sequence/functions/functions.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_FUNCTIONS_H_
#define GENESIS_SEQUENCE_FUNCTIONS_FUNCTIONS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 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/sequence/functions/codes.hpp"
#include "genesis/utils/math/bitvector.hpp"
#include "genesis/utils/tools/char_lookup.hpp"
 
#include <iosfwd>
#include <map>
#include <string>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Sequence;
class SequenceSet;
 
// =================================================================================================
//     Characteristics
// =================================================================================================
 
utils::Bitvector find_sites(
    Sequence const& seq,
    std::string const& chars
);
 
utils::Bitvector find_sites(
    Sequence const& seq,
    utils::CharLookup<bool> const& chars
);
 
utils::Bitvector gap_sites(
    Sequence const& seq,
    std::string const& gap_chars = nucleic_acid_codes_undetermined()
);
 
utils::Bitvector gap_sites(
    SequenceSet const& set,
    std::string const& gap_chars = nucleic_acid_codes_undetermined()
);
 
bool validate_chars( SequenceSet const& set, std::string const& chars );
 
size_t longest_sequence_length( SequenceSet const& set );
 
size_t total_length( SequenceSet const& set );
 
bool is_alignment( SequenceSet const& set );
 
// =================================================================================================
//     Modifiers
// =================================================================================================
 
void remove_sites( Sequence&    seq, utils::Bitvector sites );
 
void remove_sites( SequenceSet& set, utils::Bitvector sites );
 
void remove_gap_sites( SequenceSet& set, std::string const& gap_chars = nucleic_acid_codes_undetermined() );
 
void remove_characters( Sequence&    seq, std::string const& search );
 
void remove_characters( SequenceSet& set, std::string const& search );
 
void remove_all_gaps( Sequence&    seq, std::string const& gap_chars = nucleic_acid_codes_undetermined() );
 
void remove_all_gaps( SequenceSet& set, std::string const& gap_chars = nucleic_acid_codes_undetermined() );
 
void replace_characters( Sequence&    seq, std::string const& search, char replacement );
 
void replace_characters( SequenceSet& set, std::string const& search, char replacement );
 
void replace_u_with_t( Sequence&    seq );
 
void replace_u_with_t( SequenceSet& set );
 
void replace_t_with_u( Sequence&    seq );
 
void replace_t_with_u( SequenceSet& set );
 
enum class MergeDuplicateSequencesCountPolicy
{
    kDiscard,
 
    kAppendToLabel,
 
};
 
void merge_duplicate_sequences(
    SequenceSet& set,
    MergeDuplicateSequencesCountPolicy count_policy = MergeDuplicateSequencesCountPolicy::kDiscard,
    std::string const& counter_prefix = "_"
);
 
// =================================================================================================
//     Normalization
// =================================================================================================
 
void normalize_nucleic_acid_codes( Sequence& sequence, bool accept_degenerated = true );
 
void normalize_nucleic_acid_codes( SequenceSet& sequence_set, bool accept_degenerated = true );
 
void normalize_amino_acid_codes( Sequence& sequence, bool accept_degenerated = true );
 
void normalize_amino_acid_codes( SequenceSet& sequence_set, bool accept_degenerated = true );
 
// =================================================================================================
//     Filters
// =================================================================================================
 
void filter_min_sequence_length( SequenceSet& set, size_t min_length );
 
void filter_max_sequence_length( SequenceSet& set, size_t max_length );
 
void filter_min_max_sequence_length( SequenceSet& set, size_t min_length, size_t max_length );
 
// =================================================================================================
//     Print and Output
// =================================================================================================
 
std::ostream& operator << ( std::ostream& out, Sequence    const& seq );
 
std::ostream& operator << ( std::ostream& out, SequenceSet const& set );
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard