strformat.h File Reference

#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
#include <sstream>
#include <set>
#include <cstring>

Go to the source code of this file.

Functions
int	wc (const string &str)
bool	isnumber (const string &str)
bool	isnumber (const string &str, const string dc)
bool	isupper (const string &str)
void	upper (const char lo[], char *up)
string	getLower (const string &str)
void	strTolower (string &str)
void	strTolower (const string &str1, string &str2)
void	strToupper (string &str)
string	str2upper (const string &str)
string	lc (const string &str)
int	cmp_nocase (const string &s1, const string &s2)
bool	intersect (vector< string > &s1, vector< string > &s2)
string	delall (const string &str, const char c)
string	delall (const string &str, const string &c)
string	deleteChr (const string &str, char c)
string	tr (const string &str, char i, char o)
void	trim (string &str)
void	trimLeadingSpace (string &str)
void	dlc (char a[])
void	rmtsp (char a[])
void	rmsp (char a[])
void	singleSpace (string &str)
void	rmsp (const char a[], char b[])
void	rmdquote (char a[])
void	rpldquote (char a[], const char r)
void	newline (istream &ins)
int	getNumber (char *&ptr)
int	getInt (const string &str)
vector< int >	getAllInt (const string &str)
int	itoa (unsigned int n, char a[])
string	itos (int n)
template<class T>
string	toString (const T &val)
template<class T>
string	anyToString (const T &val)
vector< int >	extractInt (const string &str)
int	substr (const char ln[], int s, char sub[])
int	substr (const char ln[], int s, int f, char sub[])
void	firstwd (const char ln[], char sub[], char term=' ')
string	firstword (const string &str, const string &delim=" ,.()")
void	lastwd (const char ln[], char wd[], char sep= ' ')
string	lastword (const string &str, const string &delim=" ,.()")
string	acronym (const string &str, int n=1)
string	acronymWithDigit (const string &str, int n=1)
string	acronymWithTag (const string &str, int n=1)
void	append (char *&head, const char *tail, int &len, int &maxlen, int incr)
void	append (char *&head, const char *tail, int &len, int &maxlen)
vector< string >	split (const string &str, const char sep='\t')
vector< string >	split (const string &str, const char sep[])
vector< string >	splitOneOf (const string &str, const string &delims=",. \t")
vector< string >	dissect (const string &str, const string &delims=",. \t")
set< string >	digest2set (const string &str, const string &delims=",. \t")
pair< string, string >	breakString (const string &str, const string &sep)
void	writeSequence (const string &seq, ostream &ous, const int width=70)
int	isName (char *n)
bool	codonIsStop (const string &codon)
bool	subseqIsStop (const string &seq, int i)

---

Function Documentation

string acronym	(	const string &	str,
		int	n = 1
	)

acronym based on, at most, n letters of each word

string acronymWithDigit	(	const string &	str,
		int	n = 1
	)

string acronymWithTag	(	const string &	str,
		int	n = 1
	)

References dissect(), length, and substr().

Referenced by main().

template<class T>

string anyToString

(

const T &

val

)

[inline]

Make a long name so it will be different I tried to use name space but I have a hard time to compile and link!

Referenced by ESTAssembly::ESTAssembly(), ESTModel::ESTModel(), ESTAssembly::setName(), and ESTAssembly::setTitle().

void append	(	char *&	head,
		const char *	tail,
		int &	len,
		int &	maxlen
	)

void append	(	char *&	head,
		const char *	tail,
		int &	len,
		int &	maxlen,
		int	incr
	)

Referenced by Alnview::namesToString(), Alnview::readFile(), feature::readloc(), kzseq::readSeq(), and Alnview::toString().

pair<string,string> breakString	(	const string &	str,
		const string &	sep
	)

break a string into two parts according the the separator sep

Returns:

a pair of strings. if sep is not found inside str, then I will return two empty strings as a pair.

