jplace_writer.cpp

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/*
    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/placement/formats/jplace_writer.hpp"
 
#include <fstream>
#include <memory>
#include <sstream>
#include <stdexcept>
#include <string>
#include <vector>
 
#include "genesis/placement/function/operators.hpp"
#include "genesis/placement/formats/newick_writer.hpp"
#include "genesis/placement/sample_set.hpp"
#include "genesis/placement/sample.hpp"
 
#include "genesis/tree/formats/newick/writer.hpp"
 
#include "genesis/utils/core/fs.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/core/options.hpp"
#include "genesis/utils/core/std.hpp"
#include "genesis/utils/core/version.hpp"
#include "genesis/utils/formats/json/document.hpp"
#include "genesis/utils/formats/json/writer.hpp"
#include "genesis/utils/io/output_stream.hpp"
#include "genesis/utils/text/string.hpp"
#include "genesis/utils/tools/date_time.hpp"
 
namespace genesis {
namespace placement {
 
// =================================================================================================
//     Constructor and Rule of Five
// =================================================================================================
 
JplaceWriter::JplaceWriter()
{
    program_ = "genesis " + genesis_version();
    invocation_ = utils::Options::get().command_line_string();
}
 
// =================================================================================================
//     Printing
// =================================================================================================
 
void JplaceWriter::write( Sample const& sample, std::shared_ptr<utils::BaseOutputTarget> target ) const
{
    // Shorthand.
    auto& os = target->ostream();
 
    // Indent. Might be replaced by some setting for the class in the future.
    std::string in = "    ";
 
    // Open json document.
    os << "{\n";
 
    // Write version.
    os << in << "\"version\": 3,\n";
 
    // Write metadata.
    os << in << "\"metadata\": {\n";
    os << in << in << "\"program\": \"" << utils::escape( program_ ) << "\",\n";
    os << in << in << "\"invocation\": \"" << utils::escape( invocation_ ) << "\",\n";
    os << in << in << "\"created\": \"" << utils::escape( utils::current_date() );
    os << " " << utils::escape( utils::current_time() ) << "\"\n";
    os << in << "},\n";
 
    // Write tree.
    auto newick_writer = PlacementTreeNewickWriter();
    newick_writer.enable_names(true);
    newick_writer.enable_branch_lengths(true);
    newick_writer.branch_length_precision( branch_length_precision_ );
    newick_writer.trailing_new_line( false );
    os << in << "\"tree\": \"";
    os << utils::escape( newick_writer.to_string( sample.tree() ));
    os << "\",\n";
 
    // Write field names.
    os << in << "\"fields\": [ \"edge_num\", \"likelihood\", \"like_weight_ratio\", "
    << "\"distal_length\", \"pendant_length\" ],\n";
 
    // Write pqueries.
    os << in << "\"placements\": [\n";
    for( size_t i = 0; i < sample.size(); ++i ) {
        auto const& pquery = sample.at(i);
        os << in << in << "{\n";
 
        // Write placements.
        os << in << in << in << "\"p\": [\n";
        for( size_t j = 0; j < pquery.placement_size(); ++j ) {
            auto const& placement = pquery.placement_at(j);
            os << in << in << in << in << "[ ";
 
            os << placement.edge_num() << ", ";
            os << placement.likelihood << ", ";
            os << placement.like_weight_ratio << ", ";
 
            auto const& edge_data = placement.edge().data<PlacementEdgeData>();
            os << edge_data.branch_length - placement.proximal_length << ", ";
            os << placement.pendant_length;
 
            os << " ]";
            if( j < pquery.placement_size() - 1 ) {
                os << ",";
            }
            os << "\n";
        }
        os << in << in << in << "],\n";
 
        // Find out whether names have multiplicity.
        bool has_nm = false;
        for( auto const& pqry_name : pquery.names() ) {
            has_nm |= ( pqry_name.multiplicity != 1.0 );
        }
 
        // Write names.
        if( has_nm ) {
 
            // With multiplicity.
            os << in << in << in << "\"nm\": [\n";
            for( size_t j = 0; j < pquery.name_size(); ++j ) {
                os << in << in << in << in << "[ \"";
                os << utils::escape( pquery.name_at(j).name ) << "\", ";
                os << pquery.name_at(j).multiplicity << " ]";
 
                if( j < pquery.name_size() - 1 ) {
                    os << ", ";
                }
                os << "\n";
            }
            os << in << in << in << "]\n";
 
