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NCBI C++ ToolKit: src/algo/align/splign/splign_exon_trim.cpp Source File

= segments.size();

( ; np <

; ++np) {

( segments[np].m_exon )

;

( segments[p].m_box[3] + 1 == segments[np].m_box[2] ) {

( ; pp>=0; --pp ) {

( segments[pp].m_exon )

;

( segments[pp].m_box[3] + 1 == segments[p].m_box[2] ) {

min_query_size = 4;

(

(s.

[1] - s.

[0] + 1) <

(min_query_size)) {

( p1 >= segments.size() )

;

( p2 >= segments.size() )

;

( !segments[p1].m_exon )

;

( !segments[p2].m_exon )

;

pos1 =

( p1, p2);

pos2 =

( p1, p2);

( segments[pos1].m_box[1] >= segments[pos2].m_box[0] ||

segments[pos1].m_box[3] >= segments[pos2].m_box[2] ) {

(

pos = 0; pos < pos1; ++pos) {

new_segments.push_back(segments[pos]);

s(segments[pos1]);

s.

[1] = segments[pos2].m_box[1];

s.

[3] = segments[pos2].m_box[3];

( segments[pos1].m_box[1] + 1 < segments[pos2].m_box[0]) {

s.

.append(segments[pos2].m_box[0] - segments[pos1].m_box[1] - 1,

);

( segments[pos1].m_box[3] + 1 < segments[pos2].m_box[2]) {

s.

.append(segments[pos2].m_box[2] - segments[pos1].m_box[3] - 1,

);

s.

+= segments[pos2].m_details;

new_segments.push_back(s);

(

pos = ++pos2; pos < segments.size(); ++pos) {

new_segments.push_back(segments[pos]);

segments.swap(new_segments);

( mrna_bio_handle ) {

vector<TSeqRange> tr;

(

slit(ci->GetLocation()); slit; ++slit) {

ori = slit.GetRange();

.SetFrom(mrna_len - ori.

() - 1);

.SetTo(mrna_len - ori.

() - 1);

(tr.empty())

;

pos1 = 0, pos2 = 2;

(; pos2 < segments.size(); ++pos1, ++pos2) {

( segments[pos1].m_exon && !segments[pos1+1].m_exon && segments[pos2].m_exon ) {

p1 = segments[pos1].m_box[1];

(vector<TSeqRange>, it, tr) {

( p1 >= it->GetFrom() && p1 <= it->GetTo() ) {

cut_mrna_len = (p1 + 1 - it->GetFrom()) % 3,

= 0;

transcript = segments[pos1].m_details;

= (

)transcript.size() - 1;

(;

>=0; --

) {

(

%3 == cut_mrna_len && transcript[

] ==

) {

( transcript[

] !=

) ++

;

p2 = segments[pos2].m_box[0];

(vector<TSeqRange>, it, tr) {

( p2 >= it->GetFrom() && p2 <= it->GetTo() ) {

cut_mrna_len = ( 3 - ( p2 - it->GetFrom()) % 3 ) %3,

= 0;

transcript = segments[pos2].m_details;

( ;

< (

)transcript.size(); ++

) {

(

%3 == cut_mrna_len && transcript[

] ==

) {

( transcript[

] !=

) ++

;

(

== (

)transcript.size() ) {

( s.

[2] > 1 ) {

( s.

[2] > 0 ) {

gap_start_idx (-1);

(segments.size() && segments[0].m_exon ==

) {

(

k (0); k < segments.size(); ++k) {

& s (segments[k]);

(gap_start_idx == -1) {

gap_start_idx =

(k);

s.

[0] = segments[k-1].m_box[1] + 1;

s.

[2] = segments[k-1].m_box[3] + 1;

(gap_start_idx >= 0) {

&

= segments[gap_start_idx];

.m_box[1] = s.

[0] - 1;

.m_box[3] = s.

