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NCBI C++ ToolKit: src/algo/gnomon/glb_align.cpp Source File

istringstream istr(cigar_string);

(istr >>

>> c) {

(m_elements.empty()) {

}

(c ==

) {

(m_elements.empty()) {

cigar_string = cigar_string.substr(clip_pos);

clip_pos = (

)istr.tellg();

m_qfrom -= el.

;

m_sfrom -= el.

;

}

(el.

==

)

m_sfrom -= el.

;

m_qfrom -= el.

;

(m_elements.empty() || m_elements.front().m_type != el.

)

m_elements.push_front(el);

m_elements.front().m_len += el.

;

}

(el.

==

)

(m_elements.empty() || m_elements.back().m_type != el.

)

m_elements.push_back(el);

m_elements.back().m_len += el.

;

(list<SElement>,

, m_elements)

missingstart = qstart+m_qfrom;

(missingstart > 0)

missingend = qlen-1-m_qto-qstart;

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

(

= 0;

<

->m_len; ++

) {

((*(

+qpos) == *(

+spos)) == is_match) {

indels.push_back(indl);

is_match = !is_match;

indels.push_back(indl);

}

(

->m_type ==

) {

indels.push_back(indl);

indels.push_back(indl);

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

(

= 0;

<

->m_len; ++

) {

is_match = !is_match;

}

(

->m_type ==

) {

missingstart = qstart+m_qfrom;

(missingstart > 0)

missingend = qlen-1-m_qto-qstart;

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

align.first.insert(align.first.end(),

,

+

->m_len);

align.second.insert(align.second.end(),

,

+

->m_len);

}

(

->m_type ==

) {

align.first.insert(align.first.end(),

->m_len,

);

align.second.insert(align.second.end(),

,

+

->m_len);

align.first.insert(align.first.end(),

,

+

->m_len);

align.second.insert(align.second.end(),

->m_len,

);

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

(

= 0;

<

->m_len; ++

) {

}

(

->m_type ==

) {

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

(

= 0;

<

->m_len; ++

) {

}

(

->m_type ==

) {

(list<SElement>,

, m_elements) {

(

->m_type ==

) {

(

= 0;

<

->m_len; ++

) {

}

(

->m_type ==

) {

score -= gopen+gapextend*

->m_len;

score -= gopen+gapextend*

->m_len;

(

*

,

na,

*

,

nb,

rho,

sigma,

[256][256]) {

* s =

[nb+1];

* sm =

[nb+1];

* gapb =

[nb+1];

* mtrx =

[(na+1)*(nb+1)];

(

= 2;

<= nb; ++

)

sm[

] = sm[

-1]-sigma;

(

= 0;

<= nb; ++

)

gapb[

] = bignegative;

{Agap = 1, Bgap = 2, Astart = 4, Bstart = 8};

(

= 1;

<= nb; ++

) {

(

= 0;

< na; ++

) {

*(++m) = Bstart|Bgap;

gapa = bignegative;

* matrix =

[ai];

(

j = 0; j < nb; ) {

ss = sm[j]+matrix[(

)

[j]];

& gapbj = gapb[++j];

(sm[j]-rs > gapbj) {

m = mtrx+(na+1)*(nb+1)-1;

(ia >= 0 || ib >= 0) {

(!(*m&Astart)) {

}

(*m&Bgap) {

(!(*m&Bstart)) {

(

*

,

na,

*

,

nb,

rho,

sigma,

[256][256]) {

* s =

[nb+1];

* sm =

[nb+1];

* gapb =

[nb+1];

* mtrx =

[(na+1)*(nb+1)];

{Agap = 1, Bgap = 2, Astart = 4, Bstart = 8, Zero = 16};

(

= 0;

<= nb; ++

) {

* max_ptr = mtrx;

(

= 0;

< na; ++

) {

* matrix =

[ai];

(

j = 0; j < nb; ) {

ss = sm[j]+matrix[(

)

[j]];

& gapbj = gapb[++j];

(sm[j]-rs > gapbj) {

(ss > max_score) {

(ss > max_score) {

ia = (

)(max_ptr-mtrx)/(nb+1)-1;

ib = (max_ptr-mtrx)%(nb+1)-1;

((ia >= 0 || ib >= 0) && !(*m&Zero)) {

(!(*m&Astart)) {

}

(*m&Bgap) {

(!(*m&Bstart)) {

(

*

,

na,

*

,

nb,

rho,

sigma,

pinleft,

pinright,

[256][256]) {

* s =

[nb+1];

* sm =

[nb+1];

* gapb =

[nb+1];

* mtrx =

[(na+1)*(nb+1)];

{Agap = 1, Bgap = 2, Astart = 4, Bstart = 8, Zero = 16};

gapb[0] = bignegative;

mtrx[1] = Astart|Agap;

gapb[1] = bignegative;

(

= 2;

<= nb; ++

) {

sm[

] = sm[

-1]-sigma;

gapb[

] = bignegative;

(

= 1;

