_1 = new GSDI( g2_1, s2, false );
+ if ( sdi2_1.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_1.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_1.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_1.getNode( "e2" ), g2_1.getNode( "h2" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_2 = TestGSDI.createPhylogeny( "(e2[&&NHX:S=e2],p4[&&NHX:S=p4])" );
+ final GSDI sdi2_2 = new GSDI( g2_2, s2, false );
+ if ( sdi2_2.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_2.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_2.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_2.getNode( "e2" ), g2_2.getNode( "p4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_3 = TestGSDI.createPhylogeny( "(e2a[&&NHX:S=e2],e2b[&&NHX:S=e2])" );
+ final GSDI sdi2_3 = new GSDI( g2_3, s2, false );
+ if ( sdi2_3.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_3.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_3.getSpeciationsSum() != 0 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_3.getNode( "e2a" ), g2_3.getNode( "e2b" ) ).getNodeData().getEvent().isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_4 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),i3[&&NHX:S=i3])" );
+ final GSDI sdi2_4 = new GSDI( g2_4, s2, false );
+ if ( sdi2_4.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_4.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_4.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_4.getNode( "j1" ), g2_4.getNode( "i3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_5 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],j4[&&NHX:S=j4]),f3[&&NHX:S=f3])" );
+ final GSDI sdi2_5 = new GSDI( g2_5, s2, false );
+ if ( sdi2_5.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_5.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_5.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "j4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_5.getNode( "j1" ), g2_5.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_6 = TestGSDI.createPhylogeny( "((j3[&&NHX:S=j3],i4[&&NHX:S=i4]),f3[&&NHX:S=f3])" );
+ final GSDI sdi2_6 = new GSDI( g2_6, s2, false );
+ if ( sdi2_6.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_6.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_6.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "i4" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_6.getNode( "j3" ), g2_6.getNode( "f3" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_7 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k1[&&NHX:S=k1]),i1[&&NHX:S=i1])" );
+ final GSDI sdi2_7 = new GSDI( g2_7, s2, false );
+ if ( sdi2_7.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_7.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_7.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "k1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_7.getNode( "j1" ), g2_7.getNode( "i1" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_8 = TestGSDI.createPhylogeny( "(j1[&&NHX:S=j1],(k1[&&NHX:S=k1],i1[&&NHX:S=i1]))" );
+ final GSDI sdi2_8 = new GSDI( g2_8, s2, false );
+ if ( sdi2_8.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_8.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_8.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_8.getNode( "j1" ), g2_8.getNode( "k1" ) ).getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !pm.obtainLCA( g2_8.getNode( "k1" ), g2_8.getNode( "i1" ) ).getNodeData().getEvent().isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_9 = TestGSDI.createPhylogeny( "((j1[&&NHX:S=j1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
+ final GSDI sdi2_9 = new GSDI( g2_9, s2, false );
+ if ( sdi2_9.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_9.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_9.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_9, "j1", "k4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_9, "j1", "f2" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_10 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),f2[&&NHX:S=f2])" );
+ final GSDI sdi2_10 = new GSDI( g2_10, s2, false );
+ if ( sdi2_10.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_10.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_10.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_10, "m1", "k4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_10, "m1", "f2" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_11 = TestGSDI.createPhylogeny( "((m1[&&NHX:S=m1],k4[&&NHX:S=k4]),x[&&NHX:S=x])" );
+ final GSDI sdi2_11 = new GSDI( g2_11, s2, false );
+ if ( sdi2_11.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_11.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_11.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_11, "m1", "k4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_11, "m1", "x" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_12 = TestGSDI.createPhylogeny( "(m1[&&NHX:S=m1],(k4[&&NHX:S=k4],x[&&NHX:S=x]))" );
+ final GSDI sdi2_12 = new GSDI( g2_12, s2, false );
