Finder

Class

Finder

Holds the haystack and a current search context.

Finder

Backtracking

Pigeonhole

Swift


SwiftLocal		SwiftSemiGlobal

Finder<THaystack[, TSpec]>

Include Headers

seqan/find.h

Parameters

THaystack	The haystack type. Types: Index, String
TSpec	The index-algorithm to search with (Optional). Types: Backtracking, Pigeonhole, Swift Default: The result of DefaultFinder Remarks: Leave empty for online pattern matching (see Pattern). If THaystack is an Index, then TSpec specifies the index search algorithm.

Remarks

position(finder) returns the position of the current hit in the haystack. If THaystack is a set of strings or an index of a set of strings, then position(finder) returns a Pair (hayNo, pos), in which hayNo is the haystack index and pos the local position of the hit.

To reset the finder object and use it on another text or different text position, use clear(finder) Note that clear(finder) doesn't move the text iterator. To start the search from the beginning or somewhere else in the text, use goBegin or setPosition.

Specializations

Backtracking	Provides approximate string matching via backtracking on a substring index.
Pigeonhole	Provides a fast filter alogrithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.
Swift	Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential ε-matches. An ε-match is a matching region of minimal length and an error rate of at most ε.

Metafunctions

Container	Type of the container given an iterator.
Difference	Type of an object that stores the difference between two iterators.
Haystack	Returns the haystack type of a Finder type.
Host	Type of the object a given object depends on.
Iterator	Type of iterator objects that are used to traverse the container.
Value	Type of the items in the container or behind an iterator.

Member Functions

Finder

Constructor

Functions

begin	The begin of a container.
beginPosition	Begin position of object in host.
clear	Resets an object.
end	The end of a container.
endPosition	End position of object in host.
find	Search for a Pattern in a Finder object.
findBegin	Search the begin of an approximate match.
haystack	Returns the haystack of a Finder object.
infix	Returns the segment of the last found match in haystack.
length	The number of items/characters.
position	Position of an iterator.
setHaystack	Sets the haystack of a Finder object.
setPosition	Sets the position of a finder.

Examples

The following example shows how one can search online for a pattern in a haystack. Note that it is neccessary to reset the finder befor searching for another pattern.

File "finder_online.cpp"

1	#include <seqan/find.h>
2
3	using namespace seqan;
4
5	int main()
6	{
7	CharString hstck = "I spy with my little eye something that is yellow";
8	Finder<CharString> finder(hstck);
9
10	Pattern<CharString, Horspool> p1("y");
11
12	while(find(finder, p1))
13	std::cout << "Hit at position: " << position(finder)<<std::endl;
14
15	goBegin(finder); // move Finder to the beginning of the text
16	clear(finder); // reset Finder
17
18	Pattern<CharString, Horspool> p2("t");
19	while(find(finder, p2))
20	std::cout << "Hit at position: " << position(finder)<<std::endl;
21	}

Hit at position: 4
Hit at position: 12
Hit at position: 22
Hit at position: 43
Hit at position: 8
Hit at position: 16
Hit at position: 17
Hit at position: 29
Hit at position: 35
Hit at position: 38

In contrast to the example above the code below shows how one can use a Finder with an index as base. Again, note that it is neccessary to reset the finder befor searching for another pattern.

File "finder_index.cpp"

1	#include <seqan/find.h>
2	#include <seqan/index.h>
3
4	using namespace seqan;
5
6	int main()
7	{
8	CharString hstck = "I spy with my little eye something that is yellow";
9	Index<CharString, FMIndex<> > index(hstck);
10	Finder<Index<CharString, FMIndex<> > > finder(hstck);
11
12	while(find(finder, "y"))
13	std::cout << "Hit at position: " << position(finder)<<std::endl;
14
15	clear(finder); // reset Finder
16
17	while(find(finder, "t"))
18	std::cout << "Hit at position: " << position(finder)<<std::endl;
19	}

Hit at position: 12
Hit at position: 4
Hit at position: 22
Hit at position: 43
Hit at position: 38
Hit at position: 8
Hit at position: 35
Hit at position: 29
Hit at position: 17
Hit at position: 16

Example Programs

Index Finder, Index Finder StringSet

SeqAn - Sequence Analysis Library - www.seqan.de