Index Finder

Example Program

Index Finder

Example for using a Finder of an Index.

This example shows how to use the Finder class for an Index search.

A tutorial about find algorithms using an index.

1	#include <iostream>
2	#include <seqan/index.h>
3
4	using namespace seqan;
5
6	int main ()
7	{

The following code creates an Index of "tobeornottobe". As there is no second template parameter given to Index<..>, the default index based on an enhanced suffix array is used.

8	Index< String<char> > index_esa("tobeornottobe");
9	Finder< Index< String<char> > > finder_esa(index_esa);
10
11	std::cout << "hit at ";
12	while (find(finder_esa, "be"))
13	std::cout << position(finder_esa) << " ";
14	std::cout << std::endl;
15

Now we explicitly create a q-gram index using an ungapped 2-gram and do the same. Instead of this fixed-size shape you can use arbitrary shapes and assign them before calling find via indexShape.

16	typedef Index< String<char>, IndexQGram< UngappedShape<2> > > TQGramIndex;
17	TQGramIndex index_2gram("tobeornottobe");
18	Finder< TQGramIndex > finder_2gram(index_2gram);
19
20	std::cout << "hit at ";
21	while (find(finder_2gram, "be"))
22	std::cout << position(finder_2gram) << " ";
23	std::cout << std::endl;
24
25	return 0;
26	}

Output

weese@tanne:~/seqan$ cd demos
weese@tanne:~/seqan/demos$ make index_find
weese@tanne:~/seqan/demos$ ./index_find
hit at 11 2
hit at 2 11
weese@tanne:~/seqan/demos$

See

Index, find, Finder

SeqAn - Sequence Analysis Library - www.seqan.de