signature_specifications.hpp

Go to the documentation of this file.

#ifndef GENESIS_SEQUENCE_FUNCTIONS_SIGNATURE_SPECIFICATIONS_H_
#define GENESIS_SEQUENCE_FUNCTIONS_SIGNATURE_SPECIFICATIONS_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 "genesis/utils/tools/char_lookup.hpp"

#include <string>
#include <vector>

namespace genesis {
namespace sequence {

// =================================================================================================
//     Forwardd Declarations
// =================================================================================================

class Sequence;
class SequenceSet;

// =================================================================================================
//     Signature Specifications
// =================================================================================================

class SignatureSpecifications
{
public:

    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------

    enum class UnknownCharBehavior
    {
        kSkip,

        kThrow
    };

    static size_t const InvalidCharIndex;

    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------

    SignatureSpecifications() = default;
    SignatureSpecifications( std::string const& alphabet, size_t k );

    ~SignatureSpecifications() = default;

    SignatureSpecifications( SignatureSpecifications const& ) = default;

    SignatureSpecifications( SignatureSpecifications&& )      = default;

    SignatureSpecifications& operator= ( SignatureSpecifications const& ) = default;

    SignatureSpecifications& operator= ( SignatureSpecifications&& )      = default;

    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------

    std::string const& alphabet() const
    {
        return alphabet_;
    }

    size_t k() const
    {
        return k_;
    }

    UnknownCharBehavior unknown_char_behavior() const
    {
        return unknown_char_behavior_;
    }

    // -------------------------------------------------------------------------
    //     Derived Properties
    // -------------------------------------------------------------------------

    bool is_nucleic_acids() const
    {
        return is_nucleic_acids_;
    }

    size_t char_index( char c ) const
    {
        return index_lookup_[c];
    }

    std::vector<std::string> const& kmer_list() const;

    size_t kmer_list_size() const;

    std::vector<size_t> const& kmer_combined_reverse_complement_map() const;

    std::vector<size_t> const& kmer_reverse_complement_indices() const;

    std::vector<std::string> const& kmer_reverse_complement_list() const;

    size_t kmer_reverse_complement_list_size( bool with_palindromes = true ) const;

    // -------------------------------------------------------------------------
    //     Modifiers
    // -------------------------------------------------------------------------

    SignatureSpecifications& unknown_char_behavior( UnknownCharBehavior value )
    {
        unknown_char_behavior_ = value;
        return *this;
    }

    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------

private:

    // Direct Settings
    std::string alphabet_;
    size_t      k_ = 0;
    UnknownCharBehavior unknown_char_behavior_ = UnknownCharBehavior::kSkip;

    // Induced Settings and Helpers
    bool        is_nucleic_acids_ = false;
    utils::CharLookup<size_t> index_lookup_;

    // Cached lookup lists
    mutable std::vector<std::string> kmer_list_;
    mutable std::vector<std::string> rev_comp_list_;
    mutable std::vector<size_t> rev_comp_map_;
    mutable std::vector<size_t> rev_comp_indices_;
};

} // namespace sequence
} // namespace genesis

#endif // include guard