taxa.hpp

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#ifndef GENESIS_UTILS_FORMATS_NEXUS_TAXA_H_
#define GENESIS_UTILS_FORMATS_NEXUS_TAXA_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 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/utils/core/algorithm.hpp"
#include "genesis/utils/formats/nexus/block.hpp"
 
#include <algorithm>
#include <ostream>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class NexusTaxa;
bool operator == ( NexusTaxa const& lhs, NexusTaxa const& rhs );
bool operator != ( NexusTaxa const& lhs, NexusTaxa const& rhs );
 
// =================================================================================================
//     Nexus Block Taxa
// =================================================================================================
 
class NexusTaxa : public NexusBlock
{
 
    // -----------------------------------------------------
    //     Member Types
    // -----------------------------------------------------
 
public:
 
    using container      = std::vector<std::string>;
    using const_iterator = container::const_iterator;
 
    // -----------------------------------------------------
    //     Constructor and Rule of Five
    // -----------------------------------------------------
 
public:
 
    NexusTaxa() = default;
    virtual ~NexusTaxa() override = default;
 
    NexusTaxa( NexusTaxa const& ) = default;
    NexusTaxa( NexusTaxa&& )      = default;
 
    NexusTaxa& operator= ( NexusTaxa const& ) = default;
    NexusTaxa& operator= ( NexusTaxa&& )      = default;
 
    void swap( NexusTaxa& other )
    {
        using std::swap;
        swap( taxa_, other.taxa_ );
    }
 
    // -----------------------------------------------------
    //     Operators
    // -----------------------------------------------------
 
public:
 
    friend bool operator == ( NexusTaxa const& lhs, NexusTaxa const& rhs )
    {
        return lhs.taxa_ == rhs.taxa_;
    }
 
    friend bool operator != ( NexusTaxa const& lhs, NexusTaxa const& rhs )
    {
        return !(lhs == rhs);
    }
 
    // -----------------------------------------------------
    //     Accessors
    // -----------------------------------------------------
 
public:
 
    bool empty() const
    {
        return taxa_.empty();
    }
 
    size_t size() const
    {
        return taxa_.size();
    }
 
    bool has_taxon( std::string const& name ) const
    {
        return utils::contains( taxa_, name );
    }
 
    // -----------------------------------------------------
    //     Iterators
    // -----------------------------------------------------
 
public:
 
    const_iterator begin() const
    {
        return taxa_.cbegin();
    }
 
    const_iterator end() const
    {
        return taxa_.cend();
    }
 
    // -----------------------------------------------------
    //     Modifiers
    // -----------------------------------------------------
 
public:
 
    void add_taxon( std::string const& name )
    {
        insert_sorted( taxa_, name );
    }
 
    void add_taxa( std::vector<std::string> const& taxa )
    {
        // for( auto const& taxon : taxa ) {
        //     add_taxon( taxon );
        // }
 
        // Faster: Don't move on every insertion, and only do the sorting once.
        taxa_.insert( taxa_.end(), taxa.begin(), taxa.end() );
        std::sort( taxa_.begin(), taxa_.end() );
    }
 
    void clear()
    {
        taxa_.clear();
    }
 
    // -----------------------------------------------------
    //     Virtual Functions
    // -----------------------------------------------------
 
public:
 
    std::string block_name() const override
    {
        return "TAXA";
    }
 
    void to_stream( std::ostream& os ) const override
    {
        os << "    dimensions ntax=" << taxa_.size() << ";\n";
        os << "    taxlabels\n";
        for( auto& taxon : taxa_ ) {
            os << "        " << taxon << "\n";
        }
        os << "    ;\n";
    }
 
    // -----------------------------------------------------
    //     Data Members
    // -----------------------------------------------------
 
private:
 
    container taxa_;
 
};
 
// =================================================================================================
//     Operators
// =================================================================================================
 
inline void swap( NexusTaxa& lhs, NexusTaxa& rhs )
{
    lhs.swap(rhs);
}
 
} // namespace utils
} // namespace genesis
 
#endif // include guard