+ if ( sdi2_12.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_12.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_12.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_12, "x", "k4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_12, "m1", "x" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_13 = TestGSDI.createPhylogeny( "(x[&&NHX:S=x],(y[&&NHX:S=y],z[&&NHX:S=z]))" );
+ final GSDI sdi2_13 = new GSDI( g2_13, s2, false );
+ if ( sdi2_13.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_13.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_13.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_13, "y", "z" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_13, "x", "z" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_14 = TestGSDI.createPhylogeny( "(a1_1[&&NHX:S=a1],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
+ final GSDI sdi2_14 = new GSDI( g2_14, s2, false );
+ if ( sdi2_14.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_14.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_14.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_14, "b1", "a1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_14, "b1", "a1_1" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_15 = TestGSDI.createPhylogeny( "(a2[&&NHX:S=a2],(b1[&&NHX:S=b1],a1[&&NHX:S=a1]))" );
+ final GSDI sdi2_15 = new GSDI( g2_15, s2, false );
+ if ( sdi2_15.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_15.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_15.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_15, "b1", "a1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_15, "b1", "a2" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_16 = TestGSDI.createPhylogeny( "(n2[&&NHX:S=n2],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
+ final GSDI sdi2_16 = new GSDI( g2_16, s2, false );
+ if ( sdi2_16.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_16.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_16.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_16, "j3", "n1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_16, "j3", "n2" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_17 = TestGSDI.createPhylogeny( "(p4[&&NHX:S=p4],(j3[&&NHX:S=j3],n1[&&NHX:S=n1]))" );
+ final GSDI sdi2_17 = new GSDI( g2_17, s2, false );
+ if ( sdi2_17.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_17.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_17.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_17, "j3", "n1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_17, "j3", "p4" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_18 = TestGSDI
+ .createPhylogeny( "((n11[&&NHX:S=n1],n12[&&NHX:S=n1]),(n13[&&NHX:S=n1],n14[&&NHX:S=n1]))" );
+ final GSDI sdi2_18 = new GSDI( g2_18, s2, false );
+ if ( sdi2_18.getDuplicationsSum() != 3 ) {
+ return false;
+ }
+ if ( sdi2_18.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_18.getSpeciationsSum() != 0 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_18, "n11", "n12" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_18, "n13", "n14" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_18, "n11", "n13" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_19 = TestGSDI
+ .createPhylogeny( "((n11[&&NHX:S=n1],n21[&&NHX:S=n2]),(n12[&&NHX:S=n1],n22[&&NHX:S=n2]))" );
+ final GSDI sdi2_19 = new GSDI( g2_19, s2, false );
+ if ( sdi2_19.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_19.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_19.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_19, "n11", "n21" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_19, "n12", "n22" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_19, "n11", "n12" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_20 = TestGSDI
+ .createPhylogeny( "((n11[&&NHX:S=n1],n2[&&NHX:S=n2]),(n12[&&NHX:S=n1],n3[&&NHX:S=n3]))" );
+ final GSDI sdi2_20 = new GSDI( g2_20, s2, false );
+ if ( sdi2_20.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_20.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_20.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_20, "n11", "n2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_20, "n12", "n3" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_20, "n11", "n12" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_21 = TestGSDI
+ .createPhylogeny( "((n1[&&NHX:S=n1],n2[&&NHX:S=n2]),(n3[&&NHX:S=n3],a1[&&NHX:S=a1]))" );
+ final GSDI sdi2_21 = new GSDI( g2_21, s2, false );
+ if ( sdi2_21.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_21.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_21.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_21, "n1", "n2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_21, "n3", "a1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_21, "n2", "a1" ).isDuplication() ) {
+ return false;
+ }
