indexed_newick_reader.hpp

Go to the documentation of this file.

#ifndef GENESIS_TREE_ATTRIBUTE_TREE_INDEXED_NEWICK_READER_H_
#define GENESIS_TREE_ATTRIBUTE_TREE_INDEXED_NEWICK_READER_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 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/tree/attribute_tree/tree.hpp"
#include "genesis/tree/common_tree/newick_reader.hpp"
#include "genesis/tree/formats/newick/element.hpp"
#include "genesis/tree/formats/newick/reader.hpp"

#include <functional>
#include <map>
#include <string>
#include <vector>

namespace genesis {
namespace tree {

// =================================================================================================
//     Indexed Attribute Tree Newick Reader Plugin
// =================================================================================================

class IndexedAttributeTreeNewickReaderPlugin
{
public:

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

    using self_type = IndexedAttributeTreeNewickReaderPlugin;

    enum class Source
    {
        kValue,

        kComment,

        kTag
    };

    enum class Target
    {
        kNode,

        kEdge
    };

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

    IndexedAttributeTreeNewickReaderPlugin() = default;
    virtual ~IndexedAttributeTreeNewickReaderPlugin() = default;

    IndexedAttributeTreeNewickReaderPlugin(IndexedAttributeTreeNewickReaderPlugin const&) = default;
    IndexedAttributeTreeNewickReaderPlugin(IndexedAttributeTreeNewickReaderPlugin&&)      = default;

    self_type& operator= (IndexedAttributeTreeNewickReaderPlugin const&) = default;
    self_type& operator= (IndexedAttributeTreeNewickReaderPlugin&&)      = default;

    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------

    self_type& add_attribute(
        Source             source,
        size_t             index,
        Target             target,
        std::string const& target_key
    );

    self_type& add_attribute(
        Source             source,
        size_t             index,
        Target             target,
        std::string const& target_key,
        std::string const& default_value
    );

    self_type& add_catch_all(
        Source             source,
        Target             target,
        std::string const& target_key_prefix
    );

    self_type& add_catch_all( Target target = Target::kNode );

    void clear();

    // -------------------------------------------------------------------------
    //     Plugin Functions
    // -------------------------------------------------------------------------

    void element_to_node( NewickBrokerElement const& element, TreeNode& node ) const;

    void element_to_edge( NewickBrokerElement const& element, TreeEdge& edge ) const;

    void register_with( NewickReader& reader ) const;

    // -------------------------------------------------------------------------
    //     Internal Functions
    // -------------------------------------------------------------------------

private:

    std::vector<std::string> const& get_attribute_source_(
        NewickBrokerElement const& element,
        Source                     source
    ) const;

    void process_indexed_attributes_(
        NewickBrokerElement const& element,
        AttributeTreeMap& attributes,
        Target target
    ) const;

    void process_catch_all_attributes_(
        NewickBrokerElement const& element,
        AttributeTreeMap& attributes,
        Target target
    ) const;

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

private:

    struct AttributeDescriptor
    {
        Source      source;
        size_t      index;
        Target      target;
        std::string target_key;
        std::string default_value;
        bool        use_default;
    };

    std::vector<AttributeDescriptor> indexed_attributes_;
    std::vector<AttributeDescriptor> catch_all_attributes_;

};

// =================================================================================================
//     Attribute Tree Newick Reader
// =================================================================================================

class IndexedAttributeTreeNewickReader
    : public NewickReader
    , public CommonTreeNewickReaderPlugin
    , public IndexedAttributeTreeNewickReaderPlugin
{
public:

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

    IndexedAttributeTreeNewickReader()
    {
        // We first register the default reader, then the placement reader, because the latter
        // overwrites the data creation functions.
        CommonTreeNewickReaderPlugin::register_with( *this );
        IndexedAttributeTreeNewickReaderPlugin::register_with( *this );
    }
};

} // namespace tree
} // namespace genesis

#endif // include guard