Class
BlastMatchAn data structure to hold a blast match, also known as high-scoring segment pair (HSP)
Implements | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, EqualityComparableConcept, LessThanComparableConcept |
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All Impl'd | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, EqualityComparableConcept, LessThanComparableConcept |
Defined in | <seqan/blast.h> |
Signature |
struct BlastMatch<TAlign, TPos, TQId, TSId> { ... };
|
Template Parameters
TAlignRow0 |
Type of the first alignment row, usually Gaps |
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TAlignRow1 |
Type of the second alignment row, usually Gaps |
TPos |
Position type of the sequences, defaults to uint32_t |
TQId |
Type of qId, defaults to std::string |
TSId |
Type of sId, defaults to std::string |
TSAccs |
Type of sAccs, defaults to std::vector of std::string |
TSTaxIds |
Type of sTaxIds, defaults to String of uint32_t |
Member Function Overview
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BlastMatch::BlastMatch() BlastMatch::BlastMatch(sId) BlastMatch::BlastMatch(qId, sId) [deprecated]
Constructor, can be called with arguments for qId and sId. -
bool BlastMatch::operator< (BlastMatch const & bm2) const
The comparison operator (for sorting by bit-score).
Member Functions Inherited From AssignableConcept
Member Functions Inherited From EqualityComparableConcept
Member Functions Inherited From LessThanComparableConcept
Interface Function Overview
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void computeAlignmentStats(blastMatch, context);
Compute the alignStats member of a BlastMatch. -
double computeBitScore(blastMatch, context);
Compute the bit-score for a BlastMatch. -
double computeEValue(blastMatch, qLength, context); [[deprecated]] double computeEValue(blastMatch, context);
Compute the E-Value for a BlastMatch.
Interface Functions Inherited From AssignableConcept
Member Variable Overview
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TAlign BlastMatch::alignRow0
First alignment row (Gaps object). -
TAlign BlastMatch::alignRow1
Second alignment row (Gaps object). -
AlignmentStats BlastMatch::alignStats
An AlignmentStats object holding further stats of the alignment. -
double BlastMatch::bitScore
The bit-score of the alignment. -
double BlastMatch::eValue
The e-value of the alignment. -
TPos BlastMatch::qEnd
The end of the alignment on the (possibly translated) query sequence. -
char BlastMatch::qFrameShift
An indicator for query frame and query strand. -
TQId BlastMatch::qId
The verbose Id of the query. -
TPos BlastMatch::qLength
The length of the original query sequence (possibly before translation). -
TPos BlastMatch::qStart
The start of the alignment on the (possibly translated) query sequence. -
TSId BlastMatch::sAccs
The Accession number(s) of the subject. -
TPos BlastMatch::sEnd
The end of the alignment on the (possibly translated) subject sequence. -
char BlastMatch::sFrameShift
An indicator for subject frame and subject strand. -
TSId BlastMatch::sId
The verbose Id of the subject. -
TPos BlastMatch::sLength
The length of the original subject sequence (possibly before translation). -
TPos BlastMatch::sStart
The start of the alignment on the (possibly translated) subject sequence. -
TSId BlastMatch::sTaxIds
The taxonomic ID(s) of the subject.
Detailed Description
You should set the following members manually: qId, sId, qLength, sLength, qFrameShift and sFrameShift.
If you then also set valid alignRow-members (alignRow0, alignRow1), you can let the other members be computed by computeAlignmentStats and computeBitScore, computeEValue.
Member Functions Detail
BlastMatch::BlastMatch()
BlastMatch::BlastMatch(sId)
BlastMatch::BlastMatch(qId, sId) [deprecated]
Data Races
bool BlastMatch::operator< (BlastMatch const & bm2) const
To facilitate fast sorting of matches in a BlastRecord, only the bit-score is compared. Also large bit-score are sorted to front (i.e. operator< on BlastMatch checks operator>= on the bitScores).
Data Races
Interface Functions Detail
void computeAlignmentStats(blastMatch, context);
Parameters
blastMatch
|
A BlastMatch that has a valid align member. |
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context
|
A BlastIOContext with parameters and buffers. |
The alignRow-members (alignRow0, alignRow1) are used as in-parameter to compute the alignStats member. This includes the raw score, amount of gaps, mismatches et cetera. This is a prerequisite for printing a match to file or computing it's e-value.
Data Races
double computeBitScore(blastMatch, context);
Parameters
blastMatch
|
A BlastMatch that has a valid align member. |
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context
|
A BlastIOContext with parameters and buffers. |
Returns
double |
blastMatch.bitScore after computation |
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Remarks
This will compute the bit-score for a BlastMatch. At least the following members need to be set before calling this function:
Data Races
double computeEValue(blastMatch, qLength, context);
[[deprecated]] double computeEValue(blastMatch, context);
Parameters
blastMatch
|
A BlastMatch that has a valid align member. |
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qLength
|
The length of the query sequence (pass qLength). |
context
|
A BlastIOContext with parameters and buffers. |
Returns
double |
blastMatch.eValue after computation |
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Remarks
This will compute the e-value for a BlastMatch. At least the following members need to be set before calling this function:
Note, that in contrast to the general interface (computeEValue), this interface caches some computation steps in the context and is therefore faster.
Data Races
Member Variables Detail
TAlign BlastMatch::alignRow0
TAlign BlastMatch::alignRow1
AlignmentStats BlastMatch::alignStats
double BlastMatch::bitScore
double BlastMatch::eValue
TPos BlastMatch::qEnd
char BlastMatch::qFrameShift
one out of { -3, -2, -1, +1, +2, +3 } where the absolute value - 1 is the shift of the translation frame and a negative sign indicates the reverse complement strand [query sequence, only applies for BlastFormatProgram == BLASTX | TBLASTX]; -1 implies reverse complement for BLASTN.
TQId BlastMatch::qId
TPos BlastMatch::qLength
TPos BlastMatch::qStart
TSId BlastMatch::sAccs
TPos BlastMatch::sEnd
char BlastMatch::sFrameShift
one out of { -3, -2, -1, +1, +2, +3 } where the absolute value - 1 is the shift of the translation frame and a negative sign indicates the reverse complement strand [subject sequence, only applies for BlastFormatProgram == TBLASTN | TBLASTX].