testseq.cpp File Reference

#include "bioseq.h"
#include <string>
#include "strformat.h"
#include <sys/stat.h>
#include <cstring>
#include "codon.h"

Functions
void	testLoad (const string &file)
void	testTranslate ()
void	testLongestORF ()
void	testLongestPlus ()
void	testLongestNMissingORF ()
void	testFindORF (const string &file)
void	testcodon ()
int	main (int argc, char *argv[])

---

Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

References bioseq::assign(), bioseq::computeEntropy(), bioseq::getcode(), bioseq::length(), bioseq::printFasta(), Protein::relativeEntropy(), Protein::relativeEntropyUniform(), reverseComplementInPlace(), string(), testcodon(), testLoad(), and DNA::translate().

void testcodon

(

)

References DNA::setCodonTable().

Referenced by main().

void testFindORF

(

const string &

file

)

References findAllORFIndex(), bioseq::length(), longestORFPlus(), bioseq::read(), and bioseq::toString().

void testLoad

(

const string &

file

)

References loadFastaIntoMap(), and printFasta().

Referenced by main().

void testLongestNMissingORF

(

)

References best, longestNoStartORFPlus(), longestNoStopORFPlus(), and reverseComplementInPlace().

void testLongestORF

(

)

References DNA::longestORFForward().

void testLongestPlus

(

)

References longestNoStopORFPlus(), and longestORFPlus().

void testTranslate

(

)

References dna, DNA::longestORF(), DNA::longestORFForward(), and DNA::longestORFReverse().