output_target.hpp

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#ifndef GENESIS_UTILS_IO_OUTPUT_TARGET_H_
#define GENESIS_UTILS_IO_OUTPUT_TARGET_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    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@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/utils/io/base_output_target.hpp"
#include "genesis/utils/io/file_output_target.hpp"
#include "genesis/utils/io/gzip_output_target.hpp"
#include "genesis/utils/io/gzip_stream.hpp"
#include "genesis/utils/io/stream_output_target.hpp"
#include "genesis/utils/io/string_output_target.hpp"
 
#include "genesis/utils/core/fs.hpp"
#include "genesis/utils/core/std.hpp"
 
#include <iostream>
#include <memory>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Output Target Convenience Functions
// =================================================================================================
 
inline std::shared_ptr<BaseOutputTarget> to_file(
    std::string const& file_name,
    GzipCompressionLevel compression_level,
    // GzipCompressionLevel compression_level = GzipCompressionLevel::kNoCompression,
    bool auto_adjust_filename = true
) {
    auto fn = file_name;
    auto const ext = file_extension( fn );
 
    // With compression
    if( compression_level != GzipCompressionLevel::kNoCompression ) {
        if( auto_adjust_filename && ext != "gz" ) {
            fn += ".gz";
        }
        return std::make_shared<GzipOutputTarget>(
            std::make_shared< FileOutputTarget >( fn, std::ios_base::out | std::ios_base::binary ),
            compression_level
        );
    }
 
    // Without compression. Not in the `else` branch, to not confuse old compilers.
    if( auto_adjust_filename && ext == "gz" ) {
        fn.erase( fn.size() - 3 );
    }
    return std::make_shared< FileOutputTarget >( fn );
}
 
inline std::shared_ptr<BaseOutputTarget> to_file(
    std::string const& file_name,
    std::ios_base::openmode mode = std::ios_base::out
) {
    return std::make_shared< FileOutputTarget >( file_name, mode );
}
 
inline std::shared_ptr<BaseOutputTarget> to_gzip_file(
    std::string const& file_name
) {
    return to_file( file_name, GzipCompressionLevel::kDefaultCompression );
}
 
inline std::shared_ptr<BaseOutputTarget> to_gzip_block_file(
    std::string const& file_name,
    std::size_t block_size = GzipBlockOStream::GZIP_DEFAULT_BLOCK_SIZE,
    GzipCompressionLevel compression_level = GzipCompressionLevel::kDefaultCompression,
    std::shared_ptr<ThreadPool> thread_pool = nullptr,
    bool auto_adjust_filename = true
) {
    if( compression_level == GzipCompressionLevel::kNoCompression ) {
        throw std::invalid_argument(
            "Cannot use compression level kNoCompression with a gzip block output."
        );
    }
 
    // Adjust filename if needed and wanted
    auto fn = file_name;
    auto const ext = file_extension( fn );
    if( auto_adjust_filename && ext != "gz" ) {
        fn += ".gz";
    }
 
    // Return the wrapped streams
    return std::make_shared<GzipBlockOutputTarget>(
        std::make_shared< FileOutputTarget >( fn, std::ios_base::out | std::ios_base::binary ),
        block_size,
        compression_level,
        thread_pool
    );
}
 
inline std::shared_ptr<BaseOutputTarget> to_string(
    std::string& target_string
) {
    return std::make_shared< StringOutputTarget >( target_string );
}
 
inline std::shared_ptr<BaseOutputTarget> to_stream(
    std::ostream& target_stream,
    GzipCompressionLevel compression_level = GzipCompressionLevel::kNoCompression
) {
    if( compression_level != GzipCompressionLevel::kNoCompression ) {
        return std::make_shared<GzipOutputTarget>(
            std::make_shared< StreamOutputTarget >( target_stream ),
            compression_level
        );
    }
    return std::make_shared< StreamOutputTarget >( target_stream );
}
 
inline std::shared_ptr<BaseOutputTarget> to_stdout() {
    return std::make_shared< StreamOutputTarget >( std::cout );
}
 
inline std::shared_ptr<BaseOutputTarget> to_stderr() {
    return std::make_shared< StreamOutputTarget >( std::cerr );
}
 
} // namespace utils
} // namespace genesis
 
#endif // include guard