gatb.core-API-1.4.2
Path_t< Node > Struct Template Reference

Structure representing a path in the De Bruijn graph. More...

#include <Graph.hpp>

Public Member Functions

 Path_t (size_t n=0)
 
size_t size () const
 
void resize (size_t n)
 
char ascii (size_t i) const
 
void push_back (kmer::Nucleotide nt)
 
void clear ()
 
kmer::Nucleotideoperator[] (size_t i)
 
const kmer::Nucleotideoperator[] (size_t i) const
 

Public Attributes

Node start
 
std::vector< kmer::Nucleotidepath
 

Detailed Description

template<typename Node>
struct gatb::core::debruijn::impl::Path_t< Node >

Structure representing a path in the De Bruijn graph.

The Path structure provides information on a linear path in the DB graph. It mainly holds the succession of nucleotides that define the path.

The path start is defined by an Node object, which defines without ambiguity the first node of the path.

It can be used by clients such a contiger tool.

Note: by now, the structure is not perfect and some adaptations could come.

Constructor & Destructor Documentation

Path_t ( size_t  n = 0)
inline

Constructor (default one)

Parameters
[in]n: size of the path.

Member Function Documentation

char ascii ( size_t  i) const
inline

Get the ascii value of the ith nucleotide in the path.

Parameters
[in]i: index of the nucleotide
Returns
the ascii code for the ith nucleotide.
void clear ( )
inline

Clear the path (ie remove all the nucleotides).

kmer::Nucleotide& operator[] ( size_t  i)
inline

Retrieve a reference on the ith nucleotide in the path.

Parameters
[in]i: index od the nucleotide to be retrieved.
Returns
a reference on the ith nucleotide
const kmer::Nucleotide& operator[] ( size_t  i) const
inline

Retrieve a reference on the ith nucleotide in the path.

Parameters
[in]i: index od the nucleotide to be retrieved.
Returns
a const reference on the ith nucleotide
void push_back ( kmer::Nucleotide  nt)
inline

Add a nucleotide to the path.

Parameters
[in]nt: nucleotide to be appended to the path.
void resize ( size_t  n)
inline

Set the size of the path

Parameters
[in]n: the size of the path.
size_t size ( ) const
inline

Get the path size

Returns
the size of the path.

Member Data Documentation

std::vector<kmer::Nucleotide> path

Path definition as a succession of nucleotides.

Node start

Node defining the initial transition of the path.


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