+ 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 ( sdi2_22.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_22.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_22, "n1", "n2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_22, "n3", "n4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_22, "n1", "n3" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_23 = TestGSDI
+ .createPhylogeny( "((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),(c1[&&NHX:S=c1],d1[&&NHX:S=d1]))" );
+ final GSDI sdi2_23 = new GSDI( g2_23, s2, false );
+ if ( sdi2_23.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_23.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_23.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_23, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_23, "c1", "d1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_23, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_24 = TestGSDI
+ .createPhylogeny( "((a1[&&NHX:S=a1],e1[&&NHX:S=e1]),(i1[&&NHX:S=i1],m1[&&NHX:S=m1]))" );
+ final GSDI sdi2_24 = new GSDI( g2_24, s2, false );
+ if ( sdi2_24.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_24.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_24.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_24, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_24, "i1", "m1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_24, "a1", "i1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_25 = TestGSDI
+ .createPhylogeny( "((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),(b1[&&NHX:S=b1],c1[&&NHX:S=c1]))" );
+ final GSDI sdi2_25 = new GSDI( g2_25, s2, false );
+ if ( sdi2_25.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_25.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_25.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_25, "a1", "a4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_25, "b1", "c1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_25, "a1", "b1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_26 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),e1[&&NHX:S=e1])" );
+ final GSDI sdi2_26 = new GSDI( g2_26, s2, false );
+ if ( sdi2_26.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_26.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_26.getSpeciationsSum() != 3 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_26, "a1", "a4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_26, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_26, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_27 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],a4[&&NHX:S=a4]),b1[&&NHX:S=b1]),c1[&&NHX:S=c1])" );
+ final GSDI sdi2_27 = new GSDI( g2_27, s2, false );
+ if ( sdi2_27.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_27.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_27.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_27, "a1", "a4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_27, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_27, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_28 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),e1[&&NHX:S=e1])" );
+ final GSDI sdi2_28 = new GSDI( g2_28, s2, false );
+ if ( sdi2_28.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_28.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_28.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_28, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_28, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_28, "a1", "e1" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_29 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),d1[&&NHX:S=d1])" );
+ final GSDI sdi2_29 = new GSDI( g2_29, s2, false );
+ if ( sdi2_29.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_29.getSpeciationOrDuplicationEventsSum() != 2 ) {
+ return false;
+ }
+ if ( sdi2_29.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_29, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_29, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_29, "a1", "d1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_30 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),a2[&&NHX:S=a2])" );
+ final GSDI sdi2_30 = new GSDI( g2_30, s2, false );
+ if ( sdi2_30.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_30.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_30.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_30, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_30, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_30, "a1", "a2" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_31 = TestGSDI
+ .createPhylogeny( "(((a1[&&NHX:S=a1],b1[&&NHX:S=b1]),c1[&&NHX:S=c1]),c2[&&NHX:S=c2])" );
+ final GSDI sdi2_31 = new GSDI( g2_31, s2, false );
+ if ( sdi2_31.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_31.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_31.getSpeciationsSum() != 1 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_31, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_31, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_31, "a1", "c2" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_32 = 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]),e1[&&NHX:S=e1]),y[&&NHX:S=y]),z[&&NHX:S=z])" );
