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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/best__placement_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/util/best_placement.cpp Source File

101 odds

(

double

pos_ = 0.0,

double

neg_ = 0.0) :

pos

(pos_),

neg

(neg_) {}

108 if

(

pos

< 0 ||

neg

< 0) {

111 return log

( (

+pos)/(

neg

) );

116 return "(+"

+ std::to_string(

pos

)

117

", -"

+ std::to_string(

neg

) +

")"

;

123 _ASSERT

(0 < ratio && ratio < 1);

124 return log

( ratio / (1 - ratio) );

129 static double clamp

(

double

lo,

double

hi)

139 const bool

is_prot =

isProtSS

(aln);

143 const auto

num_gaps = gapped_len - ungapped_len;

148 const auto

num_gapopens_between_exons =

151 const auto

weighted_gaps =

154

+ 4 * num_gapopens_between_exons

155

+ 4 * num_frameshifts;

157 const odds

gaps_odds(ungapped_len, weighted_gaps);

163

matches_odds += polya_len;

172

splices_odds.pos += 1.1;

175 const bool

defect_free = matches_odds.neg == 0

176

&& gaps_odds.

neg

== 0

177

&& splices_odds.neg == 0;

196 const odds

matchrun_odds(

197 clamp

(longest_matchrun, 1, ungapped_len/4.0),

202

0.5 * matches_odds.logodds()

203

+ 0.5 * matchrun_odds.

logodds

()

205

+ splices_odds.logodds()

206

+ exons_odds.logodds()

209

clamp

(coverage, 0.05, 0.95))

213

cerr <<

"ret:"

<< ret

214

" ma"

<< matches_odds.AsString()

215

" mr"

<< matchrun_odds.

AsString

()

217

" s"

<< splices_odds.AsString()

218

" e"

<< exons_odds.AsString()

219

" "

<< (defect_free ?

"perfect"

"not-perfect"

)

220

<< (

int

)

round

(100 * ret)

230 const string

& donor,

231 const string

& acptr)

const 233 const bool

have_donor = !(donor ==

""

|| donor ==

"NN"

);

234 const bool

have_acptr = !(acptr ==

""

|| acptr ==

"NN"

);

244

(have_donor && have_acptr) ?

245

( donor ==

"GT"

&& acptr ==

"AG"

? 3.75

246

: donor ==

"AC"

&& acptr ==

"AG"

? -4.5

247

: donor ==

"AT"

&& acptr ==

"AC"

? -6.5

248

: donor ==

"GT"

|| acptr ==

"AG"

? -7.0

251

: ( !have_donor && !have_acptr ? 0.0

252

: !have_donor ? (acptr ==

"AG"

? 2.0 : -7.0)

253

: !have_acptr ? (donor ==

"GT"

? 2.0 : -7.0)

270 for

(

const auto

& chunk : exon->GetParts()) {

272 if

(chunk->IsMatch()) {

273

curr_len += chunk->GetMatch();

274

}

else if

(chunk->IsDiag()) {

275

curr_len += chunk->GetDiag();

277

max_len =

max

(max_len, curr_len);

283 return max

(curr_len, max_len);

296 return r1

.CombinationWith(

).GetLength()

303 #pragma push_macro("GET_SCORE"

)

304 #define GET_SCORE(score_name) \ 305 double score_name = 0.0; \ 306 bool have_##score_name = aln.GetNamedScore(#score_name, score_name); \ 307 (void)score_name; (void)have_##score_name 336 if

(!have_num_ident && have_num_mismatch) {

337

have_num_ident =

true

;

338

num_ident = ungapped_len - num_mismatch;

341 if

(!have_num_positives && have_num_negatives) {

342

have_num_positives =

true

;

343

num_positives = ungapped_len - num_negatives;

349 double

identity = have_num_ident ? num_ident / ungapped_len

350

: have_num_positives ? num_positives / ungapped_len

353 if

(identity < 0 || identity > 1.0) {

355 NCBI_USER_THROW

(

"Identity is outside of [0..1] range - problem with alignment scores."

);

358 return odds

(ungapped_len * identity,

359

ungapped_len * (1 - identity));

370 for

(

const auto

& chunk : exon->GetParts()) {

371 if

(chunk->IsMatch()) {

372

res.

pos

+= chunk->GetMatch();

373

}

else if

(chunk->IsMismatch()) {

374

res.

neg

+= chunk->GetMismatch();

410 if

(have_num_ident && have_num_mismatch) {

411 return odds

(num_ident,

417 if

(have_num_ident) {

418 return odds

(num_ident,

419

ungapped_len - num_ident);

422 if

(have_num_mismatch) {

423 return odds

(ungapped_len - num_mismatch,

429 if

(have_pct_identity_ungap) {

430

num_ident = pct_identity_ungap * 0.01 * ungapped_len;

431 return odds

(num_ident,

432

ungapped_len - num_ident);

437 if

(have_pct_identity_gap) {

439

num_ident = pct_identity_gap * 0.01 * gapped_len;

440 return odds

(num_ident,

441

ungapped_len - num_ident);

466 for

(

const auto

& exon : ss.

