diff --git a/src/naive_search.cpp b/src/naive_search.cpp index c6cc2c8bc5459a6c3ceb86e58b2efcdc31ddbb96..2f0a32225820bb6baeaf81b3658ad20ff8974eca 100644 --- a/src/naive_search.cpp +++ b/src/naive_search.cpp @@ -1,5 +1,8 @@ #include <sstream> +// #include <seqan/sequence.h> +// #include <seqan/stream.h> + #include <seqan3/alphabet/nucleotide/dna5.hpp> #include <seqan3/argument_parser/all.hpp> #include <seqan3/core/debug_stream.hpp> @@ -7,9 +10,38 @@ #include <seqan3/search/fm_index/fm_index.hpp> #include <seqan3/search/search.hpp> +#include <iostream> +#include <string> +using namespace std; + // prints out all occurences of query inside of ref void findOccurences(std::vector<seqan3::dna5> const& ref, std::vector<seqan3::dna5> const& query) { //!TODO ImplementMe + int m = query.vector::size(); + int total_count = 0; + std::vector<int> occurances; // number of occurences of pattern in referenc + + for(int i=0; i<ref.vector::size(); i++){ + + for(int j=0; j<m; j++){ + if(ref.at(i+j) != query.at(j)){ + break; + }else if(j=m-1) + { + std::cout << "Infix found at position: " << i <<std::endl; + // std::cout << i << std::endl; + // std::cout << "\n" << std::endl; + total_count+=1; + + } + + + } + if(total_count> 10){ + break; + } + + } } int main(int argc, char const* const* argv) {