+ final GSDI sdi2_32 = new GSDI( g2_32, s2, false );
+ if ( sdi2_32.getDuplicationsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_32.getSpeciationOrDuplicationEventsSum() != 7 ) {
+ return false;
+ }
+ if ( sdi2_32.getSpeciationsSum() != 3 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "a2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "d1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "x" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "p1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "i1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "e1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_32, "a1", "y" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ 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;
+ }
+ if ( sdi2_33.getSpeciationOrDuplicationEventsSum() != 7 ) {
+ return false;
+ }
+ if ( sdi2_33.getSpeciationsSum() != 3 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "a2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "c1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "d1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "x" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "p1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "i1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "k2" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "e1" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "y" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_33, "a1", "z" ).isSpeciationOrDuplication() ) {
+ 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 ( sdi2_34.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_34.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_34.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_34, "n1_0", "n2_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_34, "n1_1", "n3_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_34, "n1_0", "n1_1" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_34, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_35 = 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]),a1_0[&&NHX:S=a1])" );
+ final GSDI sdi2_35 = new GSDI( g2_35, s2, false );
+ if ( sdi2_35.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_35.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_35.getSpeciationsSum() != 3 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_35, "n1_0", "n2_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_35, "n1_1", "n3_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_35, "n1_0", "n1_1" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_35, "n1_0", "n4_0" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_35, "n1_0", "a1_0" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g2_36 = TestGSDI
+ .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a1_1[&&NHX:S=a1],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+ final GSDI sdi2_36 = new GSDI( g2_36, s2, false );
+ if ( sdi2_36.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_36.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_36.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_36, "a1_0", "b1_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_36, "a1_1", "c1_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_36, "a1_0", "c1_0" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_36, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_37 = TestGSDI
+ .createPhylogeny( "(((a1_0[&&NHX:S=a1],b1_0[&&NHX:S=b1]),(a2_0[&&NHX:S=a2],c1_0[&&NHX:S=c1])),d1_0[&&NHX:S=d1])" );
+ final GSDI sdi2_37 = new GSDI( g2_37, s2, false );
+ if ( sdi2_37.getDuplicationsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_37.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_37.getSpeciationsSum() != 2 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_37, "a1_0", "b1_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_37, "a2_0", "c1_0" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_37, "a1_0", "c1_0" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_37, "a1_0", "d1_0" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_38 = TestGSDI
+ .createPhylogeny( "(((([&&NHX:S=n1],[&&NHX:S=n1]),([&&NHX:S=n1],[&&NHX:S=n1])),[&&NHX:S=n1]),[&&NHX:S=n1])" );
+ final GSDI sdi2_38 = new GSDI( g2_38, s2, false );
+ if ( sdi2_38.getDuplicationsSum() != 5 ) {
+ return false;
+ }
+ if ( sdi2_38.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_38.getSpeciationsSum() != 0 ) {
+ return false;
+ }
+ final Phylogeny g2_100 = TestGSDI
+ .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],h2[&&NHX:S=h2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],b1[&&NHX:S=b1])))" );
+ final GSDI sdi2_100 = new GSDI( g2_100, s2, false );
+ if ( sdi2_100.getDuplicationsSum() != 4 ) {
+ return false;
+ }
+ if ( sdi2_100.getSpeciationOrDuplicationEventsSum() != 0 ) {
+ return false;
+ }
