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 char *	readable_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

Definition at line 189 of file AP_seq_protein.cxx.

References ap_assert, APP_DOT, APP_ILLEGAL, APP_MAX, APP_X, calcOneMutationAway(), D, AWT_distance_meter::getDistance(), hasGap(), AWT_PDP::patd, PROTEINS_TO_TEST, readable_combined_protein(), and s.

Variable Documentation

AP_PROTEINS prot2AP_PROTEIN[26]

static

Initial value:

= {
    APP_A,
    APP_B,
    APP_C,
    APP_D,
    APP_E,
    APP_F,
    APP_G,
    APP_H,
    APP_I,
    APP_ILLEGAL, 
    APP_K,
    APP_L,
    APP_M,
    APP_N,
    APP_ILLEGAL, 
    APP_P,
    APP_Q,
    APP_R,
    APP_S,
    APP_T,
    APP_ILLEGAL, 
    APP_V,
    APP_W,
    APP_X,
    APP_Y,
    APP_Z
}

Definition at line 35 of file AP_seq_protein.cxx.

AP_PROTEINS prot2test[PROTEINS_TO_TEST]

static

Initial value:

= { 
    APP_STAR,
    APP_A,
    APP_C,
    APP_D,
    APP_E,
    APP_F,
    APP_G,
    APP_H,
    APP_I,
    APP_K,
    APP_L,
    APP_M,
    APP_N,
    APP_P,
    APP_Q,
    APP_R,
    APP_S,
    APP_T,
    APP_V,
    APP_W,
    APP_Y,
    APP_GAP
}

Definition at line 66 of file AP_seq_protein.cxx.

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.