librostlab  1.0.20
Namespaces | Classes | Typedefs | Functions | Variables
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.

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