Concept AlphabetWithQualitiesConceptAn alphabet where qualities can be attached to the characters.
An alphabet where qualities can be attached to the characters.
Extends | AlphabetConcept |
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All Extended | AlphabetConcept, AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept |
Defined in | <seqan/basic.h> |
Signature |
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Interface Function Overview
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void assignQualityValue(c, q);
Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence. -
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.
Interface Functions Inherited From AssignableConcept
Interface Metafunction Overview
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HasQualities<TAlphabet>::VALUE;, HasQualities<TAlphabet>::Type;
Return whether the given type stores qualities besides the alphabet. -
QualityValueSize<TAlphabet>::VALUE;
Return the number of quality values in characters from alphabet with qualities.
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. |
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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. |
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Returns
int |
Quality value of c. The quality value is an int value between 0 and 62 (inclusive). |
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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.