librostlab-blast
1.0.0
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High-scoring segment pair. More...
#include <blast-result.h>
Public Types | |
enum | ECompoAdjustModes { eNoCompositionBasedStats = 0, eCompositionBasedStats = 1, eCompositionMatrixAdjust = 2, eCompoForceFullMatrixAdjust = 3, eNumCompoAdjustModes } |
An collection of constants that specify all permissible modes of composition adjustment. More... | |
typedef enum rostlab::blast::hsp::ECompoAdjustModes | ECompoAdjustModes |
An collection of constants that specify all permissible modes of composition adjustment. | |
Public Member Functions | |
hsp (double __bit_score=0, size_t __raw_score=0) | |
virtual | ~hsp () |
Static Public Member Functions | |
static std::string | methodstr (const ECompoAdjustModes __m) |
Translate method code to string. | |
static ECompoAdjustModes | methfromstr (std::string __m) |
Translate method description to mode code. | |
Public Attributes | |
double | bit_score |
size_t | raw_score |
double | e_value |
ECompoAdjustModes | method |
size_t | identities |
size_t | positives |
size_t | gaps |
std::string | q_strand |
Query strand [Plus|Minus]. | |
std::string | s_strand |
Subject strand [Plus|Minus]. | |
int8_t | q_frame |
Query frame. | |
int8_t | s_frame |
Subject frame. | |
size_t | q_start |
Query start (1-based). | |
std::string | q_ali |
Query alignment string. | |
size_t | q_end |
Query end (1-based). | |
std::string | match_line |
Match line. | |
size_t | s_start |
Subject start (1-based). | |
std::string | s_ali |
Subject alignment string. | |
size_t | s_end |
Subject end (1-based). |
High-scoring segment pair.
Depending on the type of blast results, fields may be unused.
Definition at line 53 of file blast-result.h.
An collection of constants that specify all permissible modes of composition adjustment.
Copied from ncbi-tools6-6.1.20090809/algo/blast/composition_adjustment/composition_constants.h in order to avoid having to depend on that library only for this.
An collection of constants that specify all permissible modes of composition adjustment.
Copied from ncbi-tools6-6.1.20090809/algo/blast/composition_adjustment/composition_constants.h in order to avoid having to depend on that library only for this.
eNoCompositionBasedStats | |
eCompositionBasedStats | |
eCompositionMatrixAdjust | |
eCompoForceFullMatrixAdjust | |
eNumCompoAdjustModes |
Definition at line 56 of file blast-result.h.
rostlab::blast::hsp::hsp | ( | double | __bit_score = 0 , |
size_t | __raw_score = 0 |
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) | [inline] |
Definition at line 96 of file blast-result.h.
virtual rostlab::blast::hsp::~hsp | ( | ) | [inline, virtual] |
Definition at line 98 of file blast-result.h.
static ECompoAdjustModes rostlab::blast::hsp::methfromstr | ( | std::string | __m | ) | [inline, static] |
Translate method description to mode code.
E.g. `Composition-based stats' => eCompositionBasedStats. The trailing dot - if present - is ignored.
Definition at line 123 of file blast-result.h.
static std::string rostlab::blast::hsp::methodstr | ( | const ECompoAdjustModes | __m | ) | [inline, static] |
Translate method code to string.
The trailing `.' is not included. eCompositionBasedStats => "Composition-based stats" eCompositionMatrixAdjust => "Compositional matrix adjust"
Default: integer code of enum value.
Definition at line 108 of file blast-result.h.
Definition at line 64 of file blast-result.h.
double rostlab::blast::hsp::e_value |
Definition at line 66 of file blast-result.h.
size_t rostlab::blast::hsp::gaps |
Definition at line 70 of file blast-result.h.
Definition at line 68 of file blast-result.h.
std::string rostlab::blast::hsp::match_line |
Match line.
Definition at line 88 of file blast-result.h.
Definition at line 67 of file blast-result.h.
Definition at line 69 of file blast-result.h.
std::string rostlab::blast::hsp::q_ali |
Query alignment string.
Definition at line 84 of file blast-result.h.
size_t rostlab::blast::hsp::q_end |
Query end (1-based).
Definition at line 86 of file blast-result.h.
int8_t rostlab::blast::hsp::q_frame |
size_t rostlab::blast::hsp::q_start |
Query start (1-based).
Definition at line 82 of file blast-result.h.
std::string rostlab::blast::hsp::q_strand |
Query strand [Plus|Minus].
Definition at line 72 of file blast-result.h.
Definition at line 65 of file blast-result.h.
std::string rostlab::blast::hsp::s_ali |
Subject alignment string.
Definition at line 92 of file blast-result.h.
size_t rostlab::blast::hsp::s_end |
Subject end (1-based).
Definition at line 94 of file blast-result.h.
int8_t rostlab::blast::hsp::s_frame |
size_t rostlab::blast::hsp::s_start |
Subject start (1-based).
Definition at line 90 of file blast-result.h.
std::string rostlab::blast::hsp::s_strand |
Subject strand [Plus|Minus].
Definition at line 74 of file blast-result.h.