taxonomy/functions/taxonomy.hpp

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#ifndef GENESIS_TAXONOMY_FUNCTIONS_TAXONOMY_H_
#define GENESIS_TAXONOMY_FUNCTIONS_TAXONOMY_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program 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 General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
 
#include <functional>
#include <iosfwd>
#include <string>
#include <unordered_map>
#include <vector>
#include <queue>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Tags for Tag Dispatch
// =================================================================================================
 
struct DepthFirstSearch{};
 
struct BreadthFirstSearch{};
 
using DFS = DepthFirstSearch;
 
using BFS = BreadthFirstSearch;
 
// =================================================================================================
//     Find Functions
// =================================================================================================
 
template< class UnaryPredicate >
Taxon const* find_taxon( Taxonomy const& tax, UnaryPredicate p )
{
    return find_taxon( tax, p, DepthFirstSearch{} );
}
 
template< class UnaryPredicate >
Taxon* find_taxon( Taxonomy& tax, UnaryPredicate p )
{
    return find_taxon(tax, p, DepthFirstSearch{} );
}
 
template< class UnaryPredicate >
Taxon const* find_taxon( Taxonomy const& tax, UnaryPredicate p, DepthFirstSearch )
{
    for( auto const& c : tax ) {
        if( p( c ) ) {
            return &c;
        }
        auto rec = find_taxon( c, p, DepthFirstSearch{} );
        if( rec != nullptr ) {
            return rec;
        }
    }
    return nullptr;
}
 
template< class UnaryPredicate >
Taxon const* find_taxon( Taxonomy const& tax, UnaryPredicate p, BreadthFirstSearch )
{
    std::queue< Taxon const* > taxa_queue;
    for( auto& t : tax ) {
        taxa_queue.push( &t );
    }
 
    while( not taxa_queue.empty() ) {
        auto const& cur = *taxa_queue.front();
        taxa_queue.pop();
 
        if( p( cur ) ) {
            return &cur;
        }
 
        for( auto const& t : cur ) {
            taxa_queue.push( &t );
        }
    }
    return nullptr;
}
 
template< class SearchStrategy, class UnaryPredicate >
Taxon* find_taxon( Taxonomy& tax, UnaryPredicate p, SearchStrategy strat )
{
    // Avoid code duplication according to Scott Meyers.
    auto const& ctax = static_cast< Taxonomy const& >( tax );
    return const_cast< Taxon* >( find_taxon( ctax, p, strat ));
}
 
Taxon const* find_taxon_by_name( Taxonomy const& tax, std::string const& name );
 
Taxon*       find_taxon_by_name( Taxonomy&       tax, std::string const& name );
 
Taxon const* find_taxon_by_id( Taxonomy const& tax, std::string const& id );
 
Taxon*       find_taxon_by_id( Taxonomy&       tax, std::string const& id );
 
template< class SearchStrategy >
Taxon const* find_taxon_by_name( Taxonomy const& tax, std::string const& name, SearchStrategy strat )
{
    return find_taxon( tax, [&name]( Taxon const& t ){
        return t.name() == name;
    }, strat );
}
 
template< class SearchStrategy >
Taxon*       find_taxon_by_name( Taxonomy&       tax, std::string const& name, SearchStrategy strat )
{
    // Avoid code duplication according to Scott Meyers.
    auto const& ctax = static_cast< Taxonomy const& >( tax );
    return const_cast< Taxon* >( find_taxon_by_name( ctax, name, strat ));
}
 
template< class SearchStrategy >
Taxon const* find_taxon_by_id( Taxonomy const& tax, std::string const& id, SearchStrategy strat )
{
    return find_taxon( tax, [&id]( Taxon const& t ){
        return t.id() == id;
    }, strat );
}
 
template< class SearchStrategy >
Taxon*       find_taxon_by_id( Taxonomy&       tax, std::string const& id, SearchStrategy strat )
{
    // Avoid code duplication according to Scott Meyers.
    auto const& ctax = static_cast< Taxonomy const& >( tax );
    return const_cast< Taxon* >( find_taxon_by_id<SearchStrategy>( ctax, id, strat ));
}
 
// =================================================================================================
//     Accessors
// =================================================================================================
 
size_t taxon_level( Taxon const& taxon );
 
size_t total_taxa_count( Taxonomy const& tax );
 
size_t taxa_count_lowest_levels( Taxonomy const& tax );
 
size_t taxa_count_at_level( Taxonomy const& tax, size_t level );
 
std::vector< size_t > taxa_count_levels( Taxonomy const& tax );
 
size_t taxa_count_with_rank(
    Taxonomy const&    tax,
    std::string const& rank,
    bool               case_sensitive = false
);
 
std::unordered_map< std::string, size_t> taxa_count_ranks(
    Taxonomy const& tax,
    bool            case_sensitive = false
);
 
bool has_unique_ids( Taxonomy const& tax );
 
// =================================================================================================
//     Modifiers
// =================================================================================================
 
void sort_by_name( Taxonomy& tax, bool recursive = true, bool case_sensitive = false );
 
void remove_taxa_at_level( Taxonomy& tax, size_t level );
 
// =================================================================================================
//     Print and Output
// =================================================================================================
 
std::ostream& operator << ( std::ostream& out, Taxonomy const& tax );
 
bool validate( Taxonomy const& taxonomy, bool stop_at_first_error = false );
 
} // namespace taxonomy
} // namespace genesis
 
#endif // include guard