ARB
Macros | Functions
ali_misc.hxx File Reference
#include <cstdio>
#include <cstdlib>
#include <unistd.h>
#include <memory.h>
#include <attributes.h>
#include <arbtools.h>
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Macros

#define ALI_A_CODE   0
 
#define ALI_C_CODE   1
 
#define ALI_G_CODE   2
 
#define ALI_U_CODE   3
 
#define ALI_GAP_CODE   4
 
#define ALI_N_CODE   5
 
#define ALI_DOT_CODE   6
 
#define ALI_UNDEF_CODE   200
 

Functions

void ali_message (const char *message)
 
void ali_warning (const char *message)
 
void ali_error (const char *message, const char *func="") __ATTR__NORETURN
 
void ali_fatal_error (const char *message, const char *func="") __ATTR__NORETURN
 
void ali_out_of_memory_if (bool cond)
 
void * CALLOC (long i, long j)
 
int ali_is_base (char c)
 
int ali_is_base (unsigned char c)
 
int ali_is_real_base (char c)
 
int ali_is_real_base (unsigned char c)
 
int ali_is_real_base_or_gap (char c)
 
int ali_is_real_base_or_gap (unsigned char c)
 
int ali_is_dot (char c)
 
int ali_is_dot (unsigned char c)
 
int ali_is_nbase (char c)
 
int ali_is_nbase (unsigned char c)
 
int ali_is_gap (char c)
 
int ali_is_gap (unsigned char c)
 
unsigned char ali_base_to_number (char c, int no_gap_flag=0)
 
char ali_number_to_base (unsigned char n)
 
void ali_string_to_sequence (char *sequence)
 
void ali_sequence_to_string (unsigned char *sequence, unsigned long length)
 
void ali_sequence_to_postree_sequence (unsigned char *sequence, unsigned long length)
 
void ali_print_sequence (unsigned char *sequence, unsigned long length)
 

Macro Definition Documentation

#define ALI_A_CODE   0

Definition at line 34 of file ali_misc.hxx.

#define ALI_C_CODE   1

Definition at line 35 of file ali_misc.hxx.

#define ALI_G_CODE   2

Definition at line 36 of file ali_misc.hxx.

#define ALI_U_CODE   3

Definition at line 37 of file ali_misc.hxx.

#define ALI_GAP_CODE   4
#define ALI_N_CODE   5

Definition at line 39 of file ali_misc.hxx.

#define ALI_DOT_CODE   6

Definition at line 40 of file ali_misc.hxx.

Referenced by ALI_MAP::sequence(), and ALI_MAP::sequence_without_inserts().

#define ALI_UNDEF_CODE   200

Definition at line 41 of file ali_misc.hxx.

Function Documentation

void ali_message ( const char message)
inline
void ali_warning ( const char message)
inline
void ali_error ( const char message,
const char func = "" 
)
void ali_fatal_error ( const char message,
const char func = "" 
)
void ali_out_of_memory_if ( bool  cond)
inline
void* CALLOC ( long  i,
long  j 
)
inline
int ali_is_base ( char  c)
inline
int ali_is_base ( unsigned char  c)
inline

Definition at line 72 of file ali_misc.hxx.

int ali_is_real_base ( char  c)
inline

Definition at line 76 of file ali_misc.hxx.

int ali_is_real_base ( unsigned char  c)
inline

Definition at line 82 of file ali_misc.hxx.

int ali_is_real_base_or_gap ( char  c)
inline

Definition at line 86 of file ali_misc.hxx.

Referenced by ALI_PROFILE::w_bind().

int ali_is_real_base_or_gap ( unsigned char  c)
inline

Definition at line 92 of file ali_misc.hxx.

int ali_is_dot ( char  c)
inline

Definition at line 96 of file ali_misc.hxx.

Referenced by ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), and convert_for_back_write().

int ali_is_dot ( unsigned char  c)
inline

Definition at line 100 of file ali_misc.hxx.

int ali_is_nbase ( char  c)
inline

Definition at line 104 of file ali_misc.hxx.

Referenced by ali_sequence_to_postree_sequence().

int ali_is_nbase ( unsigned char  c)
inline

Definition at line 108 of file ali_misc.hxx.

int ali_is_gap ( char  c)
inline

Definition at line 112 of file ali_misc.hxx.

Referenced by convert_for_back_write().

int ali_is_gap ( unsigned char  c)
inline

Definition at line 116 of file ali_misc.hxx.

unsigned char ali_base_to_number ( char  c,
int  no_gap_flag = 0 
)
inline

Definition at line 120 of file ali_misc.hxx.

References ali_warning(), and FALLTHROUGH.

Referenced by ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), and ali_string_to_sequence().

char ali_number_to_base ( unsigned char  n)
inline

Definition at line 134 of file ali_misc.hxx.

References ali_fatal_error(), and ali_warning().

Referenced by ali_sequence_to_string(), and ALI_PROFILE::cheapest_sequence().

void ali_string_to_sequence ( char sequence)
inline

Definition at line 150 of file ali_misc.hxx.

References ali_base_to_number(), and ali_is_base().

Referenced by ALI_SEQUENCE::ALI_SEQUENCE().

void ali_sequence_to_string ( unsigned char sequence,
unsigned long  length 
)
inline

Definition at line 158 of file ali_misc.hxx.

References ali_number_to_base().

Referenced by ALI_SEQUENCE::string(), and ALI_NORM_SEQUENCE::string().

void ali_sequence_to_postree_sequence ( unsigned char sequence,
unsigned long  length 
)
inline

Definition at line 163 of file ali_misc.hxx.

References ali_is_base(), ali_is_nbase(), and ali_warning().

void ali_print_sequence ( unsigned char sequence,
unsigned long  length 
)
inline

Definition at line 175 of file ali_misc.hxx.