org.forester.sdi.GSDIR Maven / Gradle / Ivy
// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2013 Christian M. Zmasek
// 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
package org.forester.sdi;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.SortedSet;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyBranch;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
import org.forester.util.BasicDescriptiveStatistics;
public class GSDIR implements GSDII {
private final int _min_duplications_sum;
private final int _speciations_sum;
private final BasicDescriptiveStatistics _duplications_sum_stats;
private Phylogeny _min_duplications_sum_gene_tree;
private final List _stripped_gene_tree_nodes;
private final List _stripped_species_tree_nodes;
private final Set _mapped_species_tree_nodes;
private final TaxonomyComparisonBase _tax_comp_base;
private final SortedSet _scientific_names_mapped_to_reduced_specificity;
public GSDIR( final Phylogeny gene_tree,
final Phylogeny species_tree,
final boolean strip_gene_tree,
final boolean strip_species_tree,
final boolean transfer_taxonomy ) throws SDIException {
final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,
species_tree,
strip_gene_tree,
strip_species_tree );
_stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();
_stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();
_mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();
_scientific_names_mapped_to_reduced_specificity = nodes_linking_result
.getScientificNamesMappedToReducedSpecificity();
_tax_comp_base = nodes_linking_result.getTaxCompBase();
final List gene_tree_branches_post_order = new ArrayList();
for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
if ( !n.isRoot() && !( n.getParent().isRoot() && ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) ) ) {
gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );
}
}
if ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) {
gene_tree_branches_post_order.add( new PhylogenyBranch( gene_tree.getRoot().getChildNode1(), gene_tree
.getRoot().getChildNode2() ) );
}
int min_duplications_sum = Integer.MAX_VALUE;
int speciations_sum = 0;
_duplications_sum_stats = new BasicDescriptiveStatistics();
for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {
reRoot( branch, gene_tree );
PhylogenyMethods.preOrderReId( species_tree );
final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
true,
min_duplications_sum );
if ( gsdi_result == null ) {
continue;
}
if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
min_duplications_sum = gsdi_result.getDuplicationsSum();
speciations_sum = gsdi_result.getSpeciationsSum();
_min_duplications_sum_gene_tree = gene_tree.copy();
if ( transfer_taxonomy ) {
transferTaxonomy( _min_duplications_sum_gene_tree );
}
}
else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {
final List l = new ArrayList();
l.add( _min_duplications_sum_gene_tree );
l.add( gene_tree );
final int index = getIndexesOfShortestTree( l ).get( 0 );
if ( index == 1 ) {
_min_duplications_sum_gene_tree = gene_tree.copy();
if ( transfer_taxonomy ) {
transferTaxonomy( _min_duplications_sum_gene_tree );
}
}
}
_duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );
}
_min_duplications_sum = min_duplications_sum;
_speciations_sum = speciations_sum;
}
public BasicDescriptiveStatistics getDuplicationsSumStats() {
return _duplications_sum_stats;
}
@Override
public Set getMappedExternalSpeciesTreeNodes() {
return _mapped_species_tree_nodes;
}
public int getMinDuplicationsSum() {
return _min_duplications_sum;
}
public Phylogeny getMinDuplicationsSumGeneTree() {
return _min_duplications_sum_gene_tree;
}
@Override
public final SortedSet getReMappedScientificNamesFromGeneTree() {
return _scientific_names_mapped_to_reduced_specificity;
}
@Override
public int getSpeciationsSum() {
return _speciations_sum;
}
@Override
public List getStrippedExternalGeneTreeNodes() {
return _stripped_gene_tree_nodes;
}
@Override
public List getStrippedSpeciesTreeNodes() {
return _stripped_species_tree_nodes;
}
@Override
public TaxonomyComparisonBase getTaxCompBase() {
return _tax_comp_base;
}
public final static List getIndexesOfShortestTree( final List assigned_trees ) {
final List shortests = new ArrayList();
boolean depth = true;
double x = Double.MAX_VALUE;
for( int i = 0; i < assigned_trees.size(); ++i ) {
final Phylogeny phy = assigned_trees.get( i );
if ( i == 0 ) {
if ( PhylogenyMethods.calculateMaxDistanceToRoot( phy ) > 0 ) {
depth = false;
}
}
final double d;
if ( depth ) {
d = PhylogenyMethods.calculateMaxDepth( phy );
}
else {
d = PhylogenyMethods.calculateMaxDistanceToRoot( phy );
}
if ( d < x ) {
x = d;
shortests.clear();
shortests.add( i );
}
else if ( d == x ) {
shortests.add( i );
}
}
return shortests;
}
/**
* Places the root of this Phylogeny on Branch b. The new root is always
* placed on the middle of the branch b.
*
*/
static final void reRoot( final PhylogenyBranch b, final Phylogeny phy ) {
final PhylogenyNode n1 = b.getFirstNode();
final PhylogenyNode n2 = b.getSecondNode();
if ( n1.isExternal() ) {
phy.reRoot( n1 );
}
else if ( n2.isExternal() ) {
phy.reRoot( n2 );
}
else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
phy.reRoot( n2 );
}
else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
phy.reRoot( n1 );
}
// else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
// && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
// phy.reRoot( n1 );
//
// }
else {
throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
}
}
private final static void transferTaxonomy( final Phylogeny gt ) {
for( final PhylogenyNodeIterator it = gt.iteratorPostorder(); it.hasNext(); ) {
GSDI.transferTaxonomy( it.next() );
}
}
}