util.cpp File Reference

#include "util.h"
#include <iostream>

Functions
void	rmspace (string &s)
vector< string >	split (const string &str)
vector< string >	split (const string &str, int nf)
vector< string >	split (const string &str, const string sep)
void	erase (string &s, const string &sub)
void	replace (string &s, const string &sub, const string &r)
bool	remove_end_mark (string &s, const char m[], int n)
string	toupper (const string &s)
bool	startWith (const string &s1, const string &s2)
bool	startWithIgnoreCase (const string &s1, const string &s2)
string	acronym (const string &s)
string	firstWord (const string &s)
void	replaceInnerQuote (string &s)

---

Function Documentation

string acronym

(

const string &

s

)

References split().

Referenced by refloc::key(), main(), book::makeKey(), and feature::shortIsGeneSymbol().

void erase	(	string &	s,
		const string &	sub
	)

Referenced by prt::getAC(), ref::process(), and prt::writeAce().

string firstWord

(

const string &

s

)

Referenced by ref::firstAuthor(), and book::makeKey().

bool remove_end_mark	(	string &	s,
		const char	m[],
		int	n
	)

Referenced by prt::next(), and ref::next().

void replace	(	string &	s,
		const string &	sub,
		const string &	r
	)

Referenced by refloc::key(), prt::next(), ref::process(), and prt::writeAce().

void replaceInnerQuote

(

string &

s

)

Referenced by book::parse(), and ref::process().

void rmspace

(

string &

s

)

when s is derived from substr it crashes s = str.substr(3); then abort Do not use this algorithm

vector<string> split	(	const string &	str,
		const string	sep
	)

vector<string> split	(	const string &	str,
		int	nf
	)

vector<string> split

(

const string &

str

)

separate the line into name and sequence parts first=name, second=sequence string with gaps

References name.

Referenced by acronym(), Aceobj::at(), Book::Book(), digestLine(), prt::getAC(), gbseq::getOrgAcronym(), Gsubrecord::Gsubrecord(), hitCount(), feature::loadGeneName(), Ref::loadKey(), Reference::loadKey(), gbseq::loadOrgmap(), main(), feature::makeGeneSymbol(), prt::next(), operator<<(), book::parse(), locseg::parse(), Aceobj::parse(), Patent::parsejl(), Reference::parseJournal(), feature::parseLoc(), ref::process(), prt::processID(), RangeChain::RangeChain(), Reference::read(), gbseq::read(), Gsubreader::read(), readandstoreSam(), readConf(), ref::readkeymap(), Ref::Ref(), refloc::refloc(), feature::RNAdump(), feature::subCDS(), table2map(), feature::wjoinseg(), gbprt::write(), prt::writeAce(), feature::writeGene(), feature::writeProtein(), feature::writeSource(), and gbseq::writeSpecies().

bool startWith	(	const string &	s1,
		const string &	s2
	)

Referenced by book::parse(), ref::process(), and startWithIgnoreCase().

bool startWithIgnoreCase	(	const string &	s1,
		const string &	s2
	)

References startWith(), and toupper().

Referenced by ref::process().

string toupper

(

const string &

s

)

References toupper().

Referenced by Protein::aminoAcidFullName(), bcd2num(), checksum(), countbase(), bioseq::getcode(), is_dchar(), load_mat(), load_seq(), load_seq_fromstr(), feature::makeGeneSymbol(), rcbase(), protein::read(), gbprt::read(), Protein::relativeEntropy(), Protein::relativeEntropyUniform(), kzseq::revcomp(), kzseq::seq2upper(), startWithIgnoreCase(), str2upper(), strToupper(), Protein::threeLetterCode(), toupper(), bioseq::toUpperCase(), upper(), and prt::writeAce().