librostlab-blast  1.0.1
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
rostlab::blast::hsp Struct Reference

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. More...
 

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. More...
 
static ECompoAdjustModes methfromstr (std::string __m)
 Translate method description to mode code. More...
 

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]. More...
 
std::string s_strand
 Subject strand [Plus|Minus]. More...
 
int8_t q_frame
 Query frame. More...
 
int8_t s_frame
 Subject frame. More...
 
size_t q_start
 Query start (1-based). More...
 
std::string q_ali
 Query alignment string. More...
 
size_t q_end
 Query end (1-based). More...
 
std::string match_line
 Match line. More...
 
size_t s_start
 Subject start (1-based). More...
 
std::string s_ali
 Subject alignment string. More...
 
size_t s_end
 Subject end (1-based). More...
 

Detailed Description

High-scoring segment pair.

Depending on the type of blast results, fields may be unused.

Definition at line 53 of file blast-result.h.

Member Typedef Documentation

◆ ECompoAdjustModes

typedef enum rostlab::blast::hsp::ECompoAdjustModes rostlab::blast::hsp::ECompoAdjustModes

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.

Member Enumeration Documentation

◆ ECompoAdjustModes

enum rostlab::blast::hsp::ECompoAdjustModes

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.

Enumerator
eNoCompositionBasedStats 
eCompositionBasedStats 
eCompositionMatrixAdjust 
eCompoForceFullMatrixAdjust 
eNumCompoAdjustModes 

Definition at line 56 of file blast-result.h.

Constructor & Destructor Documentation

◆ hsp()

rostlab::blast::hsp::hsp ( double  __bit_score = 0,
size_t  __raw_score = 0 
)
inline

Definition at line 96 of file blast-result.h.

◆ ~hsp()

virtual rostlab::blast::hsp::~hsp ( )
inlinevirtual

Definition at line 98 of file blast-result.h.

Member Function Documentation

◆ methfromstr()

static ECompoAdjustModes rostlab::blast::hsp::methfromstr ( std::string  __m)
inlinestatic

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.

◆ methodstr()

static std::string rostlab::blast::hsp::methodstr ( const ECompoAdjustModes  __m)
inlinestatic

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.

Member Data Documentation

◆ bit_score

double rostlab::blast::hsp::bit_score

Definition at line 64 of file blast-result.h.

◆ e_value

double rostlab::blast::hsp::e_value

Definition at line 66 of file blast-result.h.

◆ gaps

size_t rostlab::blast::hsp::gaps

Definition at line 70 of file blast-result.h.

◆ identities

size_t rostlab::blast::hsp::identities

Definition at line 68 of file blast-result.h.

◆ match_line

std::string rostlab::blast::hsp::match_line

Match line.

Definition at line 88 of file blast-result.h.

◆ method

ECompoAdjustModes rostlab::blast::hsp::method

Definition at line 67 of file blast-result.h.

◆ positives

size_t rostlab::blast::hsp::positives

Definition at line 69 of file blast-result.h.

◆ q_ali

std::string rostlab::blast::hsp::q_ali

Query alignment string.

Definition at line 84 of file blast-result.h.

◆ q_end

size_t rostlab::blast::hsp::q_end

Query end (1-based).

Definition at line 86 of file blast-result.h.

◆ q_frame

int8_t rostlab::blast::hsp::q_frame

Query frame.

Initialized to 32.

Definition at line 77 of file blast-result.h.

◆ q_start

size_t rostlab::blast::hsp::q_start

Query start (1-based).

Definition at line 82 of file blast-result.h.

◆ q_strand

std::string rostlab::blast::hsp::q_strand

Query strand [Plus|Minus].

Definition at line 72 of file blast-result.h.

◆ raw_score

size_t rostlab::blast::hsp::raw_score

Definition at line 65 of file blast-result.h.

◆ s_ali

std::string rostlab::blast::hsp::s_ali

Subject alignment string.

Definition at line 92 of file blast-result.h.

◆ s_end

size_t rostlab::blast::hsp::s_end

Subject end (1-based).

Definition at line 94 of file blast-result.h.

◆ s_frame

int8_t rostlab::blast::hsp::s_frame

Subject frame.

Initialized to 32.

Definition at line 80 of file blast-result.h.

◆ s_start

size_t rostlab::blast::hsp::s_start

Subject start (1-based).

Definition at line 90 of file blast-result.h.

◆ s_strand

std::string rostlab::blast::hsp::s_strand

Subject strand [Plus|Minus].

Definition at line 74 of file blast-result.h.

The documentation for this struct was generated from the following file:
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