DnaStr Class Reference

Facilitates some useful operations on a particular double stranded dna sequence (e.g. More...

#include <DnaStr.h>

List of all members.

Public Member Functions
	DnaStr (const string &str, dsu::Strand_t strnd)
	simply maintains a const reference to the double strand sequence and sets an internal variable to remember which strand to conduct operations on.
const string &	getStr () const
	get const reference to double strand
double	gcPcnt (int=1, int=-1) const
	gc
dsu::Strand_t	getStrnd () const
	query which side of the strand the object is set to operate on
const char	operator[] (int idx) const
	access a single base at a specified location in the string
unsigned	length () const
	query length of strand
bool	isStart (const char[3]) const
	check for a start codon sorry, this should be made static
bool	isStart (int) const
	check for a start codon begining at a specified location in the strand
bool	isStop (const char[3]) const
	check for a stop codon sorry, this should be made static
bool	isStop (int bp) const
	check for stop codon starting a specified locationi in strand
Friends
std::ostream &	operator<< (std::ostream &os, const DnaStr &str)
	print 5' to 3'

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Detailed Description

Facilitates some useful operations on a particular double stranded dna sequence (e.g.

positive or negative)

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Member Function Documentation

double DnaStr::gcPcnt (  int  = 1, int  = -1 )  const

gc Parameters: -  int 5' end (default = 1) -  int 3' end (default = sequence length)

bool DnaStr::isStart (  const  char[3]  )  const [inline]

check for a start codon sorry, this should be made static Parameters: const  char[3] = input codon

bool DnaStr::isStop (  const  char[3]  )  const [inline]

check for a stop codon sorry, this should be made static Parameters: const  char[3] = input codon

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

• DnaStr.h
• DnaStr.hpp