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) 2014-2019 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/io/input_source.hpp"

#include <iosfwd>
#include <memory>
#include <string>
#include <unordered_map>
#include <vector>

namespace genesis {

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

namespace utils {
    class JsonDocument;
}

namespace tree {
    class TreeEdge;
}

namespace placement {
    using PlacementTreeEdge = tree::TreeEdge;

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

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

    SampleSet read(
        std::vector<std::shared_ptr<utils::BaseInputSource>> sources
    ) const;

    void read(
        std::vector<std::shared_ptr<utils::BaseInputSource>> sources,
        SampleSet& target
    ) const;

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

private:

    int get_jplace_version_( utils::JsonDocument const& doc ) const;

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

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

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

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

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

    void process_jplace_placements_p_(
        utils::JsonDocument const&      pqry_obj,
        Pquery&                         pquery,
        std::vector<std::string> const& fields,
        std::unordered_map<size_t, PlacementTreeEdge*> const& edge_num_map
    ) const;

    void process_jplace_placements_nm_(
        utils::JsonDocument const&      pqry_obj,
        Pquery&                         pquery
    ) const;

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

public:

    enum class InvalidNumberBehaviour {
        kIgnore,

        kLog,

        kFix,

        kLogAndFix,

        kThrow
    };

    InvalidNumberBehaviour invalid_number_behaviour() const
    {
        return invalid_number_behaviour_;
    }

    JplaceReader& invalid_number_behaviour( InvalidNumberBehaviour val )
    {
        invalid_number_behaviour_ = val;
        return *this;
    }

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

private:

    InvalidNumberBehaviour invalid_number_behaviour_ = InvalidNumberBehaviour::kIgnore;

};

} // namespace placement
} // namespace genesis

#endif // include guard