| Function getFrequency Returns the number of sequences, which contain the representative as a substring. int getFrequency(iterator) Include Headers seqan/index.h Parameters
iterator | An iterator of a suffix tree. Types: VSTree Iterator
Return Values The number of different sequences containing the representative. Member of VSTree Iterator Examples The following code how getFrequency is used. Note that the result of alternative 1 and 2 is the same, however alternative one copies a string which requires more memory. File "index_getOccurrences_getFrequency_range_getFibre.cpp"
1 | #include <seqan/index.h>
2 |
3 | using namespace seqan;
4 |
5 | int main ()
6 | {
7 | typedef StringSet<String<char> > TText;
8 | typedef Index<TText> TIndex;
9 | typedef SAValue<TIndex>::Type TSAValue;
10 |
11 | TText text;
12 | appendValue(text, "MISSISSIPPI");
13 | appendValue(text, "MYMISSISAHAPPY");
14 |
15 | TIndex index(text);
16 | Iterator<TIndex, TopDown<> >::Type it(index);
17 |
18 | goDown(it, "SSI");
19 |
20 | std::cout << "SSI occurs in " << getFrequency(it) << " sequences." << std::endl;
21 |
22 | // 1 alternative to print the location of hits
23 | String<TSAValue> saPositions = getOccurrences(it);
24 | for (unsigned i = 0; i < length(saPositions); ++i)
25 | std::cout << "Hit in sequence " << saPositions[i].i1 << " at position " << saPositions[i].i2 << std::endl;
26 |
27 | std::cout << "----------------------------" << std::endl;
28 |
29 | // 2 alternative to print the location of hits
30 | Pair<unsigned> hitInterval = range(it);
31 | for (; hitInterval.i1 < hitInterval.i2; ++hitInterval.i1)
32 | std::cout << "Hit in sequence " << getFibre(index, FibreSA())[hitInterval.i1].i1 <<
33 | " at position " << getFibre(index, FibreSA())[hitInterval.i1].i2 << std::endl;
34 |
35 | return 0;
36 | }
SSI occurs in 2 sequences. Hit in sequence 0 at position 5 Hit in sequence 1 at position 4 Hit in sequence 0 at position 2 ---------------------------- Hit in sequence 0 at position 5 Hit in sequence 1 at position 4 Hit in sequence 0 at position 2 See Also getOccurrences SeqAn - Sequence Analysis Library - www.seqan.de

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