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NCBI C++ ToolKit: src/util/tables/raw_scoremat.c Source File

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48 static const char kNCBIstdaa

[] =

"-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

;

58

}

else if

(

islower

((

unsigned char

) aa)) {

59

aa =

toupper

((

unsigned char

) aa);

73  if

(i1 >=0 && i2 >= 0) {

74  return

sm->

scores

[(size_t)i1 * strlen(sm->

symbols

) + (size_t)i2];

85  int

dim,

i

, j, aa1, aa2;

88

dim = (

int

)strlen(sym);

96  for

(

i

= 0;

i

< dim; ++

i

) {

99  for

(j = 0; j < dim; ++j) {

101

fsm->

s

[aa1][aa2] = psm->

scores

[

i

* dim + j];

104  for

(aa2 = 0; aa2 <

sizeof

(

kNCBIstdaa

); ++aa2) {

107  for

(aa2 =

'a'

; aa2 <=

'z'

; ++aa2) {

108

fsm->

s

[aa1][aa2] = fsm->

s

[aa1][

toupper

((

unsigned char

) aa2)];

112  for

(aa1 = 0; aa1 <

sizeof

(

kNCBIstdaa

); ++aa1) {

115  for

(aa1 =

'a'

; aa1 <=

'z'

; ++aa1) {

123  for

( ; *pfx; ++

str

, ++pfx) {

124  if

(

tolower

((

unsigned char

)*

str

) != *pfx) {

134  case 'B'

:

case 'b'

:

144  default

:

return NULL

;

147  case 'P'

:

case 'p'

:

157  case 'I'

:

case 'i'

:

static const char * str(char *buf, int n)

unsigned int

A callback function used to compare two keys in a database.

int strcmp(const char *str1, const char *str2)

static int s_NCBISM_StartsWith(const char *str, const char *pfx)

int NCBISM_GetIndex(const SNCBIPackedScoreMatrix *sm, int aa)

Map a standard residue code into an index suitable for a particular packed score matrix.

const SNCBIPackedScoreMatrix * NCBISM_GetStandardMatrix(const char *name)

TNCBIScore NCBISM_GetScore(const SNCBIPackedScoreMatrix *sm, int aa1, int aa2)

Look up an entry in a packed score matrix.

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

static const char kNCBIstdaa[]

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

const SNCBIPackedScoreMatrix NCBISM_Blosum50

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

const SNCBIPackedScoreMatrix NCBISM_Blosum80

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

const SNCBIPackedScoreMatrix NCBISM_Identity

const SNCBIPackedScoreMatrix NCBISM_Blosum90

int TNCBIScore

data types

const TNCBIScore * scores

strlen(symbols) x strlen(symbols)

TNCBIScore defscore

score for unknown residues

const char * symbols

order of residues

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