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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/psl__record_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/psl_record.cpp Source File

69 int

& productInsertionSize,

70 int

& genomicInsertionSize)

73 switch

(chunk.

Which

()) {

124 const auto

& exonList = splicedSeg.

GetExons

();

125 for

(

auto

pExon: exonList) {

126 for

(

auto

pPart: pExon->GetParts()) {

129 if

(pPart->IsProduct_ins()) {

132 else if

(pPart->IsGenomic_ins()) {

139 int

lastExonBoundT = -1;

141 for

(

auto

pExon: exonList) {

142 if

(lastExonBoundT == -1) {

143

lastExonBoundT = pExon->GetGenomic_end() + 1;

146 int

exonStart = pExon->GetGenomic_start();

147 if

(exonStart > lastExonBoundT) {

150

lastExonBoundT = pExon->GetGenomic_end() + 1;

154 for

(

auto

pExon: exonList) {

155 if

(lastExonBoundT == -1) {

156

lastExonBoundT = pExon->GetGenomic_start();

159 int

exonEnd = pExon->GetGenomic_end() + 1;

160 if

(exonEnd < lastExonBoundT) {

163

lastExonBoundT = pExon->GetGenomic_start();

166 mNumInsertT

static_cast<int>

((exonList.size() - 1));

179 if

(!querySeqHandle) {

181 "Unable to resolve given query id"

eDiag_Error

);

183 mSizeQ

= querySeqHandle.GetInst_Length();

190 if

(!targetSeqHandle) {

192 "Unable to resolve given target id"

eDiag_Error

);

194 mSizeT

= targetSeqHandle.GetInst_Length();

206 const auto

& exonList = splicedSeg.

GetExons

();

209 for

(

auto

pExon: exonList) {

211 int

exonStartQ =

static_cast<int>

(pExon->GetProduct_start().AsSeqPos());

212 int

exonStartT =

static_cast<int>

(pExon->GetGenomic_start());

216 int

productInsertionPending = 0;

217 int

genomicInsertionPending = 0;

218 for

(

auto

pPart: pExon->GetParts()) {

219 if

(productInsertionPending || genomicInsertionPending) {

222 mBlockStartsQ

.push_back(exonStartQ + blockSize + productInsertionPending);

224

exonStartT + blockSize + genomicInsertionPending);

225

exonStartQ += blockSize + productInsertionPending;

226

exonStartT += blockSize + genomicInsertionPending;

228

productInsertionPending = 0;

229

genomicInsertionPending = 0;

232

*pPart, blockSize, blockSize, productInsertionPending, genomicInsertionPending);

235

exonStartQ += blockSize;

236

exonStartT += blockSize;

247 const auto

& exonList = splicedSeg.

GetExons

();

250 for

(

auto

pExon: exonList) {

251 int

exonEndT =

static_cast<int>

(pExon->GetGenomic_end() + 1);

252 int

exonEndQ =

mSizeQ

static_cast<int>

(pExon->GetProduct_end().AsSeqPos() + 1);

254 int

productInsertionPending = 0;

255 int

genomicInsertionPending = 0;

256 for

(

auto

pPart: pExon->GetParts()) {

257 if

(productInsertionPending || genomicInsertionPending) {

262

exonEndQ -= (blockSize + productInsertionPending);

263

exonEndT -= (blockSize + genomicInsertionPending);

265

productInsertionPending = 0;

266

genomicInsertionPending = 0;

269

*pPart, blockSize, blockSize, productInsertionPending, genomicInsertionPending);

271

exonEndT -= blockSize;

274

exonEndQ -= blockSize;

297 const auto

& exonList = splicedSeg.

GetExons

();

319 "Unsupported alignment product type \"protein\""

eDiag_Error

);

322 const auto

& exonList = splicedSeg.

GetExons

();

323 for

(

auto

pExon: exonList) {

324 if

(!pExon->CanGetProduct_start() || !pExon->CanGetProduct_end()) {

326 "Mandatory product information missing"

eDiag_Error

);

328 if

(!pExon->CanGetGenomic_start() || !pExon->CanGetGenomic_end()) {

330 "Mandatory target information missing"

eDiag_Error

);

357 for

(

const auto

& pScore: scores) {

358 if

(!pScore->CanGetId() || !pScore->GetId().IsStr()) {

361 if

(!pScore->CanGetValue()) {

364 const auto

key

= pScore->GetId().GetStr();

365 const auto

value

= pScore->GetValue();

396 if

(denseSeg.

GetDim

() != 2) {

398 "PSL supports only pairwaise alignments"

eDiag_Error

);

423 mSizeQ

= seqHandleQ.GetInst_Length();

430 mSizeT

= seqHandleT.GetInst_Length();

443 for

(

auto

length: denseSeg.

GetLens

()) {

448 auto

lens = denseSeg.

GetLens

();

450 if

(starts[2*

] != -1 && starts[2*

+1] != -1) {

479 if

(startOfThisQ - endOfLastQ != 0) {

489 if

(startOfThisT - endOfLastT != 0) {

516 const string

& message,

User-defined methods of the data storage class.

const CSeq_id & GetSeq_id(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

TSeqPos GetSeqStop(TDim row) const

TSeqPos GetSeqStart(TDim row) const

bool GetBestId(CSeq_id_Handle, CScope &, string &) const

vector< int > mBlockSizes

void xInitializeSequenceInfo(CScope &, const CSpliced_seg &)

void xInitializeBlocksStrandNegative(CScope &, const CSpliced_seg &)

void xInitializeStatsAndBlocks(CScope &, const CDense_seg &)

CGenbankIdResolve & mIdResolve

void Initialize(CScope &scope, const CSpliced_seg &splicedSeg)

CWriterListener * mpMessageListener

vector< int > mBlockStartsQ

void xInitializeStrands(CScope &, const CSpliced_seg &)

void xInitializeStats(CScope &, const CSpliced_seg &)

void xValidateSegment(CScope &, const CSpliced_seg &)

void xInitializeBlocksStrandPositive(CScope &, const CSpliced_seg &)

vector< int > mBlockStartsT

void xPutMessage(const string &message, EDiagSev severity)

void xInitializeBlocks(CScope &, const CSpliced_seg &)

TSeqPos GetSeqStop(TDim row) const

TSeqPos GetSeqStart(TDim row) const

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

#define NCBI_THROW(exception_class, err_code, message)

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

vector< CRef< CScore > > TScore

TMatch GetMatch(void) const

Get the variant data.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetProduct_type(void) const

Check if it is safe to call GetProduct_type method.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

TDim GetDim(void) const

Get the Dim member data.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

const TExons & GetExons(void) const

Get the Exons member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

bool CanGetGenomic_strand(void) const

Check if it is safe to call GetGenomic_strand method.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

static void sExonChunkAppendStats(const CSpliced_exon_chunk &chunk, int &matchSize, int &misMatchSize, int &productInsertionSize, int &genomicInsertionSize)

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