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