C++ (Cpp) findIntervalWithCache Examples

Example #1

File: BWTAlgorithms.cpp Project: Nanapeel/StriDe

// Count the number of occurrences of string w, including the reverse complement using a BWTInterval cache
size_t BWTAlgorithms::countSequenceOccurrencesWithCache(const std::string& w, const BWT* pBWT, const BWTIntervalCache* pIntervalCache)
{
    BWTInterval fwd_interval = findIntervalWithCache(pBWT, pIntervalCache, w);
    BWTInterval rc_interval = findIntervalWithCache(pBWT, pIntervalCache, reverseComplement(w));

    size_t count = 0;
    if(fwd_interval.isValid())
        count += fwd_interval.size();
    if(rc_interval.isValid())
        count += rc_interval.size();
    return count;
}

Example #2

File: BWTAlgorithms.cpp Project: Nanapeel/StriDe

// Delegate the findInterval call based on what indices are loaded
BWTInterval BWTAlgorithms::findInterval(const BWTIndexSet& indices, const std::string& w)
{
    if(indices.pCache != NULL)
        return findIntervalWithCache(indices.pBWT, indices.pCache, w);
    else
        return findInterval(indices.pBWT, w);
}

Example #3

File: BWTAlgorithms.cpp Project: zhangzhen/sga

size_t BWTAlgorithms::countSequenceOccurrencesSingleStrand(const std::string& w, const BWTIndexSet& indices)
{
    assert(indices.pBWT != NULL);
    assert(indices.pCache != NULL);

    BWTInterval interval = findIntervalWithCache(indices.pBWT, indices.pCache, w);
    return interval.isValid() ? interval.size() : 0;
}