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//![includes]
#include <iostream>
#include <random>
#include <seqan/align.h>
#include <seqan/index.h>
using namespace seqan2;
//![includes]
//![matrix_init]
template <typename TStringSet, typename TIndexSpec>
void qgramCounting(TStringSet & set, TIndexSpec)
{
typedef Index<TStringSet, TIndexSpec> TIndex;
typedef typename Fibre<TIndex, QGramCounts>::Type TCounts;
typedef typename Fibre<TIndex, QGramCountsDir>::Type TCountsDir;
typedef typename Value<TCountsDir>::Type TDirValue;
typedef typename Iterator<TCounts, Standard>::Type TIterCounts;
typedef typename Iterator<TCountsDir, Standard>::Type TIterCountsDir;
TIndex index(set);
indexRequire(index, QGramCounts());
// initialize distance matrix
int seqNum = countSequences(index);
Matrix<int, 2> distMat;
setLength(distMat, 0, seqNum);
setLength(distMat, 1, seqNum);
resize(distMat, 0);
std::cout << std::endl << "Length of the CountsDir fibre: " << length(indexCountsDir(index)) << std::endl;
TIterCountsDir itCountsDir = begin(indexCountsDir(index), Standard());
TIterCountsDir itCountsDirEnd = end(indexCountsDir(index), Standard());
TIterCounts itCountsBegin = begin(indexCounts(index), Standard());
//![matrix_init]
//![matrix_calculation]
// for each bucket count common q-grams for each sequence pair
TDirValue bucketBegin = *itCountsDir;
for (++itCountsDir; itCountsDir != itCountsDirEnd; ++itCountsDir)
{
TDirValue bucketEnd = *itCountsDir;
// q-gram must occur in at least 2 different sequences
if (bucketBegin != bucketEnd)
{
TIterCounts itA = itCountsBegin + bucketBegin;
TIterCounts itEnd = itCountsBegin + bucketEnd;
for (; itA != itEnd; ++itA)
for (TIterCounts itB = itA; itB != itEnd; ++itB)
distMat((*itA).i1, (*itB).i1) += _min((*itA).i2, (*itB).i2);
}
bucketBegin = bucketEnd;
}
std::cout << std::endl << "Common 5-mers for Seq_i, Seq_j" << std::endl;
std::cout << distMat;
}
//![matrix_calculation]
//![initialization]
int main()
{
// for the sake of reproducibility
std::mt19937 rng;
// create StringSet of 3 random sequences
StringSet<DnaString> stringSet;
reserve(stringSet, 3);
for (int seqNo = 0; seqNo < 3; ++seqNo)
{
DnaString tmp;
int len = rng() % 100 + 10;
for (int i = 0; i < len; ++i)
appendValue(tmp, Dna(rng() % 4));
appendValue(stringSet, tmp);
std::cout << ">Seq" << seqNo << std::endl << tmp << std::endl;
}
qgramCounting(stringSet, IndexQGram<UngappedShape<5> >());
qgramCounting(stringSet, IndexQGram<UngappedShape<5>, OpenAddressing>());
return 0;
}
//![initialization]
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