[2] - 1;

.m_len =

.m_box[1] -

.m_box[0] + 1;

.m_details.resize(0);

new_segments.push_back(

);

new_segments.push_back(s);

(gap_start_idx >= 0) {

&

(segments[gap_start_idx]);

.m_box[1] = segments[segments.size()-1].m_box[1];

.m_box[3] = segments[segments.size()-1].m_box[3];

.m_len =

.m_box[1] -

.m_box[0] + 1;

.m_details.resize(0);

new_segments.push_back(

);

segments.swap(new_segments);

(

== 0)

;

string::iterator irs, irs0, irs1;

(irs1 - irs0 <= (

)

) {

(irs = irs0; irs != irs1; ++irs) {

c1 = j1 >= 0?

[j1]:

;

c2 = j2 >= 0?

[j2]:

;

(

== 0)

;

string::reverse_iterator irs, irs0, irs1;

(irs1 - irs0 <= (

)

) {

(irs = irs0; irs != irs1; ++irs) {

adim = s.

.size();

(adim > 2 && s.

[adim - 3] ==

) {

(pos == string::npos) {

(pos == string::npos) {

score = 0, maxscore = -2;

string::reverse_iterator rirs0, rirs1, rirs, rirs_max;

(rirs = rirs0; rirs != rirs1; ++rirs) {

(score >= maxscore) {

= rirs1 - rirs_max - 1;

score = 0, maxscore = -2;

string::iterator irs0, irs1, irs, irs_max;

(irs = irs0; irs != irs1; ++irs) {

(score >= maxscore) {

= irs1 - irs_max - 1;

(len_total <= 20)

;

string::iterator irs0 = s.

.begin(),

(irs = irs0; irs != irs1; ++irs) {

minlen =

(20, len_total/5);

pos = irs1 - irs0 - minlen;

( pos == string::npos )

;

pos = s.

.find_last_not_of(

, pos);

( pos == string::npos )

;

irs1 = irs0 + pos + 1;

string::iterator irs_tr = s.

.end();

(irs = irs0; irs != irs1; ++irs) {

rid = (match_total -

) / (

)(len_total -

);

match_total -=

;

(irs_tr == s.

.end())

;

(len_total <= 20)

;

string::reverse_iterator irs0 = s.

.rbegin(),

(irs = irs0; irs != irs1; ++irs) {

pos =

(20, len_total/5) - 1;

( pos == string::npos )

;

pos = s.

.find_first_not_of(

, pos);

( pos == string::npos )

;

string::reverse_iterator irs_tr = s.

.rend();

(irs = irs0; irs != irs1; ++irs) {

lid = (match_total -

) / (

)(len_total -

);

match_total -=

;

( irs_tr == s.

.rend() )

;

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

void ImproveFromLeft(TSeg &s)

const double m_MaxPartExonIdentDrop

void Cut50FromLeft(TSeg &s)

void CutToMatchRight(TSeg &s)

void UpdateAnnot(TSeg &s)

static bool HasAbuttingExonOnLeft(TSegs segments, TSeqPos p)

void Cut50FromRight(TSeg &s)

void TrimHolesToCodons(TSegs &segments, objects::CBioseq_Handle &mrna_bio_handle, bool mrna_strand, TSeqPos mrna_len)

void ImproveFromRight(TSeg &s)

CConstRef< CSplicedAligner > m_aligner

bool ThrowAway20_28_90(TSeg &s)

void JoinExons(TSegs &segments, TSeqPos p1, TSeqPos p2)

void AdjustGaps(TSegs &segments)

static bool HasAbuttingExonOnRight(TSegs segments, TSeqPos p)

bool ThrowAwayShortExon(TSeg &s)

void CutFromLeft(size_t len, TSeg &s)

void CutToMatchLeft(TSeg &s)

void CutFromRight(size_t len, TSeg &s)

void Update(const CNWAligner *aligner)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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)

const char g_msg_InvalidRange[]

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

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