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#include <iostream>
#include <cstdlib>
#include <fstream>
#include <string>
#include <map>
#include <algorithm>
#include "fasta.hpp"
#include <boost/program_options.hpp>
namespace po = boost::program_options;
struct longer_sequence
{
bool operator()(const sequence::FastaRecord &r1, const sequence::FastaRecord &r2)
{
return r1.sequence.length() > r2.sequence.length();
}
};
int main(int argc, char *argv[])
{
bool produce_help = false;
bool do_random_shuffle = false;
// bool lexicographic = false;
po::options_description desc("Options");
desc.add_options()
("help,h", po::bool_switch(&produce_help), "Produce help message.")
("random-shuffle,r", po::bool_switch(&do_random_shuffle), "Randomly shuffle sequences.")
// ("lexicographic,l", po::bool_switch(&lexicographic), "Sort sequences in lexicographical order.")
;
po::variables_map vm;
po::store(po::command_line_parser(argc, argv).options(desc).run(), vm);
notify(vm);
if (produce_help) {
std::cerr << "Usage: fastasort [OPTIONS]\n"
<< " The FASTA sequences are read from the STDIN.\n"
<< " The sorted sequences are written to the STDOUT in FASTA format.\n"
<< desc << '\n';
exit(EXIT_FAILURE);
}
sequence::Fasta sequences;
std::cin >> sequences;
if (do_random_shuffle) {
std::random_shuffle(sequences.begin(), sequences.end());
std::cout << sequences;
} else {
// sort by length. the first sequence is the longest.
typedef std::pair<size_t, size_t> length_index_pair;
std::vector<length_index_pair> length_indexes;
for (size_t i = 0; i < sequences.size(); ++i)
length_indexes.push_back(std::make_pair(sequences[i].sequence.length(), i));
std::sort(length_indexes.begin(), length_indexes.end(), std::greater<length_index_pair>());
for (size_t i = 0; i < length_indexes.size(); ++i)
std::cout << sequences[length_indexes[i].second];
}
return EXIT_SUCCESS;
}
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