Referenced by Gmapath::Gmapath(), and readandstoreGmap().

int cmp_nocase	(	const string &	s1,
		const string &	s2
	)

compare to string and ignoring case

Referenced by Aceobj::at(), find(), and feature::isGoodGeneSymbol().

bool codonIsStop

(

const string &

codon

)

References strToupper().

string delall	(	const string &	str,
		const string &	c
	)

delete all string c from str

string delall	(	const string &	str,
		const char	c
	)

delete all character from a string

See also:

also deleteChr

if str is very long, this operation will be slow

Referenced by main(), and feature::makeGeneSymbol().

string deleteChr	(	const string &	str,
		char	c
	)

alias for delall

Referenced by Gmapath::Gmapath().

set<string> digest2set	(	const string &	str,
		const string &	delims = ",. \t"
	)

Referenced by deflineBetter().

vector<string> dissect	(	const string &	str,
		const string &	delims = ",. \t"
	)

anything in delims will be discarded only the none-delims char are left, and packed in the vector more or less digestions same as split, but will use any of the characters as separators leading and trailing separators are discarded

Referenced by acedbinfo::acedbinfo(), feature::acronymWithAllDigits(), acronymWithTag(), dumpFromModel(), getinslen(), dbinfo::init(), Journal::Journal(), main(), feature::makeGeneSymbol(), Refreader::newRef(), Reference::parseJournal(), parseOneFile(), pgdbinfo::pgdbinfo(), gbseq::read(), Matrix::read(), readconf(), and readUnwantedTaxid().

void dlc

(

char

a[]

)

delete last character from an C-string a

Referenced by head::getHead().

vector<int> extractInt

(

const string &

str

)

Referenced by main(), and locseg::parse().

void firstwd	(	const char	ln[],
		char	sub[],
		char	term = ' '
	)

Referenced by head::loadSeqInfo().

string firstword	(	const string &	str,
		const string &	delim = " ,.()"
	)

Referenced by gbseq::getLocusName(), feature::isGoodGeneSymbol(), Journal::Journal(), feature::makeGeneSymbol(), Reference::parseJournal(), and Submission::Submission().

vector<int> getAllInt

(

const string &

str

)

extract all integer numbers in the string

Referenced by Gmapalnseg::Gmapalnseg(), Gmapath::Gmapath(), and readandstoreGmap().

int getInt

(

const string &

str

)

return the first integer number in the string

Referenced by readandstoreGmap().

string getLower

(

const string &

str

)

Referenced by feature::writeAceProtein(), and feature::writeSource().

int getNumber

(

char *&

ptr

)

Conversion to other types such as integer, double

Referenced by Date::gbstr(), and feature::readloc().

bool intersect	(	vector< string > &	s1,
		vector< string > &	s2
	)

int isName

(

char *

n

)

References isupper().

bool isnumber	(	const string &	str,
		const string	dc
	)

bool isnumber

(

const string &

str

)

Referenced by feature::acronymWithAllDigits(), main(), and feature::makeGeneSymbol().

bool isupper

(

const string &

str

)

References isupper().

Referenced by feature::acronymWithAllDigits(), ref::au2list(), isName(), isupper(), feature::makeGeneSymbol(), and feature::shortIsGeneSymbol().

int itoa	(	unsigned int	n,
		char	a[]
	)

reverse of atoi convert into an array of char

Referenced by seqinfo::getcntstr(), main(), feature::wjoinseg(), feature::writeAllele(), feature::writeRNA(), feature::writeSource(), and feature::writeToken().

string itos

(

int

n

)

convert integer type to string type the toString() method is more generic

Referenced by alignProtein(), breakonecl(), ESTAssembly::breakPrefixModel(), ESTAssembly::breakSuffixModel(), ESTAssemblyid::breakup(), ESTAssembly::budMinusPrefixModel(), ESTAssembly::budMinusSuffixModel(), ESTAssembly::budPlusPrefixModel(), ESTAssembly::budPlusSuffixModel(), Dynaln::buildAlnInfo(), checkBadStopIndex(), constructJGIModel(), create_modelaln(), ChainAvgrange::dbrows(), dumpFromModel(), RNAModel::genomicIndex(), Progparam::getBadExonTable(), Progparam::getBadModelFile(), Progparam::getBadModelTable(), Progparam::getGoodExonTable(), Progparam::getGoodModelFile(), Progparam::getGoodModelTable(), Progparam::getModelClusterFile(), Progparam::getModelClusterTable(), locseg::getOperation(), feature::goodGeneSymbol(), mRNAModel::growCDS3Prime(), JGIModel::JGIModel(), main(), Refwithty::makeKey(), mergeNeighbor(), mRNAModelUpdate::name(), mRNAModel::name(), feature::nextGeneSymbol(), alignmentRunner::operator()(), RNAModel::RNAIndex(), Coverdepth::searchDip(), mRNAModel::setRNACDS(), Noschain::subchain(), bioseq::subseq(), Noschain::subsequence(), mRNAModelUpdate::title(), Noschain::trimBeforePoint(), feature::writeCDS(), feature::writeImmuno(), writeJobInstruction(), feature::writemRNA(), feature::writeRNA(), feature::writeSegCDS(), feature::writeSegmRNA(), and feature::writeSource().

