libfreecontact 1.0.21
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Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
freecontact::ali_t Class Reference

Protein sequence alignment. More...

#include <freecontact.h>

Inheritance diagram for freecontact::ali_t:

Public Member Functions

 ali_t (const uint16_t __alilen=0)
 
virtual ~ali_t ()
 
uint8_t & operator() (uint32_t __k, uint16_t __ai)
 
const uint8_t & operator() (uint32_t __k, uint16_t __ai) const
 
ali_tpush (const std::vector< uint8_t > &__al)
 Push a sequence to the alignment.
 
ali_tpush (const std::string &__l)
 Push a sequence to the alignment.
 

Static Public Member Functions

static std::vector< uint8_t > read_a_seq (const std::string &__l)
 Convert alignment string to amino acid codes with aamap.
 

Public Attributes

uint32_t seqcnt
 
uint16_t alilen
 
uint16_t alilen16
 
uint16_t alilenpad
 

Detailed Description

Protein sequence alignment.

Definition at line 69 of file freecontact.h.

Constructor & Destructor Documentation

◆ ali_t()

freecontact::ali_t::ali_t ( const uint16_t  __alilen = 0)
inline

Definition at line 80 of file freecontact.h.

◆ ~ali_t()

virtual freecontact::ali_t::~ali_t ( )
inlinevirtual

Definition at line 84 of file freecontact.h.

Member Function Documentation

◆ operator()() [1/2]

uint8_t & freecontact::ali_t::operator() ( uint32_t  __k,
uint16_t  __ai 
)
inline

Definition at line 86 of file freecontact.h.

◆ operator()() [2/2]

const uint8_t & freecontact::ali_t::operator() ( uint32_t  __k,
uint16_t  __ai 
) const
inline

Definition at line 90 of file freecontact.h.

◆ push() [1/2]

ali_t & freecontact::ali_t::push ( const std::string &  __l)
inline

Push a sequence to the alignment.

Definition at line 116 of file freecontact.h.

◆ push() [2/2]

ali_t & freecontact::ali_t::push ( const std::vector< uint8_t > &  __al)

Push a sequence to the alignment.

Definition at line 1001 of file freecontact.cpp.

◆ read_a_seq()

static std::vector< uint8_t > freecontact::ali_t::read_a_seq ( const std::string &  __l)
inlinestatic

Convert alignment string to amino acid codes with aamap.

Definition at line 97 of file freecontact.h.

Member Data Documentation

◆ alilen

uint16_t freecontact::ali_t::alilen

Definition at line 76 of file freecontact.h.

◆ alilen16

uint16_t freecontact::ali_t::alilen16

Definition at line 77 of file freecontact.h.

◆ alilenpad

uint16_t freecontact::ali_t::alilenpad

Definition at line 78 of file freecontact.h.

◆ seqcnt

uint32_t freecontact::ali_t::seqcnt

Definition at line 75 of file freecontact.h.


The documentation for this class was generated from the following files: