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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/nw__spliced__aligner_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/nw/nw_spliced_aligner.cpp Source File

46

m_IntronMinSize(GetDefaultIntronMinSize()),

47

m_cds_start(0), m_cds_stop(0)

54  const char

* seq2,

size_t

len2)

56

m_IntronMinSize(GetDefaultIntronMinSize())

64

m_IntronMinSize(GetDefaultIntronMinSize())

78

eInvalidSpliceTypeIndex,

92

eInvalidSpliceTypeIndex,

114  const

vector<Uint2> ascii (0xFF, 0xFFFF);

120  Uint2

cA(0x00), cG(0x01), cC(0x02), cT(0x03);

122  for

(

Uint1

k (0); k < 4; ++k) {

164  static const char

* splice_sites[] = {

176  static size_t weight

[] = {

190  for

(

size_t i

= 0;

weight

[

i

] > 0; ++

i

) {

191  const char

* acceptor = strchr(splice_sites[

i

]+2,

'-'

)+1;

192  if

(splice_sites[

i

][0]==dnr[0] &&

193

splice_sites[

i

][1]==dnr[1] &&

194

(splice_sites[

i

][2] ==

'-'

|| splice_sites[

i

][2] == dnr[2]) &&

195

acceptor[0]==acc[0] &&

245  int

ti (

static_cast<int>

(

t

- 1));

247  const int

ilen (

static_cast<int>

(

t

- ti));

248  const char

* p2e (p2 + ilen);

259  for

(j = -1; *(p1 + j) == *(p2e + j) && j >= -csq_matches; --j) {

269

&& *(p1 + j - 1) == *(p2 + j - 1); ++j)

284  const int

incr (jmaxpr < 0? -1: 1);

285  for

(

int

k (0); k != jmaxpr; k += incr) {

290

p2 = p2 + ilen + jmaxpr;

Uint2 x_GetIdx(const char splice[4]) const

TRank GetRank(const char *donor, const char *acceptor) const

vector< vector< Uint2 > > m_Char2Bits

static bool s_IsConsensusSplice(const char *donor, const char *acceptor, bool semi_as_cons=false)

virtual bool x_CheckMemoryLimit(void)

const char * GetSeq2(void) const

const char * GetSeq1(void) const

void SetEndSpaceFree(bool Left1, bool Right1, bool Left2, bool Right2)

virtual size_t GetSpliceTypeCount(void)=0

void CheckPreferences(void)

TScore GetWi(unsigned char splice_type)

void SetWi(unsigned char splice_type, TScore value)

virtual TScore * x_GetSpliceScores()=0

virtual bool x_CheckMemoryLimit(void)

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const GenericPointer< typename T::ValueType > T2 value

size_t GetSplicePriority(const char *dnr, const char *acc)

const char g_msg_NoAlignment[]

const char g_msg_InvalidSpliceTypeIndex[]

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