<= nb; ++

) {

gapb[

] = bignegative;

* max_ptr = mtrx;

(

= 0;

< na; ++

) {

*(++m) = pinleft ? Bstart|Bgap : Zero;

gapa = bignegative;

* matrix =

[ai];

(

j = 0; j < nb; ) {

ss = sm[j]+matrix[(

)

[j]];

& gapbj = gapb[++j];

(sm[j]-rs > gapbj) {

(ss > max_score) {

(ss > max_score) {

(*sp <= 0 && !pinleft) {

maxa = (

)(max_ptr-mtrx)/(nb+1)-1;

maxb = (max_ptr-mtrx)%(nb+1)-1;

((ia >= 0 || ib >= 0) && !(*m&Zero)) {

(!(*m&Astart)) {

}

(*m&Bgap) {

(!(*m&Bstart)) {

* s =

[nb+1];

* sm =

[nb+1];

* gapb =

[nb+1];

* mtrx =

[(na+1)*(nb+1)];

{Agap = 1, Bgap = 2, Astart = 4, Bstart = 8, Zero = 16};

(

= 0;

<= nb; ++

) {

* max_ptr = mtrx;

* matrix =

[ai];

bleft = blimits->

();

bright = blimits->

();

(

j = bleft; j <= bright; ) {

ss = sm[j]+matrix[(

)

[j]];

& gapbj = gapb[++j];

(sm[j]-rs > gapbj) {

(ss > max_score) {

(ss > max_score) {

(++blimits ==

)

( ; bright <

-1; ++bright)

ia = (

)(max_ptr-mtrx)/(nb+1)-1;

ib = (max_ptr-mtrx)%(nb+1)-1;

((ia >= 0 || ib >= 0) && !(*m&Zero)) {

(!(*m&Astart)) {

}

(*m&Bgap) {

(!(*m&Bstart)) {

(

= 0;

< 256; ++

) {

(

j = 0; j < 256; ++j) {

matrix[

][j] = -mismatch;

aa(

);

4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-2,-1, 0,-4,

-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-1, 0,-1,-4,

-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3, 3, 0,-1,-4,

-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3, 4, 1,-1,-4,

0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4,

-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2, 0, 3,-1,-4,

-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2, 1, 4,-1,-4,

0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-1,-2,-1,-4,

-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3, 0, 0,-1,-4,

-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-3,-3,-1,-4,

-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-3,-1,-4,

-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2, 0, 1,-1,-4,

-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-3,-1,-1,-4,

-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-3,-3,-1,-4,

-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-2,-1,-2,-4,

1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2, 0, 0, 0,-4,

0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-1,-1, 0,-4,

-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-3,-2,-4,

-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-3,-2,-1,-4,

0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-3,-2,-1,-4,

-2,-1, 3, 4,-3, 0, 1,-1, 0,-3,-4, 0,-3,-3,-2, 0,-1,-4,-3,-3, 4, 1,-1,-4,

-1, 0, 0, 1,-3, 3, 4,-2, 0,-3,-3, 1,-1,-3,-1, 0,-1,-3,-2,-2, 1, 4,-1,-4,

0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-1,-1,-1,-4,

-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1

(

= 0;

< 256; ++

) {

(

j = 0; j < 256; ++j) {

num = (

)aa.size();

(

= 0;

< num; ++

) {

(

j = 0; j < num; ++j) {

score = scores[num*j+

];

matrix[(

)c][(

)d] = score;

matrix[(

)c][(

)

(d)] = score;

length = (

)seq.size();

: tA += 1;

;

: tC += 1;

;

: tG += 1;

;

: tT += 1;

;

entropy = -(tA*

(tA/length)+tC*

(tC/length)+tG*

(tG/length)+tT*

(tT/length))/(length*

(4.));

void PushFront(const SElement &el)

TCharAlign ToAlign(const char *query, const char *subject) const

void PushBack(const SElement &el)

int Distance(const char *query, const char *subject) const

CCigar(int qto=-1, int sto=-1)

TInDels GetInDels(int sstart, const char *const query, const char *subject) const

string CigarString(int qstart, int qlen) const

int Score(const char *query, const char *subject, int gopen, int gapextend, const char delta[256][256]) const

string DetailedCigarString(int qstart, int qlen, const char *query, const char *subject) const

int Matches(const char *query, const char *subject) const

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

double Entropy(const string &seq)

CCigar LclAlign(const char *a, int na, const char *b, int nb, int rho, int sigma, const char delta[256][256])

CCigar VariBandAlign(const char *a, int na, const char *b, int nb, int rho, int sigma, const char delta[256][256], const TSignedSeqRange *blimits)

CCigar GlbAlign(const char *a, int na, const char *b, int nb, int rho, int sigma, const char delta[256][256])

pair< string, string > TCharAlign

vector< CInDelInfo > TInDels

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

Magic spell ;-) needed for some weird compilers... very empiric.

Int4 delta(size_t dimension_, const Int4 *score_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

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

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