我想解析一个如下所示的文件（类似 FASTA 的文本格式）：
>InfoHeader
"Some text sequence that has a line break after every 80 characters"
>InfoHeader
"Some text sequence that has a line break after every 80 characters"
...
e.g.:
>gi|31563518|ref|NP_852610.1| microtubule-associated proteins 1A/1B light chain 3A isoform b [Homo sapiens]
MKMRFFSSPCGKAAVDPADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKI
IRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGFIRENE
我用 boost::spirit 为此编写了一个解析器。解析器正确地将标题行和以下文本序列存储在std::vector< std::pair< string, string >>但对于较大的文件来说需要很长时间（100MB 文件需要 17 秒）。作为比较，我编写了一个没有 boost::spirit （只是 STL 函数）的程序，它只是将 100MB 文件的每一行复制到一个std::vector。整个过程只需不到一秒钟。用于比较的“程序”没有达到目的，但我认为解析器不应该花那么长时间......
我知道还有很多其他 FASTA 解析器，但我很好奇为什么我的代码很慢。
.hpp 文件：
#include <boost/filesystem/path.hpp>
namespace fs = boost::filesystem;
class FastaReader {
public:
typedef std::vector< std::pair<std::string, std::string> > fastaVector;
private:
fastaVector fV;
fs::path file;
public:
FastaReader(const fs::path & f);
~FastaReader();
const fs::path & getFile() const;
const fastaVector::const_iterator getBeginIterator() const;
const fastaVector::const_iterator getEndIterator() const;
private:
void parse();
};
和 .cpp 文件：
#include <iomanip>
#include <boost/date_time/posix_time/posix_time.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/path.hpp>
#include <boost/spirit/include/classic_position_iterator.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/spirit/include/phoenix_core.hpp>
#include <boost/spirit/include/phoenix_fusion.hpp>
#include <boost/spirit/include/phoenix_operator.hpp>
#include <boost/spirit/include/qi.hpp>
#include "fastaReader.hpp"
using namespace std;
namespace fs = boost::filesystem;
namespace qi = boost::spirit::qi;
namespace pt = boost::posix_time;
template <typename Iterator, typename Skipper>
struct FastaGrammar : qi::grammar<Iterator, FastaReader::fastaVector(), qi::locals<string>, Skipper> {
qi::rule<Iterator> infoLineStart;
qi::rule<Iterator> inputEnd;
qi::rule<Iterator> lineEnd;
qi::rule<Iterator, string(), Skipper> infoLine;
qi::rule<Iterator, string(), Skipper> seqLine;
qi::rule<Iterator, FastaReader::fastaVector(), qi::locals<string>, Skipper> fasta;
FastaGrammar() : FastaGrammar::base_type(fasta, "fasta") {
using boost::spirit::standard::char_;
using boost::phoenix::bind;
using qi::eoi;
using qi::eol;
using qi::lexeme;
using qi::_1;
using qi::_val;
using namespace qi::labels;
infoLineStart = char_('>');
inputEnd = eoi;
/* grammar */
infoLine = lexeme[*(char_ - eol)];
seqLine = *(char_ - infoLineStart);
fasta = *(infoLineStart > infoLine[_a = _1]
> seqLine[bind(&FastaGrammar::addValue, _val, _a, _1)]
)
> inputEnd
;
infoLineStart.name(">");
infoLine.name("sequence identifier");
seqLine.name("sequence");
}
static void addValue(FastaReader::fastaVector & fa, const string & info, const string & seq) {
fa.push_back(make_pair(info, seq));
}
};
FastaReader::FastaReader(const fs::path & f) {
this->file = f;
this->parse();
}
FastaReader::~FastaReader() {}
const fs::path & FastaReader::getFile() const {
return this->file;
}
const FastaReader::fastaVector::const_iterator FastaReader::getBeginIterator() const {
return this->fV.cbegin();
}
const FastaReader::fastaVector::const_iterator FastaReader::getEndIterator() const {
return this->fV.cend();
}
void FastaReader::parse() {
if ( this->file.empty() ) throw string("FastaReader: No file specified.");
if ( ! fs::is_regular_file(this->file) ) throw (string("FastaReader: File not found: ") + this->file.string());
typedef boost::spirit::istream_iterator iterator_type;
typedef boost::spirit::classic::position_iterator2<iterator_type> pos_iterator_type;
typedef FastaGrammar<pos_iterator_type, boost::spirit::ascii::space_type> fastaGr;
fs::ifstream fin(this->file);
if ( ! fin.is_open() ) {
throw (string("FastaReader: Access denied: ") + this->file.string());
}
fin.unsetf(ios::skipws);
iterator_type begin(fin);
iterator_type end;
pos_iterator_type pos_begin(begin, end, this->file.string());
pos_iterator_type pos_end;
fastaGr fG;
try {
std::cerr << "Measuring: Parsing." << std::endl;
const pt::ptime startMeasurement = pt::microsec_clock::universal_time();
qi::phrase_parse(pos_begin, pos_end, fG, boost::spirit::ascii::space, this->fV);
const pt::ptime endMeasurement = pt::microsec_clock::universal_time();
pt::time_duration duration (endMeasurement - startMeasurement);
std::cerr << duration << std::endl;
} catch (std::string str) {
cerr << "error message: " << str << endl;
}
}
所以语法执行以下操作：
它查找“>”符号，然后存储所有后续字符，直到检测到 EOL。 EOL 之后，文本序列开始，并在检测到“>”符号时结束。然后，通过调用将两个字符串（标题行和文本序列）存储在 std::vector 中FastaReader::addValue().
我使用带有 -O2 和 -std=c++11 标志的 g++ 版本 4.8.2 编译了我的程序。
那么我的代码中的性能问题在哪里？
