getFrequency

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