+ if ( sdi2_100.getSpeciationsSum() != 4 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "e1", "f2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "d3", "g4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "e1", "d3" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "a1", "h2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "a1", "c3" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "i4", "b1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "a1", "i4" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_100, "e1", "a1" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny g2_101 = TestGSDI
+ .createPhylogeny( "(((e1[&&NHX:S=e1],f2[&&NHX:S=f2]),(d3[&&NHX:S=d3],g4[&&NHX:S=g4])),(((a1[&&NHX:S=a1],b2[&&NHX:S=b2]),c3[&&NHX:S=c3]),(i4[&&NHX:S=i4],j1[&&NHX:S=j1])))" );
+ final GSDI sdi2_101 = new GSDI( g2_101, s2, false );
+ if ( sdi2_101.getDuplicationsSum() != 2 ) {
+ return false;
+ }
+ if ( sdi2_101.getSpeciationOrDuplicationEventsSum() != 1 ) {
+ return false;
+ }
+ if ( sdi2_101.getSpeciationsSum() != 5 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "e1", "f2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "d3", "g4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "e1", "d3" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "a1", "b2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "a1", "c3" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "i4", "j1" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "a1", "i4" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g2_101, "e1", "a1" ).isDuplication() ) {
+ return false;
+ }
+ final Phylogeny s_7_4 = DevelopmentTools.createBalancedPhylogeny( 7, 4 );
+ DevelopmentTools.numberSpeciesInOrder( s_7_4 );
+ final Phylogeny g_7_4_1 = TestGSDI
+ .createPhylogeny( "(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+ + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+ + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+ + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+ + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+ + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+ + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+ + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+ + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+ + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+ + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+ + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65])" );
+ final GSDI sdi7_4_1 = new GSDI( g_7_4_1, s_7_4, false );
+ if ( sdi7_4_1.getDuplicationsSum() != 54 ) {
+ return false;
+ }
+ if ( sdi7_4_1.getSpeciationOrDuplicationEventsSum() != 6 ) {
+ return false;
+ }
+ if ( sdi7_4_1.getSpeciationsSum() != 4 ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "2" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "3" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "4" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "5" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "6" ).isDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "9" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "13" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "17" ).isSpeciation() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "33" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "49" ).isSpeciationOrDuplication() ) {
+ return false;
+ }
+ if ( !TestGSDI.getEvent( g_7_4_1, "1", "65" ).isSpeciation() ) {
+ return false;
+ }
+ final Phylogeny g_7_4_2 = TestGSDI
+ .createPhylogeny( "((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((("
+ + "1[&&NHX:S=1],2[&&NHX:S=2]),3[&&NHX:S=3]),4[&&NHX:S=4]),5[&&NHX:S=5]),"
+ + "6[&&NHX:S=6]),7[&&NHX:S=7]),8[&&NHX:S=8]),9[&&NHX:S=9]),10[&&NHX:S=10]),11[&&NHX:S=11]),"
+ + "12[&&NHX:S=12]),13[&&NHX:S=13]),14[&&NHX:S=14]),15[&&NHX:S=15]),16[&&NHX:S=16]),17[&&NHX:S=17]),"
+ + "18[&&NHX:S=18]),19[&&NHX:S=19]),20[&&NHX:S=20]),21[&&NHX:S=21]),22[&&NHX:S=22]),23[&&NHX:S=23]),"
+ + "24[&&NHX:S=24]),25[&&NHX:S=25]),26[&&NHX:S=26]),27[&&NHX:S=27]),28[&&NHX:S=28]),29[&&NHX:S=29]),"
+ + "30[&&NHX:S=30]),31[&&NHX:S=31]),32[&&NHX:S=32]),33[&&NHX:S=33]),34[&&NHX:S=34]),35[&&NHX:S=35]),"
+ + "36[&&NHX:S=36]),37[&&NHX:S=37]),38[&&NHX:S=38]),39[&&NHX:S=39]),40[&&NHX:S=40]),41[&&NHX:S=41]),"
+ + "42[&&NHX:S=42]),43[&&NHX:S=43]),44[&&NHX:S=44]),45[&&NHX:S=45]),46[&&NHX:S=46]),47[&&NHX:S=47]),"
+ + "48[&&NHX:S=48]),49[&&NHX:S=49]),50[&&NHX:S=50]),51[&&NHX:S=51]),52[&&NHX:S=52]),53[&&NHX:S=53]),"
+ + "54[&&NHX:S=54]),55[&&NHX:S=55]),56[&&NHX:S=56]),57[&&NHX:S=57]),58[&&NHX:S=58]),59[&&NHX:S=59]),"
+ + "60[&&NHX:S=60]),61[&&NHX:S=61]),62[&&NHX:S=62]),63[&&NHX:S=63]),64[&&NHX:S=64]),65[&&NHX:S=65]),"
+ + "66[&&NHX:S=66]),257[&&NHX:S=257]),258[&&NHX:S=258]),513[&&NHX:S=513]),514[&&NHX:S=514]),769[&&NHX:S=769]),770[&&NHX:S=770])" );
+ final GSDI sdi7_4_2 = new GSDI( g_7_4_2, s_7_4, false );
+ if ( sdi7_4_2.getDuplicationsSum() != 58 ) {
+ return false;
+ }
+ if ( sdi7_4_2.getSpeciationOrDuplicationEventsSum() != 8 ) {
+ return 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_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;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / commitdiff