signatures.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_SIGNATURES_H_
#define GENESIS_SEQUENCE_FUNCTIONS_SIGNATURES_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 <iosfwd>
#include <string>
#include <vector>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class SignatureSpecifications;
class Sequence;
class SequenceSet;
 
// =================================================================================================
//     Signature Counts and Frequencies
// =================================================================================================
 
std::vector<size_t> signature_counts(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_frequencies(
    Sequence const& sequence,
    SignatureSpecifications const& settings
);
 
// =================================================================================================
//     Signature Symmetrized
// =================================================================================================
 
std::vector<size_t> signature_symmetrized_counts(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_symmetrized_frequencies(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
// =================================================================================================
//     Signature Ranks
// =================================================================================================
 
std::vector<size_t> signature_ranks(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<size_t> signature_symmetrized_ranks(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
// =================================================================================================
//     Signature Min Max Reverse Complements
// =================================================================================================
 
std::vector<double> signature_minimal_complementarity_frequencies(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_maximal_complementarity_frequencies(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_reverse_identity_frequencies(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
// =================================================================================================
//     Signature Misc
// =================================================================================================
 
std::vector<double> signature_frequency_ratios_1(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_frequency_ratios_2(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
std::vector<double> signature_jensen_shannon(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
// =================================================================================================
//     Kmer Strings
// =================================================================================================
 
std::string kmer_string_overlapping(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
void kmer_string_overlapping(
    Sequence const&                sequence,
    SignatureSpecifications const& settings,
    std::ostream&                  out
);
 
std::vector<std::string> kmer_strings_non_overlapping(
    Sequence const&                sequence,
    SignatureSpecifications const& settings
);
 
void kmer_strings_non_overlapping(
    Sequence const&                sequence,
    SignatureSpecifications const& settings,
    std::ostream&                  out
);
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard