bioseq.cpp File Reference

#include "bioseq.h"
#include <cctype>
#include "strformat.h"
#include <fstream>
#include <math.h>

Functions
void	translate (string &pep, const string &seq, int begin, int end)
int	countInternalStops (const string &seq)
int	aachar2num (char a)
char	aanum2char (int c)
string	reverseComplement (const string &seq)
char	complementChar (char ch)
void	reverseComplementInPlace (string &seq)
void	printFasta (ostream &ous, const string &seq, int width)
ostream &	operator<< (ostream &ous, const bioseq &s)
pair< int, int >	longestORFIndex (const Protein &p)
void	loadFastaIntoMap (const string &file, map< string, string > &store)

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Function Documentation

int aachar2num

(

char

a

)

used by encode function

Referenced by Matrix::lookup(), and Matrix::read().

char aanum2char

(

int

c

)

convert amino acid number to character

char complementChar

(

char

ch

)

Referenced by reverseComplementInPlace().

int countInternalStops

(

const string &

seq

)

global function to be used in a more flexible way

Referenced by JGIModel::valid().

void loadFastaIntoMap	(	const string &	file,
		map< string, string > &	store
	)

load all the sequences in the file into a map for later usage. Only the id is used, title information is not cached.

References ifstream(), and bioseq::seq.

Referenced by main(), and testLoad().

pair<int,int> longestORFIndex

(

const Protein &

p

)

References bioseq::getSequence().

Referenced by DNA::longestORFForward().

ostream& operator<<	(	ostream &	ous,
		const bioseq &	s
	)

fasta format, 70 residues per line. If the sequence has name it will produce a full fasta file, otherwise only the sequence.

References bioseq::name, bioseq::printFasta(), bioseq::seq, and bioseq::title.

void printFasta	(	ostream &	ous,
		const string &	seq,
		int	width = 70
	)

class wide function that can be used without constructing a bioseq object. This will increase the performance if you are only interested in the operation but not in using the bioseq object and its derived classes

Referenced by extractInter(), main(), testLoad(), and ESTAssembly::write().

string reverseComplement

(

const string &

seq

)

operation only make sense on DNA or RNA sequences

Referenced by GenModel::CDSSeq(), and main().

void reverseComplementInPlace

(

string &

seq

)

a version for better performance

References complementChar().

Referenced by main(), DNA::revcomp(), RNAModel::seqGenomic(), and Noschain::subsequence().

void translate	(	string &	pep,
		const string &	seq,
		int	begin,
		int	end = -1
	)

helper function to be used by other methods Uses more basic type, for convinience

References ct, and DNA::getCodonTable().

Referenced by mRNAModel::mRNAModel(), and JGIModel::valid().