        } else {
 
            // Without multiplicity.
            os << in << in << in << "\"n\": [ ";
            for( size_t j = 0; j < pquery.name_size(); ++j ) {
                os << "\"" << utils::escape( pquery.name_at(j).name ) << "\"";
 
                if( j < pquery.name_size() - 1 ) {
                    os << ", ";
                }
            }
            os << " ]\n";
 
        }
 
        // Write end of placement stuff.
        os << in << in << "}";
        if( i < sample.size() - 1 ) {
            os << ",";
        }
        os << "\n";
    }
    os << in << "]\n";
 
    // Close json document.
    os << "}\n";
}
 
utils::JsonDocument JplaceWriter::to_document( Sample const& smp ) const
{
    using namespace utils;
    JsonDocument doc = JsonDocument::object();
 
    // set tree
    auto newick_writer = PlacementTreeNewickWriter();
    newick_writer.enable_names(true);
    newick_writer.enable_branch_lengths(true);
    newick_writer.branch_length_precision( branch_length_precision_ );
    newick_writer.trailing_new_line( false );
    doc[ "tree" ] = newick_writer.to_string( smp.tree() );
 
    // set placements
    auto& placements_arr = doc[ "placements" ];
    for( auto const& pqry : smp.pqueries() ) {
        auto jpqry = JsonDocument::object();
 
        // set placements
        auto pqry_p_arr = JsonDocument::array();
        for( auto const& pqry_place : pqry.placements() ) {
            auto pqry_fields = JsonDocument::array();
 
            pqry_fields.push_back( JsonDocument::number_unsigned( pqry_place.edge_num() ));
            pqry_fields.push_back( JsonDocument::number_float( pqry_place.likelihood ));
            pqry_fields.push_back( JsonDocument::number_float( pqry_place.like_weight_ratio ));
 
            // convert from proximal to distal length.
            auto const& edge_data = pqry_place.edge().data<PlacementEdgeData>();
            pqry_fields.push_back( JsonDocument::number_float(
                edge_data.branch_length - pqry_place.proximal_length
            ));
            pqry_fields.push_back( JsonDocument::number_float( pqry_place.pendant_length ));
 
            pqry_p_arr.push_back( pqry_fields );
        }
        jpqry[ "p" ] = pqry_p_arr;
 
        // find out whether names have multiplicity
        bool has_nm = false;
        for( auto const& pqry_name : pqry.names() ) {
            has_nm |= ( pqry_name.multiplicity != 1.0 );
        }
 
        // set named multiplicity / name
        if (has_nm) {
            auto pqry_nm_arr = JsonDocument::array();
            for( auto const& pqry_name : pqry.names() ) {
                auto pqry_nm_val = JsonDocument::array();
                pqry_nm_val.push_back( pqry_name.name );
                pqry_nm_val.push_back( JsonDocument::number_float( pqry_name.multiplicity ));
                pqry_nm_arr.push_back( pqry_nm_val );
            }
            jpqry[ "nm" ] = pqry_nm_arr;
        } else {
            auto pqry_n_arr  = JsonDocument::array();
            for( auto const& pqry_name : pqry.names() ) {
                pqry_n_arr.push_back( pqry_name.name );
            }
            jpqry[ "n" ] = pqry_n_arr;
        }
 
        placements_arr.push_back( jpqry );
    }
 
    // set fields
    auto jfields = JsonDocument::array();
    jfields.push_back( "edge_num" );
    jfields.push_back( "likelihood" );
    jfields.push_back( "like_weight_ratio" );
    jfields.push_back( "distal_length" );
    jfields.push_back( "pendant_length" );
    doc[ "fields" ] = jfields;
 
    // set version
    doc[ "version" ] = 3;
 
    // set metadata
    auto jmetadata = JsonDocument::object();
    jmetadata[ "program" ] = program_;
    jmetadata[ "invocation" ] = invocation_;
    jmetadata[ "created" ] = utils::current_date() + " " + utils::current_time();
    doc[ "metadata" ] = jmetadata;
 
    return doc;
}
 
} // namespace placement
} // namespace genesis