sequence/functions/stats.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_STATS_H_
#define GENESIS_SEQUENCE_FUNCTIONS_STATS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2017 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 <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include <map>
#include <string>
#include <vector>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Sequence;
class SiteCounts;
class SequenceSet;
 
// =================================================================================================
//     Characteristics
// =================================================================================================
 
std::map<char, size_t> site_histogram( Sequence    const& seq );
 
std::map<char, size_t> site_histogram( SequenceSet const& set );
 
std::map<char, double> base_frequencies( Sequence    const& seq, std::string const& plain_chars );
 
std::map<char, double> base_frequencies( SequenceSet const& set, std::string const& plain_chars );
 
size_t count_chars( SequenceSet const& set, std::string const& chars );
 
double gapyness( SequenceSet    const& set, std::string const& gap_chars );
 
size_t gap_site_count( SiteCounts const& counts );
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard