rostlab Namespace Reference

Namespaces
namespace	bio
Classes
class	cwd_resource
struct	cxx_group
class	gid_not_found_error
class	gname_not_found_error
struct	cxx_passwd
class	uid_not_found_error
class	uname_not_found_error
class	euid_egid_resource
class	file_lock_resource
class	error_backtracer
class	exception
class	runtime_error
class	umask_resource
Typedefs
typedef std::vector< std::string >	argvec_type
Functions
template<typename _Tp >
std::basic_string< _Tp >	join (const std::basic_string< _Tp > &__sep, typename std::vector< std::basic_string< _Tp > >::const_iterator __begin, typename std::vector< std::basic_string< _Tp > >::const_iterator __end)
template<typename _Tp >
std::basic_string< _Tp >	join (const std::basic_string< _Tp > &__sep, const std::vector< std::basic_string< _Tp > > &__v)
template<typename _Tp >
std::basic_string< _Tp >	join (const _Tp *__sep, const std::vector< std::basic_string< _Tp > > &__v)
template<typename _Tp >
std::basic_string< _Tp >	join (const _Tp __sep, const std::vector< std::basic_string< _Tp > > &__v)
std::vector< std::string >	split (const std::string &__str, char __c)
template<typename _Tk , typename _Tv >
std::vector< _Tk >	map_keys (const std::map< _Tk, _Tv > &__map)
void	split_in_2 (const std::string &__str, char __c, std::string &__left, std::string &__right)
std::map< std::string, std::string >	map_split_in_2 (const std::vector< std::string > &__svec, char __c)
template<class _T1 , class _T2 >
std::ostream &	operator<< (std::ostream &os, const std::pair< _T1, _T2 > &v)
	std::pair output operator.
template<typename K , typename V , class C , class A >
std::ostream &	operator<< (std::ostream &os, const std::map< K, V, C, A > &m)
	std::map output operator.
template<typename _Tp , typename _Alloc >
std::ostream &	operator<< (std::ostream &os, const std::vector< _Tp, _Alloc > &v)
	std::vector output operator.
std::string	getgrgid_r (gid_t __gid)
std::string	getgrgid_r (gid_t __gid, cxx_group &__group)
gid_t	getgrnam_r (const std::string &__gname)
gid_t	getgrnam_r (const std::string &__gname, struct cxx_group &__group)
uid_t	getpwnam_r (const std::string &__uname)
uid_t	getpwnam_r (const std::string &__uname, cxx_passwd &__passwd)
std::string	getpwuid_r (uid_t __uid)
std::string	getpwuid_r (uid_t __uid, cxx_passwd &__passwd)
char	int2AAchar (int __aanum)
int	AAchar2int (char __aachar)
template<typename _Tp >
void	fwrite (const _Tp &__v, FILE *__out)
template<typename _Tp , typename _Alloc >
void	fwrite (const vector< _Tp, _Alloc > &__v, FILE *__out)
template<>
void	fwrite< string > (const string &__str, FILE *__out)
void	fwrite (const char *__c, FILE *__out)
template<typename _Tp >
void	fread (_Tp &__v, FILE *__in)
template<typename _Tp , typename _Alloc >
void	fread (vector< _Tp, _Alloc > &__v, FILE *__in)
template<>
void	fread< string > (string &__v, FILE *__in)
template<typename _Tp >
_Tp	fread (FILE *__in)
argvec_type	mkargvec (const char *__path,...)
bool	file_exists (const std::string &__path)
int	system (const char *__path,...)
int	system (const std::vector< std::string > &__args)
std::string	tolower (std::string __str)
Variables
const signed char	blosum62 [27][27]
	BLOSUM62 matrix at a scale of ln(2)/2.0.

---

Typedef Documentation

typedef std::vector<std::string> rostlab::argvec_type

Definition at line 38 of file rostlab_stdlib.h.

---

Function Documentation

int rostlab::AAchar2int

(

char

__aachar

)

[inline]

Definition at line 77 of file mapAA2int.h.

bool rostlab::file_exists

(

const std::string &

__path

)

[inline]

Definition at line 48 of file rostlab_stdlib.h.

template<typename _Tp >

void rostlab::fread	(	_Tp &	__v,
		FILE *	__in
	)		[inline]

Definition at line 46 of file rostlab_stdio.h.

template<typename _Tp , typename _Alloc >

void rostlab::fread	(	vector< _Tp, _Alloc > &	__v,
		FILE *	__in
	)		[inline]

Definition at line 51 of file rostlab_stdio.h.

template<typename _Tp >

_Tp rostlab::fread

(

FILE *

__in

)

[inline]

Definition at line 70 of file rostlab_stdio.h.

template<>

void rostlab::fread< string >	(	string &	__v,
		FILE *	__in
	)		[inline]

Definition at line 58 of file rostlab_stdio.h.

template<typename _Tp >

void rostlab::fwrite	(	const _Tp &	__v,
		FILE *	__out
	)		[inline]

Definition at line 28 of file rostlab_stdio.h.

template<typename _Tp , typename _Alloc >

void rostlab::fwrite	(	const vector< _Tp, _Alloc > &	__v,
		FILE *	__out
	)		[inline]

Definition at line 30 of file rostlab_stdio.h.

