Calculate shortest path between 2 codons. More...

#include <Sequence/shortestPath.hpp>

Public Types
enum	pathType : std::int8_t { S, N, SS, SN, NN, SSS, SSN, SNN, NNN, NONE, AMBIG }

typedef std::vector< std::string >::const_iterator	const_iterator

Public Member Functions
	shortestPath (const std::string &codon1, const std::string &codon2, const Sequence::GeneticCodes &code=GeneticCodes::UNIVERSAL)

pathType	type () const

double	path_distance () const

const_iterator	begin () const

const_iterator	end () const

Detailed Description

Calculate shortest path between 2 codons.

A class which calculates the shortest path between two codons. The length of a path is in terms of the sum of the Grantham's distances along it's branches.

Note: It is often the case (esp. when codons differ at all three sites) that the various paths are of equal length. What this means is that the order in which the changes occur don't matter. In such cases, one of the paths is returned arbitrarily.

Definition at line 55 of file shortestPath.hpp.

Member Enumeration Documentation

◆ pathType

enum Sequence::shortestPath::pathType : std::int8_t

strong

An enum type to describe the shortest path between 2 codons. An S refers to a synonymous change, N nonsynonymous. For example, SSN means that the shortest path b/w 2 codons requires 2 synonymous and 1 nonsynonymous change. If the 2 codons don't differ, the value is NONE. If the path cannot be determined, the value is AMBIG

Definition at line 69 of file shortestPath.hpp.

Constructor & Destructor Documentation

◆ shortestPath()

Sequence::shortestPath::shortestPath	(	const std::string &	codon1,
		const std::string &	codon2,
		const Sequence::GeneticCodes &	code = `GeneticCodes::UNIVERSAL`
	)

explicit

Parameters

codon1	a std::string of length 3
codon2	a std::string of length 3
code	which genetic code to use

Precondition: (codon1.length() == 3 && codon2.length() ==3)

Note: If either codon1 or codon2 contain characters other than {A,G,C,T}, the pathway type will be assigned shortestPath::AMBIG

Definition at line 249 of file shortestPath.cc.

Member Function Documentation

◆ begin()

shortestPath::const_iterator Sequence::shortestPath::begin ( ) const

Returns: an iterator to the beginning of the shortest path between the 2 codons. The value type if the iterator is std::string

Definition at line 294 of file shortestPath.cc.

◆ end()

shortestPath::const_iterator Sequence::shortestPath::end ( ) const

Returns: an iterator to the end of the shortest path between the 2 codons. The value type if the iterator is std::string

Definition at line 304 of file shortestPath.cc.

◆ path_distance()

double Sequence::shortestPath::path_distance ( ) const

Returns: the total Grantham's distance of the shortest path

Definition at line 314 of file shortestPath.cc.

◆ type()

shortestPath::pathType Sequence::shortestPath::type ( ) const

Returns: a value from the enum type shortestPath::pathType representing the type of the shortest path.

Definition at line 285 of file shortestPath.cc.

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

Public Types

Public Member Functions