GetExons

()) {

477 prev

->IsSetDonor_after_exon()

478

->GetDonor_after_exon().GetBases() :

""

480

exon->IsSetAcceptor_before_exon()

481

? exon->GetAcceptor_before_exon().GetBases() :

""

);

503 for

(

const auto

& exon : ss.

GetExons

()) {

505 const bool

is_terminal = exon == ss.

GetExons

().front()

508 const size_t len

= exon->GetRowSeq_range(1,

true

).GetLength();

511

(exon->IsSetPartial() && exon->GetPartial())

512

|| (

len

<= (is_terminal ? 15 : 5))

515

res += is_poor ? -1 : 1;

568 if

(have_pct_coverage_hiqual) {

569 return

pct_coverage_hiqual / 100;

573 if

(have_pct_coverage) {

574 return

pct_coverage / 100;

577 const bool

is_prot =

isProtSS

(aln);

585 return

ung_aln_len * 1.0 /

len

;

595 #pragma pop_macro("GET_SCORE"

)

603 return

get_score(aln);

612 if

(sas.

Get

().empty()) {

616 using

pair_t = pair<int, CRef<CSeq_align> >;

619 for

(

const auto

aln : sas.

Set

()) {

621 _ASSERT

( aln->GetSeq_id(0).Equals(

622

sas.

Get

().front()->GetSeq_id(0)));

624

v.emplace_back(score_fn(*aln), aln);

629

[](

const

pair_t

const

pair_t

) {

630

return b.first < a.first;

633 const auto

rank1_count = std::count_if(

635

[&v](pair_t p) { return p.first == v.front().first; });

641 for

(

const auto

& p : v) {

644 if

(rank1_count > 1 && p.first == v.front().first) {

645

aln->SetNamedScore(

"rank"

, 1);

646

aln->SetNamedScore(

"rank1_index"

, rank1_index++);

647

aln->SetNamedScore(

"rank1_count"

, (

int

)rank1_count);

649

aln->SetNamedScore(

"rank"

, rank);

654

aln->SetNamedScore(

"best_placement_score"

, p.first);

656

sas.

Set

().emplace_back(aln);

User-defined methods of the data storage class.

#define GET_SCORE(score_name)

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

TSeqPos GetNumFrameshifts(TDim row=-1) const

Retrieves the number of times a given row shifts frames; i.e.

TSeqPos GetNumGapOpenings(TDim row=-1) const

Retrieves the number of gap openings in a given row in an alignment (ignoring how many gaps are in th...

TSeqRange GetRowSeq_range(CSeq_align::TDim row, bool always_as_nuc) const

Return exon's range within this row.

static void Rank(objects::CSeq_align_set &sas, score_fn_t score_fn=&NBestPlacement::GetScore)

Adds the following scores: `best_placement_score` as computed by score_fn `rank` - all top scoring al...

std::function< int(const objects::CSeq_align &)> score_fn_t

static int GetScore(const objects::CSeq_align &aln)

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

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

#define MSerial_AsnText

I/O stream manipulators â.

int64_t Int8

8-byte (64-bit) signed integer

Tdata & Set(void)

Assign a value to data member.

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

bool IsSetPoly_a(void) const

start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= ...

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

const TExons & GetExons(void) const

Get the Exons member data.

bool IsDisc(void) const

Check if variant Disc is selected.

bool IsSetProduct_length(void) const

length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length...

TPoly_a GetPoly_a(void) const

Get the Poly_a member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

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

static const sljit_gpr r1

static const sljit_gpr r2

#define row(bind, expected)

void operator+=(double x)

odds(double pos_=0.0, double neg_=0.0)

double logodds(int a=2) const

static size_t GetPolyA_length(const CSeq_align &aln)

static bool isProtSS(const CSeq_align &aln)

double GetSpliceConsensusScore(const string &donor, const string &acptr) const

static odds s_GetIdentOdds_protSS(const CSeq_align &aln)

odds GetExonsOdds(const CSeq_align &aln) const

pos + neg = count of exons.

static double clamp(double x, double lo, double hi)

static odds s_GetIdentOdds_nucSS(const CSeq_align &aln)

static odds s_GetIdentOdds_disc(const CSeq_align &aln)

int operator()(const CSeq_align &aln) const

static odds GetIdentOdds(const CSeq_align &aln)

double GetScore(const CSeq_align &aln) const

static double as_logodds(double ratio)

static double GetCoverage(const CSeq_align &aln, size_t ung_aln_len)

odds GetSplicesOdds(const CSeq_align &aln) const

static Int8 GetGapLengthOnRow(const CSpliced_exon &exon1, const CSpliced_exon &exon2, CSeq_align::TDim row)

static size_t GetLongestMatchrunLen(const CSeq_align &aln)

static size_t GetNumGapopensBetweenExons(const CSeq_align &aln)

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