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//![include]
#include <iostream>
#include <seqan/stream.h>
#include <seqan/journaled_string_tree.h>
//![include]
//![match_printer]
template <typename TTraverser>
struct MatchPrinter
{
TTraverser & trav;
MatchPrinter(TTraverser & _trav) : trav(_trav)
{}
void
operator()()
{
auto pos = position(trav);
for (auto p : pos)
{
std::cout << "Seq: " << p.i1 << " Pos: " << p.i2 << std::endl;
}
}
};
//![match_printer]
//![typedef]
using namespace seqan;
int main()
{
typedef JournaledStringTree<DnaString> TJst;
typedef Pattern<DnaString, Horspool> TPattern;
typedef Traverser<TJst>::Type TTraverser;
//![typedef]
//![init]
DnaString seq = "AGATCGAGCGAGCTAGCGACTCAG";
TJst jst(seq, 10);
insert(jst, 1, 3, std::vector<unsigned>{1, 3, 5, 6, 7}, DeltaTypeDel());
insert(jst, 8, "CGTA", std::vector<unsigned>{1, 2}, DeltaTypeIns());
insert(jst, 10, 'C', std::vector<unsigned>{4, 9}, DeltaTypeSnp());
insert(jst, 15, 2, std::vector<unsigned>{0, 4, 7}, DeltaTypeDel());
insert(jst, 20, 'A', std::vector<unsigned>{0, 9}, DeltaTypeSnp());
insert(jst, 20, Pair<unsigned, DnaString>(1, "CTC"), std::vector<unsigned>{1, 2, 3, 7}, DeltaTypeSV());
//![init]
//![prepare_search]
DnaString ndl = "AGCGT";
TTraverser trav(jst, length(ndl));
TPattern pat(ndl);
JstExtension<TPattern> ext(pat);
//![prepare_search]
//![search]
MatchPrinter<TTraverser> delegate(trav);
find(trav, ext, delegate);
return 0;
}
//![search]
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