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// Provide a generic print function which is used when the input type is not String<int>.
#include <iostream>
#include <seqan/file.h>
#include <seqan/sequence.h>
#include <seqan/score.h>
using namespace seqan;
template <typename TText>
int computeLocalScore(TText const & subText, String<AminoAcid> const & pattern)
{
int localScore = 0;
for (unsigned i = 0; i < length(pattern); ++i)
localScore += score(Blosum62(), subText[i], pattern[i]);
return localScore;
}
template <typename TText, typename TPattern>
int computeLocalScore(TText const & subText, TPattern const & pattern)
{
int localScore = 0;
for (unsigned i = 0; i < length(pattern); ++i)
if (subText[i] == pattern[i])
++localScore;
return localScore;
}
template <typename TText, typename TPattern>
String<int> computeScore(TText const & text, TPattern const & pattern)
{
String<int> score;
resize(score, length(text) - length(pattern) + 1, 0);
for (unsigned i = 0; i < length(text) - length(pattern) + 1; ++i)
score[i] = computeLocalScore(infix(text, i, i + length(pattern)), pattern);
return score;
}
template <typename TText>
void print(TText const & text)
{
std::cout << text << std::endl;
}
void print(String<int> const & text)
{
for (unsigned i = 0; i < length(text); ++i)
std::cout << text[i] << " ";
std::cout << std::endl;
}
int main()
{
String<char> text = "This is an awesome tutorial to get to now SeqAn!";
String<char> pattern = "tutorial";
String<int> score = computeScore(text, pattern);
print(text);
// > This is an awesome tutorial to get to now SeqAn!
print(pattern);
// > tutorial
print(score);
// > 1 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 8 0 1 0 0 0 0 2 0 1 0 0 1 0 3 0 1 1 0 0 0 0
return 0;
}
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