本文整理汇总了C++中KmerCounter::add_sequence方法的典型用法代码示例。如果您正苦于以下问题：C++ KmerCounter::add_sequence方法的具体用法？C++ KmerCounter::add_sequence怎么用？C++ KmerCounter::add_sequence使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类KmerCounter的用法示例。
在下文中一共展示了KmerCounter::add_sequence方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: populate_kmer_counter_from_reads
void populate_kmer_counter_from_reads (KmerCounter& kcounter, string& fasta_filename) {
unsigned int kmer_length = kcounter.get_kmer_length();
int i, myTid;
unsigned long sum,
*record_counter = new unsigned long[omp_get_max_threads()];
unsigned long start, end;
// init record counter
for (int i = 0; i < omp_get_max_threads(); i++) {
record_counter[i] = 0;
}
cerr << "-storing Kmers..." << "\n";
start = time(NULL);
Fasta_reader fasta_reader(fasta_filename);
unsigned int entry_num = 0;
#pragma omp parallel private (myTid)
{
myTid = omp_get_thread_num();
record_counter[myTid] = 0;
while (fasta_reader.hasNext()) {
Fasta_entry fe = fasta_reader.getNext();
string accession = fe.get_accession();
#pragma omp atomic
entry_num++;
record_counter[myTid]++;
if (IRKE_COMMON::MONITOR >= 4) {
cerr << "[" << entry_num << "] acc: " << accession << ", by thread no: " << myTid << "\n";;
}
else if (IRKE_COMMON::MONITOR) {
if (myTid == 0 && record_counter[myTid] % 1000 == 0)
{
sum = record_counter[0];
for (i=1; i<omp_get_num_threads(); i++)
sum+= record_counter[i];
cerr << "\r [" << sum << "] sequences parsed. ";
}
}
string seq = fe.get_sequence();
if (seq.length() < KMER_SIZE + 1) {
continue;
}
kcounter.add_sequence(seq);
}
cerr << "\n" << " done parsing " << sum << " sequences, extracted " << kcounter.size() << " kmers, taking " << (end-start) << " seconds." << "\n";
}
return;
}