input_source.hpp

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#ifndef GENESIS_UTILS_IO_INPUT_SOURCE_H_
#define GENESIS_UTILS_IO_INPUT_SOURCE_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_input_source.hpp"
#include "genesis/utils/io/file_input_source.hpp"
#include "genesis/utils/io/gzip_input_source.hpp"
#include "genesis/utils/io/gzip.hpp"
#include "genesis/utils/io/stream_input_source.hpp"
#include "genesis/utils/io/string_input_source.hpp"
 
#include "genesis/utils/core/std.hpp"
 
#include <iostream>
#include <memory>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Input Source Convenience Functions
// =================================================================================================
 
inline std::shared_ptr<BaseInputSource> from_file(
    std::string const& file_name,
    bool detect_compression = true
) {
    if( detect_compression && is_gzip_compressed_file( file_name )) {
        return std::make_shared<utils::GzipInputSource>(
            std::make_shared< FileInputSource >( file_name )
        );
    } else {
        return std::make_shared< FileInputSource >( file_name );
    }
}
 
inline std::vector<std::shared_ptr<BaseInputSource>> from_files(
    std::vector<std::string> const& file_names,
    bool detect_compression = true
) {
    std::vector<std::shared_ptr<BaseInputSource>> ret;
    for( size_t i = 0; i < file_names.size(); ++i ) {
        ret.emplace_back( from_file( file_names[i], detect_compression ));
    }
    return ret;
}
 
template<typename InputIterator>
inline std::vector<std::shared_ptr<BaseInputSource>> from_files(
    InputIterator first,
    InputIterator last,
    bool detect_compression = true
) {
    std::vector<std::shared_ptr<BaseInputSource>> ret;
    while( first != last ) {
        ret.emplace_back( from_file( *first, detect_compression ));
        ++first;
    }
    return ret;
}
 
inline std::shared_ptr<BaseInputSource> from_string(
    std::string const& input_string
) {
    return std::make_shared< StringInputSource >( input_string );
}
 
inline std::vector<std::shared_ptr<BaseInputSource>> from_strings(
    std::vector<std::string> const& input_strings
) {
    std::vector<std::shared_ptr<BaseInputSource>> ret;
    for( size_t i = 0; i < input_strings.size(); ++i ) {
        ret.emplace_back( from_string( input_strings[i] ));
    }
    return ret;
}
 
template<typename InputIterator>
inline std::vector<std::shared_ptr<BaseInputSource>> from_strings(
    InputIterator first,
    InputIterator last
) {
    std::vector<std::shared_ptr<BaseInputSource>> ret;
    while( first != last ) {
        ret.emplace_back( from_string( *first ));
        ++first;
    }
    return ret;
}
 
inline std::shared_ptr<BaseInputSource> from_stream(
    std::istream& input_stream
) {
    return std::make_shared< StreamInputSource >( input_stream );
}
 
inline std::shared_ptr<BaseInputSource> from_stdin() {
    return std::make_shared< StreamInputSource >( std::cin );
}
 
} // namespace utils
} // namespace genesis
 
#endif // include guard