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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/nw__spliced__aligner32_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/nw/nw_spliced_aligner32.cpp Source File

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[(

char)c1][(

)c2] =

;

m_Wd1(GetDefaultWd1()),

m_Wd2(GetDefaultWd2())

* seq2,

len2)

m_Wd1(GetDefaultWd1()),

m_Wd2(GetDefaultWd2())

m_Wd1(GetDefaultWd1()),

m_Wd2(GetDefaultWd2())

(splice_type) {

eInvalidSpliceTypeIndex,

where (len_dif < 0? 0: 1);

shift (

(len_dif) / 2);

band (

(len_dif) + 2*(

(

->m_len1,

->m_len2)/20 + 1));

cds_penalty_extra = -2e-6;

N1 =

->m_len1 + 1;

N2 =

->m_len2 + 1;

vector<TScore> stl_rowV (N2), stl_rowF (N2);

* rowV = &stl_rowV[0];

* rowF = &stl_rowF[0];

* seq1 =

+

->m_offset1 - 1;

* seq2 =

+

->m_offset2 - 1;

bFreeGapLeft1 =

->m_esf_L1 &&

->m_offset1 == 0;

bFreeGapRight1 =

->m_esf_R1 &&

bFreeGapLeft2 =

->m_esf_L2 &&

->m_offset1 == 0;

bFreeGapRight2 =

->m_esf_R2 &&

wg1 = wgleft1, ws1 = wsleft1;

jAllDonors[

] = &stl_jAllDonors[

*N2];

vAllDonors[

] = &stl_vAllDonors[

*N2];

vector<size_t> stl_del_start(N2);

* del_start = &stl_del_start[0];

* dnr_acc_matrix = g_dnr_acc_matrix.GetMatrix();

(k = 0; k < N2; k++) {

rowV[k] = rowF[k] = kInfMinus;

(cds_start < cds_stop) {

cds_start -=

->m_offset1;

cds_stop -=

->m_offset1;

, j = 0, k0;

(

= 0;

< N1; ++

, j = 0) {

V =

> 0? (V0 += wsleft2) : 0;

ci =

> 0? seq1[

]:

;

jTail[

] = jHead[

] = 0;

vBestDonor[

] = kInfMinus;

(

== N1 - 1 && bFreeGapRight1) {

d1 = seq2[1], d2 = seq2[2];

dnr_type = 0xF0 & dnr_acc_matrix[(size_t(d1)<<8)|d2];

jAllDonors[

][jTail[

]] = j;

(dnr_type & (0x10 <<

)) {

vAllDonors[

][jTail[

]] =

vAllDonors[

][jTail[

]] = V +

;

(cds_start <=

&&

< cds_stop) {

(

!= 0 || ! bFreeGapLeft1) {

ws1 += cds_penalty_extra;

(j != 0 || ! bFreeGapLeft2) {

ws2 += cds_penalty_extra;

(j = 1; j < N2; ++j, ++k) {

= pV[j] + sm[ci][(

char)seq2[j]];

(j == N2 - 1 && bFreeGapRight2) {

(jTail[

] > jHead[

]) {

(vAllDonors[

][jHead[

]] > vBestDonor[

]) {

vBestDonor[

] = vAllDonors[

][jHead[

]];

jBestDonor[

] = jAllDonors[

][jHead[

]];

c1 = seq2[j-1], c2 = seq2[j];

acc_mask = 0x0F & dnr_acc_matrix[(size_t(c1)<<8)|c2];

(acc_mask & (0x01 <<

)) {

dnr_pos = k0 + jBestDonor[

];

dnr_pos = k0 + jBestDonor[

];

backtrace_matrix[k] =

(

);

d1 = seq2[j+1], d2 = seq2[j+2];

dnr_mask = 0xF0 & dnr_acc_matrix[(size_t(d1)<<8)|d2];

( dnr_mask & (0x10 <<

) ) {

(V > vBestDonor[

]) {

jAllDonors[

][jTail[

]] = j;

vAllDonors[

][jTail[

]] = V;

(v > vBestDonor[

]) {

jAllDonors[

][jTail[

]] = j;

vAllDonors[

][jTail[

]] = v;

(v > vBestDonor[

]) {

jAllDonors[

][jTail[

]] = j;

vAllDonors[

][jTail[

]] = v;

N1 =

->m_len1 + 1;

N2 =

->m_len2 + 1;

->m_transcript.clear();

->m_transcript.reserve(N1 + N2);

k = N1*N2 - 1;

i1 =

->m_offset1 +

->m_len1 - 1;

i2 =

->m_offset2 +

->m_len2 - 1;

mask_jump = 0x3FFFFFFF;

mask_type = ~mask_jump;

Key = backtrace_matrix[k];

k2 = (Key & mask_jump);

kdel = k / N2, k2del = k2 / N2;

kmod = k % N2, k2mod = k2 % N2;

(kmod == k2mod) {

(; k > k2; k -= decr) {

->m_transcript.push_back(ts);

start1,

start2)

dim = transcript.size();

* p1 =

+ start1;

* p2 =

+ start2;

( transcript[0] ) {

state1 = 1; state2 = 0; score +=

;

state1 = 0; state2 = 0;

state1 = 0; state2 = 1; score +=

;

(

= 0;

< dim; ++

) {

c1 = *p1;

c2 = *p2;

(state1 != 1) score +=

;

state1 = 1; state2 = 0;

(state2 != 1) score +=

;

state1 = 0; state2 = 1;

state1 = 2; state2 = 0;

(

= dim - 1;

>= 0; --

) {

(

= dim - 1;

>= 0; --

) {

(

= 0;

< dim; ++

) {

(

= 0;

< dim; ++

) {

const Uint1 * GetMatrix() const

void x_Set(char c1, char c2, Uint1 val)

void SetBand(size_t band)

virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const

SNCBIFullScoreMatrix m_ScoreMatrix

void SetShift(Uint1 where, size_t offset)

virtual TScore x_Align(CNWAligner::SAlignInOut *data)

vector< ETranscriptSymbol > TTranscript

virtual TScore x_Align(CNWAligner::SAlignInOut *data)

TScore m_Wi[splice_type_count_32]

void x_DoBackTrace(const Uint4 *backtrace_matrix, CNWAligner::SAlignInOut *data)

virtual TScore ScoreFromTranscript(const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const

const size_t splice_type_count_32

static TScore GetDefaultWi(unsigned char splice_type)

#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

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const unsigned char g_nwspl32_acceptor[splice_type_count_32][2]

const unsigned char g_nwspl32_donor[splice_type_count_32][2]

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

int TNCBIScore

data types

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

const char g_msg_InconsistentArguments[]

const char g_msg_InvalidTranscriptSymbol[]

const char g_msg_InvalidSpliceTypeIndex[]

const char g_msg_InvalidBacktraceData[]

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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