void rostlab::fwrite	(	const char *	__c,
		FILE *	__out
	)		[inline]

Definition at line 43 of file rostlab_stdio.h.

template<>

void rostlab::fwrite< string >	(	const string &	__str,
		FILE *	__out
	)		[inline]

Definition at line 37 of file rostlab_stdio.h.

std::string rostlab::getgrgid_r

(

gid_t

__gid

)

[inline]

Definition at line 100 of file cxxgrp.h.

std::string rostlab::getgrgid_r	(	gid_t	__gid,
		cxx_group &	__group
	)		[inline]

Definition at line 66 of file cxxgrp.h.

gid_t rostlab::getgrnam_r

(

const std::string &

__gname

)

[inline]

Definition at line 142 of file cxxgrp.h.

gid_t rostlab::getgrnam_r	(	const std::string &	__gname,
		struct cxx_group &	__group
	)		[inline]

Definition at line 107 of file cxxgrp.h.

uid_t rostlab::getpwnam_r

(

const std::string &

__uname

)

[inline]

Definition at line 84 of file cxxpwd.h.

uid_t rostlab::getpwnam_r	(	const std::string &	__uname,
		cxx_passwd &	__passwd
	)		[inline]

Definition at line 91 of file cxxpwd.h.

std::string rostlab::getpwuid_r

(

uid_t

__uid

)

[inline]

Definition at line 58 of file cxxpwd.h.

std::string rostlab::getpwuid_r	(	uid_t	__uid,
		cxx_passwd &	__passwd
	)		[inline]

Definition at line 65 of file cxxpwd.h.

char rostlab::int2AAchar

(

int

__aanum

)

[inline]

Definition at line 28 of file mapAA2int.h.

template<typename _Tp >

std::basic_string<_Tp> rostlab::join	(	const std::basic_string< _Tp > &	__sep,
		typename std::vector< std::basic_string< _Tp > >::const_iterator	__begin,
		typename std::vector< std::basic_string< _Tp > >::const_iterator	__end
	)		[inline]

Definition at line 31 of file aux_functions.h.

template<typename _Tp >

std::basic_string<_Tp> rostlab::join	(	const std::basic_string< _Tp > &	__sep,
		const std::vector< std::basic_string< _Tp > > &	__v
	)		[inline]

Definition at line 44 of file aux_functions.h.

template<typename _Tp >

std::basic_string<_Tp> rostlab::join	(	const _Tp *	__sep,
		const std::vector< std::basic_string< _Tp > > &	__v
	)		[inline]

Definition at line 52 of file aux_functions.h.

template<typename _Tp >

std::basic_string<_Tp> rostlab::join	(	const _Tp	__sep,
		const std::vector< std::basic_string< _Tp > > &	__v
	)		[inline]

Definition at line 60 of file aux_functions.h.

template<typename _Tk , typename _Tv >

std::vector<_Tk> rostlab::map_keys

(

const std::map< _Tk, _Tv > &

__map

)

[inline]

Definition at line 79 of file aux_functions.h.

std::map<std::string, std::string> rostlab::map_split_in_2	(	const std::vector< std::string > &	__svec,
		char	__c
	)		[inline]

Definition at line 104 of file aux_functions.h.

argvec_type rostlab::mkargvec	(	const char *	__path,
			...
	)		[inline]

Definition at line 57 of file rostlab_stdlib.h.

template<class _T1 , class _T2 >

std::ostream& rostlab::operator<<	(	std::ostream &	os,
		const std::pair< _T1, _T2 > &	v
	)		[inline]

std::pair output operator.

The flags are:

• tabdelim This makes sense for example when printing maps.

Definition at line 155 of file aux_functions.h.

template<typename K , typename V , class C , class A >

std::ostream& rostlab::operator<<	(	std::ostream &	os,
		const std::map< K, V, C, A > &	m
	)		[inline]

std::map output operator.

Definition at line 165 of file aux_functions.h.

template<typename _Tp , typename _Alloc >

std::ostream& rostlab::operator<<	(	std::ostream &	os,
		const std::vector< _Tp, _Alloc > &	v
	)		[inline]

std::vector output operator.

Definition at line 181 of file aux_functions.h.

std::vector<std::string> rostlab::split	(	const std::string &	__str,
		char	__c
	)		[inline]

Definition at line 67 of file aux_functions.h.

void rostlab::split_in_2	(	const std::string &	__str,
		char	__c,
		std::string &	__left,
		std::string &	__right
	)		[inline]

Definition at line 88 of file aux_functions.h.

int rostlab::system	(	const char *	__path,
			...
	)		[inline]

Definition at line 76 of file rostlab_stdlib.h.

int rostlab::system

(

const std::vector< std::string > &

__args

)

[inline]

Definition at line 94 of file rostlab_stdlib.h.

std::string rostlab::tolower

(

std::string

__str

)

[inline]

Definition at line 114 of file rostlab_stdlib.h.

---

Variable Documentation

const signed char rostlab::blosum62[27][27]

BLOSUM62 matrix at a scale of ln(2)/2.0.

'*' is column/row 0; other capital letters are in column ( letter & 0x1f ). Columns/rows for non-aa letters such as o and u are 0. The matrix is symmetrical.