counts.hpp

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#ifndef GENESIS_SEQUENCE_COUNTS_H_
#define GENESIS_SEQUENCE_COUNTS_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/containers/matrix.hpp"
#include "genesis/utils/tools/char_lookup.hpp"
 
#include <cstdint>
#include <string>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwardd Declarations
// =================================================================================================
 
class Sequence;
class SequenceSet;
 
// =================================================================================================
//     Sequence Counts
// =================================================================================================
 
class SiteCounts
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using CountsIntType = uint32_t;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    SiteCounts() = default;
 
    SiteCounts( std::string const& characters, size_t length );
 
    ~SiteCounts() = default;
 
    SiteCounts( SiteCounts const& ) = default;
 
    SiteCounts( SiteCounts&& )      = default;
 
    SiteCounts& operator= ( SiteCounts const& ) = default;
 
    SiteCounts& operator= ( SiteCounts&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    size_t        length() const;
 
    std::string   characters() const;
 
    CountsIntType added_sequences_count() const;
 
    CountsIntType count_of( char character, size_t site_index ) const;
 
    CountsIntType count_at( size_t character_index, size_t site_index ) const;
 
    // std::vector< CountsIntType> counts_at( size_t site_index ) const;
 
    // -------------------------------------------------------------------------
    //     Modifiers
    // -------------------------------------------------------------------------
 
    void add_sequence( Sequence const& sequence, bool use_abundance = true );
 
    void add_sequence( std::string const& sites, CountsIntType weight = 1 );
 
    void add_sequences( SequenceSet const& sequences, bool use_abundances = true );
 
    void clear();
 
    void clear_counts();
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::string                        characters_;
    utils::CharLookup< unsigned char > lookup_;
    utils::Matrix< CountsIntType >     counts_;
    CountsIntType                      num_seqs_ = 0;
 
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard