consensus.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_CONSENSUS_H_
#define GENESIS_SEQUENCE_FUNCTIONS_CONSENSUS_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 <string>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Sequence;
class SiteCounts;
class SequenceSet;
 
// =================================================================================================
//     Consensus
// =================================================================================================
 
// ------------------------------------------------------
//     Majorities
// ------------------------------------------------------
 
std::string consensus_sequence_with_majorities(
    SiteCounts const&     counts,
    bool                  allow_gaps = true,
    char                  gap_char   = '-'
);
 
std::string consensus_sequence_with_majorities(
    SequenceSet const&    sequences,
    std::string const&    characters,
    bool                  allow_gaps = true,
    char                  gap_char   = '-'
);
 
std::string consensus_sequence_with_majorities(
    SequenceSet const&    sequences,
    bool                  allow_gaps = true
);
 
// ------------------------------------------------------
//     Ambiguities
// ------------------------------------------------------
 
std::string consensus_sequence_with_ambiguities(
    SiteCounts const&     counts,
    double                similarity_factor = 0.9,
    bool                  allow_gaps        = true
);
 
std::string consensus_sequence_with_ambiguities(
    SequenceSet const&    sequences,
    double                similarity_factor = 0.9,
    bool                  allow_gaps        = true
);
 
// ------------------------------------------------------
//     Threshold
// ------------------------------------------------------
 
std::string consensus_sequence_with_threshold(
    SiteCounts const&     counts,
    double                frequency_threshold = 0.6,
    bool                  allow_gaps          = true,
    bool                  use_ambiguities     = true
);
 
std::string consensus_sequence_with_threshold(
    SequenceSet const&    sequences,
    double                frequency_threshold = 0.6,
    bool                  allow_gaps          = true,
    bool                  use_ambiguities     = true
);
 
// ------------------------------------------------------
//     Cavener
// ------------------------------------------------------
 
std::string consensus_sequence_cavener(
    SiteCounts const&     counts,
    bool                  allow_gaps        = true
);
 
std::string consensus_sequence_cavener(
    SequenceSet const&    sequences,
    bool                  allow_gaps        = true
);
 
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard