1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
|
#include <iostream>
#include <seqan/align_profile.h>
using namespace seqan;
int main()
{
typedef ProfileChar<Dna, int> TDnaProfile;
typedef String<TDnaProfile> TProfileString;
TProfileString profile = "CGAT";
DnaString seq = "CGGAAT";
Gaps<TProfileString> gapsH(profile);
Gaps<DnaString> gapsV(seq);
Score<int, ProfileSeqScore> sScheme(profile);
int val = globalAlignment(gapsH, gapsV, sScheme, NeedlemanWunsch());
std::cout << "score value = " << val << "\n";
std::cout << "gaps in profile/sequence\n"
<< "pos\tG\tS\n";
for (unsigned i = 0; i < length(gapsH); ++i)
std::cerr << i << "\t" << isGap(gapsH, i) << "\t" << isGap(gapsV, i) << "\n";
return 0;
}
|
