phylip_reader.hpp

Go to the documentation of this file.

#ifndef GENESIS_SEQUENCE_FORMATS_PHYLIP_READER_H_
#define GENESIS_SEQUENCE_FORMATS_PHYLIP_READER_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 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/utils/tools/char_lookup.hpp"
#include "genesis/utils/io/input_source.hpp"

#include <iosfwd>
#include <string>

namespace genesis {

// =================================================================================================
//     Forward Declarations
// =================================================================================================

namespace utils {

class InputStream;

} // namespace utils

namespace sequence {

class SequenceSet;
class Sequence;

// =================================================================================================
//     Phylip Reader
// =================================================================================================

class PhylipReader
{
public:

    // ---------------------------------------------------------------------
    //     Types and Enums
    // ---------------------------------------------------------------------

    struct Header
    {
        size_t      num_sequences = 0;

        size_t      len_sequences = 0;

        std::string options;
    };

    enum class Mode
    {
        kSequential,

        kInterleaved
    };

    enum class SiteCasing
    {
        kUnchanged,

        kToUpper,

        kToLower
    };

    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------

    PhylipReader();

    ~PhylipReader() = default;

    PhylipReader( PhylipReader const& ) = default;
    PhylipReader( PhylipReader&& )      = default;

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

    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------

    SequenceSet read( std::shared_ptr<utils::BaseInputSource> source ) const;

    void read( std::shared_ptr<utils::BaseInputSource> source, SequenceSet& target ) const;

    // ---------------------------------------------------------------------
    //     Parsing
    // ---------------------------------------------------------------------

    Header parse_phylip_header(
        utils::InputStream& it
    ) const;

    std::string parse_phylip_label(
        utils::InputStream& it
    ) const;

    std::string parse_phylip_sequence_line(
        utils::InputStream& it
    ) const;

    void parse_phylip_sequential(
        utils::InputStream& it,
        SequenceSet& sset
    ) const;

    void parse_phylip_interleaved(
        utils::InputStream& it,
        SequenceSet& sset
    ) const;

    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------

    PhylipReader& mode( Mode value );

    Mode mode() const;

    PhylipReader& label_length( size_t value );

    size_t        label_length() const;

    PhylipReader& site_casing( SiteCasing value );

    SiteCasing site_casing() const;

    PhylipReader& remove_digits( bool value );

    bool remove_digits() const;

    PhylipReader& valid_chars( std::string const& chars );

    std::string   valid_chars() const;

    utils::CharLookup<bool>& valid_char_lookup();

    // ---------------------------------------------------------------------
    //     Members
    // ---------------------------------------------------------------------

private:

    Mode                    mode_           = Mode::kSequential;
    size_t                  label_length_   = 0;

    SiteCasing              site_casing_    = SiteCasing::kToUpper;
    bool                    remove_digits_ = false;
    bool                    use_validation_ = false;
    utils::CharLookup<bool> lookup_;

};

} // namespace sequence
} // namespace genesis

#endif // include guard