Class BlastMatchField
A "meta" datastructure that contains information about members of BlastMatches

Defined in seqan/blast.h
Signature template <typename TVoidSpec = void> struct BlastMatchField;

Template Parameters

TVoidSpec An extra spec to prevent global inclusion of statics members (you can safely ignore this)

Member Variable Overview

Detailed Description

This data structure conveniently gives access to all possible fields used in BLAST-compatabile tabular output formats. BlastMatchField::Enum is needed to specify a custom field composition for a BlastIOContext.

The member variables offer the correct labels for the tabular formats' I/O and strings to interact with the user on the command line.

Please note that for the legacyFormat (legacyFormat) specifying or reading custom fields is not supported and the columnsLabels will always be printed as legacyColumnLabels.

Table overview

0STDstdquery id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit scoreDefault 12 columns (Query Seq-id, Subject Seq-id, Percentage of identical matches, Alignment length, Number of mismatches, Number of gap openings, Start of alignment in query, End of alignment in query, Start of alignment in subject, End of alignment in subject, Expect value, Bit score)
1Q_SEQ_IDqseqidquery idQuery Seq-id
2Q_GIqgiquery giQuery GI
3Q_ACCqaccquery acc.Query accesion
4Q_ACCVERqaccverquery acc.verQuery accesion.version
5Q_LENqlenquery lengthQuery sequence length
6S_SEQ_IDsseqidsubject idSubject Seq-id
7S_ALL_SEQ_IDsallseqidsubject idsAll subject Seq-id(s), separated by a ';'
8S_GIsgisubject giSubject GI
9S_ALL_GIsallgisubject gisAll subject GIs
10S_ACCsaccsubject acc.Subject accession
11S_ACCVERsaccversubject acc.verSubject accession.version
12S_ALLACCsallaccsubject accs.All subject accessions
13S_LENslensubject lengthSubject sequence length
14Q_STARTqstartq. startStart of alignment in query
15Q_ENDqendq. endEnd of alignment in query
16S_STARTsstarts. startStart of alignment in subject
17S_ENDsends. endEnd of alignment in subject
18Q_SEQqseqquery seqAligned part of query sequence
19S_SEQsseqsubject seqAligned part of subject sequence
20E_VALUEevalueevalueExpect value
21BIT_SCOREbitscorebit scoreBit score
22SCOREscorescoreRaw score
23LENGTHlengthalignment lengthAlignment length
24P_IDENTpident% identityPercentage of identical matches
25N_IDENTnidentidenticalNumber of identical matches
26MISMATCHmismatchmismatchesNumber of mismatches
27POSITIVEpositivepositivesNumber of positive-scoring matches
28GAP_OPENgapopengap opensNumber of gap openings
29GAPSgapsgapsTotal number of gaps
30P_POSppos% positivesPercentage of positive-scoring matches
31FRAMESframesquery/sbjct framesQuery and subject frames separated by a '/'
32Q_FRAMEqframequery frameQuery frame
33S_FRAMEsframesbjct frameSubject frame
34BTOPbtopBTOPBlast traceback operations (BTOP)
35S_TAX_IDSstaxidssubject tax idsunique Subject Taxonomy ID(s), separated by a ';' (in numerical order)
36S_SCI_NAMESsscinamessubject sci namesunique Subject Scientific Name(s), separated by a ';'
37S_COM_NAMESscomnamessubject com namesunique Subject Common Name(s), separated by a ';'
38S_BLAST_NAMESsblastnamessubject blast namesunique Subject Blast Name(s), separated by a ';' (in alphabetical order)
39S_S_KINGDOMSsskingdomssubject super kingdomsunique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)
40S_TITLEstitlesubject titleSubject Title
41S_ALL_TITLESsalltitlessubject titlesAll Subject Title(s), separated by a '<>'
42S_STRANDsstrandsubject strandSubject Strand
43Q_COV_Sqcovs% subject coverageQuery Coverage Per Subject
45Q_COV_HSPqcovhsp% hsp coverageQuery Coverage Per HSP
46LCA_IDlcaidlca idString ID (e.g. scientific name) of the lowest common ancestor of all matches of a query
47LCA_TAX_IDlcataxidlca tax idNumeric Taxonomy ID of the lowest common ancestor of all matches of a query

LCA_IC and LCA_TAX_ID are non available in NCBI Blast.

Member Variables Detail

static_constexpr_const_std::array<char_const*,47> BlastMatchField::columnLabels[]

An array of CStrings representing the column label of each possible field; for the legacyFormat, use legacyColumnLabels instead.

static_constexpr_std::array<Enum_const,12> BlastMatchField::defaults

An std::array of BlastMatchField::Enum indicating the fields that are default
static constexpr std::array<Enum const, 12> defaults

static_constexpr_const_std::array<char_const*,47> BlastMatchField::descriptions[]

An array of CStrings representing the human-readable descriptions of each field

static_constexpr_const_std::array<bool,47> BlastMatchField::implemented[]

An array of bools revealing whether the Blast I/O module supports printing this field

static_constexpr_char_const_*_const BlastMatchField::legacyColumnLabels

A single CString representing the column labels of the legacyFormat.

static_constexpr_const_std::array<char_const*,47> BlastMatchField::optionLabels[]

An array of CStrings representing the command line parameter name of each field