hashInit

Function

hashInit

Preprocessing step of a pure hashNext loop.

Overlapping q-grams can efficiently be hashed by calling hash on the first text position and hashNext on succeeding, adjacent positions. One drawback of this scenario is that for-loops cannot start with the first position directly and become more complicated. As a remedy, hashInit was introduced which initializes the Shape to be used with hashNext on the first position directly.

hashInit(shape, it)

Include Headers

seqan/index.h

Parameters

shape	Shape to be used for hashing. Types: Shape
it	Sequence iterator pointing to the first text character of the shape.

Member of

Shape

Examples

Two hash loop examples. The first loop uses hash/hashNext while the second use hashInit/hashNext and can process all hashes within the loop.

File "shape_hash_init.cpp"

1	#include <seqan/sequence.h>
2	#include <seqan/index.h>
3
4	using namespace seqan;
5
6	int main ()
7	{
8	DnaString text = "AAAACACAGTTTGA";
9	Shape<Dna, UngappedShape<3> > myShape;
10
11	// loop using hash() and hashNext() starts at position 1
12	std::cout << hash(myShape, begin(text)) << '\t';
13	for (unsigned i = 1; i < length(text) - length(myShape) + 1; ++i)
14	std::cout << hashNext(myShape, begin(text) + i) << '\t';
15	std::cout << std::endl;
16
17	// loop using hashInit() and hashNext() starts at position 0
18	hashInit(myShape, begin(text));
19	for (unsigned i = 0; i < length(text) - length(myShape) + 1; ++i)
20	std::cout << hashNext(myShape, begin(text) + i) << '\t';
21	std::cout << std::endl;
22
23	return 0;
24	}

The two loops produce the same hash values:

0 0 1 4 17 4 18 11 47 63 62 56
0 0 1 4 17 4 18 11 47 63 62 56