jplace_reader.hpp

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#ifndef GENESIS_PLACEMENT_FORMATS_JPLACE_READER_H_
#define GENESIS_PLACEMENT_FORMATS_JPLACE_READER_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 <iosfwd>
#include <string>
#include <unordered_map>
#include <vector>

namespace genesis {

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

namespace utils {
    class InputStream;
    class JsonDocument;
}

namespace placement {
    class Sample;
    class SampleSet;
}

// =================================================================================================
//     Jplace Reader
// =================================================================================================

namespace placement {

class JplaceReader
{
    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------

public:

    JplaceReader()  = default;
    ~JplaceReader() = default;

    JplaceReader( JplaceReader const& ) = default;
    JplaceReader( JplaceReader&& )      = default;

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

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

public:

    Sample from_stream( std::istream& is ) const;

    Sample from_file( std::string const& fn ) const;

    Sample from_string( std::string const& jplace ) const;

    Sample from_document( utils::JsonDocument& doc ) const;

    SampleSet from_files( std::vector<std::string> const& fns ) const;

    SampleSet from_strings( std::vector<std::string> const& jps ) const;

    void from_files    ( std::vector<std::string> const& fns, SampleSet& set ) const;

    void from_strings  ( std::vector<std::string> const& jps, SampleSet& set ) const;

    // ---------------------------------------------------------------------
    //     Processing
    // ---------------------------------------------------------------------

private:

    void process_json_version(    utils::JsonDocument const& doc ) const;

    void process_json_metadata( utils::JsonDocument const& doc, Sample& smp ) const;

    void process_json_tree(       utils::JsonDocument const& doc, Sample& smp ) const;

    std::vector<std::string> process_json_fields( utils::JsonDocument const& doc ) const;

    void process_json_placements(
        utils::JsonDocument&       doc,
        Sample&                    smp,
        std::vector<std::string>   fields
    ) const;

    // ---------------------------------------------------------------------
    //     Jplace Version
    // ---------------------------------------------------------------------

public:

    static std::string version   ();

    static bool        check_version ( size_t             version );

    static bool        check_version ( std::string const& version );

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

public:

    enum class InvalidNumberBehaviour {
        kIgnore,

        kLog,

        kCorrect,

        kLogAndCorrect,

        kThrow
    };

    InvalidNumberBehaviour invalid_number_behaviour() const;

    JplaceReader&          invalid_number_behaviour( InvalidNumberBehaviour val );

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

private:

    InvalidNumberBehaviour invalid_number_behaviour_ = InvalidNumberBehaviour::kIgnore;

};

} // namespace placement
} // namespace genesis

#endif // include guard