Concept AlphabetWithQualitiesConcept
An alphabet where qualities can be attached to the characters.

Extends AlphabetConcept
All Extended AlphabetConcept, AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept
Defined in <seqan/basic.h>
Signature

Member Function Overview

Member Functions Inherited From AssignableConcept

Interface Function Overview

Interface Functions Inherited From AssignableConcept

Interface Metafunction Overview

Interface Metafunctions Inherited From AlphabetConcept

Interface Functions Detail

void assignQualityValue(c, q);

Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence.

Parameters

c Target character to assign quality to.
q Quality to assign to the character. The quality value is an integral value between 0 and 62 (inclusive).

If q is a char then '!' is subtracted from q. This is useful for ASCII encoded PHRED scores.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

int getQualityValue(c);

Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence.

Parameters

c Character to retrieve the quality from.

Returns

int Quality value of c. The quality value is an int value between 0 and 62 (inclusive).

Examples

String<Dna5Q> seq = "TATA";
// Assign quality value to first 'T' in sequence seq
assignQualityValue(seq[0], 35);
// Print quality value of first 'T', and default quality value of first 'A'
std::cout << getQualityValue(seq[0]) << std::endl; // Defined as 35
std::cout << getQualityValue(seq[1]) << std::endl; // Default value 60

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

Interface Metafunctions Detail

HasQualities<TAlphabet>::VALUE; HasQualities<TAlphabet>::Type;

Return whether the given type stores qualities besides the alphabet.

Template Parameters

TAlphabet The alphabe to query.

Returns

VALUE true or false
Type True or False

QualityValueSize<TAlphabet>::VALUE;

Return the number of quality values in characters from alphabet with qualities.

Template Parameters

TAlphabet The alphabet to query for its value size.

Returns

VALUE The cardinality of the set of qualities.