void lastwd	(	const char	ln[],
		char	wd[],
		char	sep = ' '
	)

string lastword	(	const string &	str,
		const string &	delim = " ,.()"
	)

Referenced by feature::isGoodGeneSymbol(), Journal::Journal(), feature::makeGeneSymbol(), feature::nojunkGene(), and Reference::parseJournal().

string lc

(

const string &

str

)

void newline

(

istream &

ins

)

This function is not so good and should be removed in the future

void rmdquote

(

char

a[]

)

Referenced by head::getHead().

void rmsp	(	const char	a[],
		char	b[]
	)

remove all spaces

void rmsp

(

char

a[]

)

References aa, and rmtsp().

void rmtsp

(

char

a[]

)

Referenced by rmsp().

void rpldquote	(	char	a[],
		const char	r
	)

Referenced by head::getHead().

void singleSpace

(

string &

str

)

Referenced by feature::cleanGene(), main(), and feature::nojunkGene().

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

separate str into an array of strings using sep as delimiter sep is a string Same behavior as the char version seprator. Anything in betwee sep will be an array element. For example, if sep is ?? then ??tabc?? will have three elements, the first and the third are empty strings

Parameters:

sep

is the delimiter that is a c_string as compare to the single character version.

vector<string> split	(	const string &	str,
		const char	sep = '\t'
	)

A version of split that will separate a string into elements separated by sep that is a single character. It even returns empty string as elements if nothing is in between sep.

vector<string> splitOneOf	(	const string &	str,
		const string &	delims = ",. \t"
	)

use one of the separators ( ,.;), no more will discard the leading separators This function should be removed, it is confusing All split functions should not discard leading fields. Needs to redefine.

Referenced by Alnchain::Alnchain().

string str2upper

(

const string &

str

)

References toupper().

Referenced by mRNAModel::guessStrand().

void strTolower	(	const string &	str1,
		string &	str2
	)

void strTolower

(

string &

str

)

void strToupper

(

string &

str

)

References toupper().

Referenced by codonIsStop(), feature::shortIsGeneSymbol(), subseqIsStop(), and gbprtseq::writeAce().

bool subseqIsStop	(	const string &	seq,
		int	i
	)

seq must be in upper case

Parameters:

i.

is the index of the subsequence of 3 nt.

References strToupper().

Referenced by mRNAModel::trimCDSStop(), and mRNAModel::trimCDSTail().

int substr	(	const char	ln[],
		int	s,
		int	f,
		char	sub[]
	)

picks non-whitespace substring from s to f returns the length of the substring s starting index, f ending index (inclusive)

int substr	(	const char	ln[],
		int	s,
		char	sub[]
	)

Extraction picks substring from index s to a white space of ln, copy to sub sub is set to the substring without any whitespace at beginning or end. If from s to the end is all whitespace, then return 0 and sub is set to empty C string. returns strlen of the substr, 0 if no substr, or substr is empty s is 0-based index

Referenced by acronymWithTag(), Book::Book(), feature::getTaxid(), head::loadSeqInfo(), main(), Refreader::newRef(), locseg::parse(), Reference::parseJournal(), RangeChain::RangeChain(), Gsubreader::read(), readandstoreSam(), feature::readloc(), feature::RNAdump(), prt::writeAce(), and feature::writeAceDNA().

template<class T>

string toString

(

const T &

val

)

[inline]

this can be used to conver most of the build-in types to string

string tr	(	const string &	str,
		char	i,
		char	o
	)

converting all character i to o in str

Referenced by feature::insertGeneSymbol(), feature::insertQualifier(), feature::makeGeneSymbol(), gbseq::read(), and feature::writeFeature().

void trim

(

string &

str

)

removing trailing spaces if exist

void trimLeadingSpace

(

string &

str

)

remove all leading spaces

Referenced by readandstoreGmap().

void upper	(	const char	lo[],
		char *	up
	)

References toupper().

Referenced by align_get_dist(), align_path(), exon_cores(), extend_bw(), extend_fw(), Date::smtoi(), Xextend_bw(), and Xextend_fw().

int wc

(

const string &

str

)

Referenced by feature::getGeneSymbol(), main(), feature::makeGeneSymbol(), feature::separateAllele(), and feature::shortIsGeneSymbol().

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

Referenced by gbdnaseq::writeAce(), gbprtseq::writeAce(), and feature::writeProtein().