StringSet

Class

StringSet

A container class for a set of strings.

StringSet

Dependent

Owner

ConcatDirect

StringSet<TString, TSpec>

Include Headers

sequence.h

Parameters

TString	The string type. Types: String
TSpec	The specializing type for the StringSet. Metafunctions: Spec Default: Owner<Generous>.

Specializations

Dependent	A string set storing references of the strings.
Owner	A string set storing the strings as members.

Metafunctions

Concatenator	Returns the type of the concatenation sequence of all sequences in a StringSet.
SAValue	The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.

Functions

alignmentFreeComparison	Computes the pairwise similarity scores for a set of sequences
appendSeqs	Appends all sequences stored in files of directory to a StringSet.
appendValue	Appends a value to a container.
assignValueById	Adds a new string to the StringSet and returns an id.
bandedChainAlignment	Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
begin	The begin of a container.
clear	Resets an object.
complement	Complement a sequence or a StringSet in-place.
completeProfile	Concatenates the background frequency with the profile for the motif component.
concat	Returns the concatenation sequence of all sequences in a StringSet.
convertPatternToProfile	Converts a pattern into a profile which consists of a set of frequency distributions.
convertSetOfPatternsToProfile	Converts a set of sequence patterns into a profile.
createCountArray	Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
createPrefixSumTable	Creates the prefix sum table
determineConsensusSeq	Determines the consensus pattern of a given profile.
display	Displays a given set of strings.
em	Represents the EM algorithm as used by MEME.
end	The end of a container.
expectation	Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
findMotif	Represents the main function which is used to start the search for noticeable motif patterns.
findRepeats	Search for repeats in a text.
generateSequence	Generates random state and alphabet sequences of a given HMM.
getValueById	Retrieves a string from the StringSet given an id.
globalAlignment	Computes the best global pairwise alignment.
globalAlignmentScore	Computes the best global pairwise alignment score.
idToPosition	Retrieves the position of a string in the StringSet given an id.
infix	Creates infix object.
infixWithLength	Creates infix object.
iter	Iterator to item at given position.
length	The number of items/characters.
loadContigs	Loads contigs into fragment store.
matchRefinement	Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
normalize	Determines the normalized frequencies.
positionToId	Retrieves the id of a string in the StringSet given a position.
prefix	Creates prefix object.
readAll	Read all sequence records from a SequenceStream object.
readBatch	Read a given number of sequence records from SequenceStream.
removeValueById	Removes a string from the StringSet given an id.
resize	Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
reverseComplement	Reverse and complement a sequence or a StringSet in-place.
setStrings	Loads the sequences of a stringset into an alignment.
stringSetLimits	Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
stringSplit	Append a list of the words in the string, using sep as the delimiter string StringSet.
stringToStringSet	Transform a String into a StringSet containing this String.
suffix	Creates suffix object.
swap	Swaps the contents of two values.
toLower	Convert characters in sequence or StringSet to lower case in-place.
toUpper	Convert characters in sequence or StringSet to lower case in-place.
value	Reference to the value.
valueById	Retrieves a string from the StringSet given an id.
variance	Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel
write2	Write FASTA or FASTQ records.
writeAll	Write sequence records from to a SequenceStream object.
zscore	Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel

Examples

File "stringset.cpp"

1	#include <seqan/basic.h>
2	#include <seqan/sequence.h>
3	#include <seqan/file.h>
4
5	using namespace seqan;
6
7	int main()
8	{
9	StringSet<String<char> > stringSet;
10	appendValue(stringSet, "Hello World!"); // Append string to the end of the string set.
11
12	std::cout << "Number of elements: " << length(stringSet) << std::endl;
13
14	resize(stringSet, 3, Exact()); // Adapt the size of the container, while keeping existing values.
15
16	String<char> seq = "To be or not to be!";
17	stringSet[1] = seq; // Use subscript operator to assign a new value.
18	stringSet[2] = "A man, a plan, a canal - Panama!";
19
20	std::cout << "Number of elements: " << length(stringSet) << std::endl;
21
22	typedef Iterator<StringSet<String<char> >, Standard>::Type TIterator;
23	for(TIterator it = begin(stringSet, Standard()); it != end(stringSet, Standard()); ++it)
24	std::cout << "Element " << position(it, stringSet) << ": " << *it << std::endl;
25
26	clear(stringSet); // Clear the contents of the StringSet.
27
28	std::cout << "Number of elements: " << length(stringSet) << std::endl;
29
30	return 0;
31	}
32

The output is as follows:

Number of elements: 1
Number of elements: 3
Element 0: Hello World!
Element 1: To be or not to be!
Element 2: A man, a plan, a canal - Panama!
Number of elements: 0

Example Programs

Mummy, Maximal Unique Matches, Index Finder StringSet

SeqAn - Sequence Analysis Library - www.seqan.de