sequence_set.hpp

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#ifndef GENESIS_SEQUENCE_SEQUENCE_SET_H_
#define GENESIS_SEQUENCE_SEQUENCE_SET_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2023 Lucas Czech
 
    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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/sequence/sequence.hpp"
 
#include <stdexcept>
#include <vector>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     SequenceSet
// =================================================================================================
 
class SequenceSet
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using       iterator = std::vector<Sequence>::iterator;
    using const_iterator = std::vector<Sequence>::const_iterator;
 
    using       reference = Sequence&;
    using const_reference = Sequence const&;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    SequenceSet() = default;
    ~SequenceSet() = default;
 
    SequenceSet( SequenceSet const& ) = default;
    SequenceSet( SequenceSet&& )      = default;
 
    SequenceSet& operator= ( SequenceSet const& ) = default;
    SequenceSet& operator= ( SequenceSet&& )      = default;
 
    friend void swap( SequenceSet& lhs, SequenceSet& rhs )
    {
        using std::swap;
        swap( lhs.sequences_, rhs.sequences_ );
    }
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    size_t size() const
    {
        return sequences_.size();
    }
 
    bool empty() const
    {
        return sequences_.empty();
    }
 
    reference at ( size_t index )
    {
        return sequences_.at( index );
    }
 
    const_reference at ( size_t index ) const
    {
        return sequences_.at( index );
    }
 
    reference operator[] ( size_t index )
    {
        return sequences_[ index ];
    }
 
    const_reference operator[] ( size_t index ) const
    {
        return sequences_[ index ];
    }
 
    // -------------------------------------------------------------------------
    //     Modifiers
    // -------------------------------------------------------------------------
 
    reference add( Sequence const& s )
    {
        sequences_.push_back( s );
        return sequences_.back();
    }
 
    reference add( Sequence&& s )
    {
        sequences_.push_back( std::move(s) );
        return sequences_.back();
    }
 
    void remove( size_t index )
    {
        if( index >= sequences_.size() ) {
            throw std::out_of_range( "Index out of range for removing from SequenceSet." );
        }
 
        sequences_.erase( sequences_.begin() + index );
    }
 
    void remove( size_t first_index, size_t last_index )
    {
        if( first_index    >= sequences_.size()
            || last_index  >= sequences_.size()
            || first_index >= last_index
        ) {
            throw std::out_of_range( "Invalid indices for removing from SequenceSet." );
        }
 
        sequences_.erase( sequences_.begin() + first_index, sequences_.begin() + last_index );
    }
 
    void remove( iterator position )
    {
        sequences_.erase( position );
    }
 
    void remove( iterator first, iterator last )
    {
        sequences_.erase( first, last );
    }
 
    void clear()
    {
        sequences_.clear();
    }
 
    // -------------------------------------------------------------------------
    //     Iterators
    // -------------------------------------------------------------------------
 
    iterator begin()
    {
        return sequences_.begin();
    }
 
    iterator end()
    {
        return sequences_.end();
    }
 
    const_iterator begin() const
    {
        return sequences_.cbegin();
    }
 
    const_iterator end() const
    {
        return sequences_.cend();
    }
 
    const_iterator cbegin() const
    {
        return sequences_.cbegin();
    }
 
    const_iterator cend() const
    {
        return sequences_.cend();
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::vector<Sequence> sequences_;
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard