ARB
Macros | Functions | Variables
AP_seq_protein.cxx File Reference
#include "AP_seq_protein.hxx"
#include <AP_pro_a_nucs.hxx>
#include <AP_filter.hxx>
#include <ARB_Tree.hxx>
#include <arb_str.h>
#include <climits>
Include dependency graph for AP_seq_protein.cxx:

Go to the source code of this file.

Macros

#define PROTEINS_TO_TEST   22
 
#define OMA_SLOW_LOWMEM
 
#define IMPL_OMA_SLOW_LOWMEM
 

Functions

bool hasGap (AP_PROTEINS c)
 
bool isGap (AP_PROTEINS c)
 
bool notHasGap (AP_PROTEINS c)
 
bool notIsGap (AP_PROTEINS c)
 
const charreadable_combined_protein (AP_PROTEINS p)
 
 STATIC_ASSERT (APP_MAX==4194303)
 
 STATIC_ASSERT (sizeof(AP_PROTEINS)==4)
 
AP_PROTEINS calcOneMutationAway (AP_PROTEINS p)
 
AP_PROTEINS oneMutationAway (AP_PROTEINS p)
 
static void update_min_mutations (int code_nr, const AWT_distance_meter *distance_meter)
 

Variables

static AP_PROTEINS prot2AP_PROTEIN [26]
 
static AP_PROTEINS prot2test [PROTEINS_TO_TEST]
 
static int prot_idx [PROTEINS_TO_TEST]
 
static char prot_mindist [PROTEINS_TO_TEST][PROTEINS_TO_TEST]
 
static int min_mutations_initialized_for_codenr = -1
 
static AP_PROTEINS one_mutation_away_0_7 [256]
 
static AP_PROTEINS one_mutation_away_8_15 [256]
 
static AP_PROTEINS one_mutation_away_16_23 [256]
 

Macro Definition Documentation

#define PROTEINS_TO_TEST   22

Definition at line 64 of file AP_seq_protein.cxx.

Referenced by readable_combined_protein(), and update_min_mutations().

#define OMA_SLOW_LOWMEM

Definition at line 139 of file AP_seq_protein.cxx.

#define IMPL_OMA_SLOW_LOWMEM

Definition at line 150 of file AP_seq_protein.cxx.

Function Documentation

bool hasGap ( AP_PROTEINS  c)
inline

Definition at line 10 of file AP_seq_protein.cxx.

References APP_GAP.

Referenced by notHasGap(), and update_min_mutations().

bool isGap ( AP_PROTEINS  c)
inline

Definition at line 11 of file AP_seq_protein.cxx.

References APP_GAP.

Referenced by notIsGap().

bool notHasGap ( AP_PROTEINS  c)
inline

Definition at line 13 of file AP_seq_protein.cxx.

References hasGap().

bool notIsGap ( AP_PROTEINS  c)
inline

Definition at line 14 of file AP_seq_protein.cxx.

References isGap().

const char* readable_combined_protein ( AP_PROTEINS  p)
inline

Definition at line 117 of file AP_seq_protein.cxx.

References APP_DOT, APP_X, buffer, PROTEINS_TO_TEST, and arb_test::readable().

Referenced by update_min_mutations().

STATIC_ASSERT ( APP_MAX  = =4194303)
STATIC_ASSERT ( sizeof(AP_PROTEINS = =4)
AP_PROTEINS calcOneMutationAway ( AP_PROTEINS  p)
inline

Definition at line 172 of file AP_seq_protein.cxx.

Referenced by oneMutationAway(), and update_min_mutations().

AP_PROTEINS oneMutationAway ( AP_PROTEINS  p)
inline

Definition at line 181 of file AP_seq_protein.cxx.

References calcOneMutationAway().

static void update_min_mutations ( int  code_nr,
const AWT_distance_meter distance_meter 
)
static

Variable Documentation

AP_PROTEINS prot2AP_PROTEIN[26]
static
AP_PROTEINS prot2test[PROTEINS_TO_TEST]
static
int prot_idx[PROTEINS_TO_TEST]
static
Initial value:
= {
0,
1,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
23
}

Definition at line 91 of file AP_seq_protein.cxx.

char prot_mindist[PROTEINS_TO_TEST][PROTEINS_TO_TEST]
static

Definition at line 134 of file AP_seq_protein.cxx.

int min_mutations_initialized_for_codenr = -1
static

Definition at line 135 of file AP_seq_protein.cxx.

AP_PROTEINS one_mutation_away_0_7[256]
static

Definition at line 168 of file AP_seq_protein.cxx.

AP_PROTEINS one_mutation_away_8_15[256]
static

Definition at line 169 of file AP_seq_protein.cxx.

AP_PROTEINS one_mutation_away_16_23[256]
static

Definition at line 170 of file AP_seq_protein.cxx.