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

m_Pssm1(0), m_Freq1(0),

m_Seq2(0), m_Freq2(0),

m_StartWg(GetDefaultWg()),

m_StartWs(GetDefaultWs()),

m_EndWg(GetDefaultWg()),

m_EndWs(GetDefaultWs())

* seq2,

len2)

m_Pssm1(pssm1), m_Freq1(0),

m_Seq2(seq2), m_Freq2(0),

m_StartWg(GetDefaultWg()),

m_StartWs(GetDefaultWs()),

m_EndWg(GetDefaultWg()),

m_EndWs(GetDefaultWs())

** freq2,

len2,

m_Pssm1(0), m_Freq1(freq1),

m_Seq2(0), m_Freq2(freq2),

m_StartWg(GetDefaultWg()),

m_StartWs(GetDefaultWs()),

m_EndWg(GetDefaultWg()),

m_EndWs(GetDefaultWs())

* seq2,

len2,

* seq2,

len2,

(!pssm1 || !len1 || !seq2 || !len2) {

(

= 0;

< len2;

++) {

** freq2,

len2,

(!freq1 || !len1 || !freq2 || !len2) {

N1 =

->m_len1 + 1;

N2 =

->m_len2 + 1;

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

* rowV = &stl_rowV[0];

* rowF = &stl_rowF[0];

* seq2 =

+

->m_offset2 - 1;

(

->m_offset1 == 0) {

(

->m_esf_L1) {

(

->m_esf_R1) {

(

->m_offset2 == 0) {

(

->m_esf_L2) {

(

->m_esf_R2) {

backtrace_matrix.

(0, 0);

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

rowV[k] = pV[k] + wsleft1;

backtrace_matrix.

(k);

tracer;

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

= pV[j] + pssm_row[

][(

char)seq2[j]];

backtrace_matrix.

(k, tracer);

backtrace_matrix.

(k);

N1 =

->m_len1 + 1;

N2 =

->m_len2 + 1;

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

* rowV = &stl_rowV[0];

* rowF = &stl_rowF[0];

* pV = rowV - 1;

** freq1_row =

+

->m_offset1 - 1;

** freq2_row =

+

->m_offset2 - 1;

(

->m_offset1 == 0) {

(

->m_esf_L1) {

(

->m_esf_R1) {

(

->m_offset2 == 0) {

(

->m_esf_L2) {

(

->m_esf_R2) {

rowV[0] = wgleft1 * (1.0 - freq2_row[1][0]);

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

rowV[k] = pV[k] + wsleft1;

backtrace_matrix.

(k);

V = rowV[N2 - 1];

tracer;

V0 = wgleft2 * (1.0 - freq1_row[1][0]);

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

*profile1 = freq1_row[

];

*profile2 = freq2_row[j];

scaled_wg1 = wg1 * (1.0 - profile2[0]);

scaled_ws1 = ws1;

scaled_wg2 = wg2 * (1.0 - profile1[0]);

scaled_ws2 = ws2;

accum = 0.0, sum = 0.0;

num_zeros1 = 0, num_zeros2 = 0;

(profile1[m] < profile2[m]) {

diff_freq2[m] = profile2[m] - profile1[m];

diff_freq1[m] = profile1[m] - profile2[m];

(profile1[0] <= profile2[0]) {

sum += diff_freq1[m];

sum += diff_freq2[m];

(profile1[0] <= profile2[0]) {

diff_freq1[m] *= sum;

diff_freq2[m] *= sum;

(num_zeros1 > num_zeros2) {

(diff_freq1[m] > 0) {

sum += diff_freq2[

] * matrix_row[

];

accum += diff_freq1[m] * sum;

(diff_freq2[m] > 0) {

sum += diff_freq1[

] * matrix_row[

];

accum += diff_freq2[m] * sum;

profile1[0] *

* (1-profile2[0]) +

profile2[0] *

* (1-profile1[0]);

n0 = rowV[j] + scaled_wg2;

rowF[j] += scaled_ws2;

rowF[j] = n0 + scaled_ws2;

backtrace_matrix.

(k, tracer);

backtrace_matrix.

(k);

(

)(V + 0.5);

start1,

start2)

dim = transcript.size();

(

= 0;

< dim; ++

) {

}

(offset2 < 0) {

}

(offset1 == (

)

- 1) {

}

(offset2 == (

)

- 1) {

++offset1; ++offset2;

score +=

[offset1][(

char)

[offset2]];

(state1 != 1) score += wg;

state1 = 1; state2 = 0;

(state2 != 1) score += wg;

state1 = 0; state2 = 1;

(

= 0;

< dim; ++

) {

}

(offset1 == (

)

- 1) {

}

(offset2 == (

)

- 1) {

++offset1; ++offset2;

accum = 0.0, sum = 0.0;

accum +=

[offset1][m] * (double)sm[m][m];

diff_freq2[m] =

[offset2][m] -

accum +=

[offset2][m] * (double)sm[m][m];

diff_freq1[m] =

[offset1][m] -

sum += diff_freq1[m];

sum += diff_freq2[m];

diff_freq1[m] /= sum;

diff_freq2[m] /= sum;

accum += diff_freq1[m] *

(state1 != 1) dscore += wg1 * (1.0 -

[offset2][0]);

state1 = 1; state2 = 0;

(state2 != 1) dscore += wg2 * (1.0 -

[offset1][0]);

state1 = 0; state2 = 1;

score = (

)(dscore + 0.5);

void SetAt(size_t i, Uint1 v)

virtual bool x_CheckMemoryLimit(void)

double m_DScoreMatrix[kPSSM_ColumnSize][kPSSM_ColumnSize]

static const int kPSSM_ColumnSize

virtual TScore x_Align(SAlignInOut *data)

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

virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const

virtual void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)

SNCBIFullScoreMatrix m_ScoreMatrix

virtual CNWAligner::TScore Run(void)

virtual TScore ScoreFromTranscript(const TTranscript &transcript, size_t start1=0, size_t start2=0) const

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

FProgressCallback m_prg_callback

virtual TScore x_Run(void)

TScore x_AlignProfile(SAlignInOut *data)

vector< ETranscriptSymbol > TTranscript

virtual TScore x_Align(SAlignInOut *data)

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)

virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const

void x_DoBackTrace(const CBacktraceMatrix4 &backtrace, SAlignInOut *data)

TScore x_AlignPSSM(SAlignInOut *data)

#define NCBI_THROW(exception_class, err_code, message)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const unsigned char kMaskFc

const unsigned char kMaskEc

const unsigned char kMaskE

const unsigned char kMaskD

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

int TNCBIScore

data types

const char g_msg_HitSpaceLimit[]

const char g_msg_InvalidTranscriptSymbol[]

const char g_msg_NullParameter[]

const char g_msg_InvalidSequenceChars[]

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