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NCBI C++ ToolKit: src/objtools/import/ftable/bed_line_reader.cpp Source File

61

mColumnDelimiter(

" \t"

62

mSplitFlags(

NStr

::fSplit_MergeDelimiters),

65

mColorByStrand(

false

)

88 string

nextLine =

""

;

89 while

(!lineReader.

AtEOF

()) {

90

nextLine = *(++lineReader);

120 const string

& line)

const 143 string

track, values;

145 if

(track !=

"track"

) {

149 throw

errorTrackLineOutOfOrder;

153 if

(values.empty()) {

157

vector<string> trackPieces;

161 for

(

int i

= 1;

< trackPieces.size() - 1; ++

) {

162

vector<string> words;

164 auto

pendingKey = words.back();

174 mUseScore

= (!useScore.empty() && useScore !=

"0"

&& useScore !=

"false"

);

177 mItemRgb

= (itemRgb ==

"on"

|| itemRgb ==

"On"

);

178 if

(!itemRgb.empty() && !

mItemRgb

) {

179

errorInvalidTrackValue.

AmendMessage

(

"Bad itemRgb value --- ignored"

);

184 if

(!colorByStrand.empty()) {

186 string

colorStrandPlus, colorStrandMinus;

188

colorByStrand,

" "

, colorStrandPlus, colorStrandMinus);

189

vector<string> rgbComponents;

190 NStr::Split

(colorStrandPlus,

","

, rgbComponents);

191 if

(rgbComponents.size() != 3) {

192 throw

std::exception();

197

rgbComponents.clear();

198 NStr::Split

(colorStrandMinus,

","

, rgbComponents);

199 if

(rgbComponents.size() != 3) {

200 throw

std::exception();

206 catch

(std::exception&) {

208 "Bad colorByStrand value --- ignored"

);

233 throw

errorInvalidColumnCount;

239 throw

errorInvalidColumnCount;

246 const

vector<string>&

columns

269 throw

errorInvalidChromStartValue;

276 throw

errorInvalidChromEndValue;

281 const auto

& strand =

columns

[5];

282 if

(strand !=

"+"

&& strand !=

"-"

&& strand !=

"."

) {

283 throw

errorInvalidStrandValue;

285 if

(strand ==

"-"

) {

294 const

vector<string>&

columns

319 const

vector<string>&

columns

335

rgbValue.

= rgbValue.

= -1;

341 const

vector<string>&

columns

347 "Invalid strand value- setting color to BLACK."

353

rgbValue.

= rgbValue.

= 0;

371 const

vector<string>&

columns

387

rgbValue.

= rgbValue.

= 0;

396

rgbValue.

= rgbValue.

= 0;

400 if

(scoreValue < 0) {

404 else if

(scoreValue > 1000) {

408 if

(scoreValue == 0) {

409

rgbValue.

= rgbValue.

= 0;

412 if

(scoreValue > 998) {

413

rgbValue.

= rgbValue.

= 255;

417

scoreValue =

static_cast<int>

(scoreValue / 111);

418

rgbValue.

= rgbValue.

= (13 + 29*scoreValue);

425 const

vector<string>&

columns

433

rgbValue.

= rgbValue.

= 0;

440

vector<string > rgbSplits;

442 switch

(rgbSplits.size()) {

444 throw

errorInvalidRgbValue;

446 unsigned long

rgbInt = 0;

448 auto

hexDigits = rgb.substr(2, string::npos);

452 auto

hexDigits = rgb.substr(1, string::npos);

459

rgbValue.

= (rgbInt & 0xff0000) >> 16;

460

rgbValue.

= (rgbInt & 0x00ff00) >> 8;

461

rgbValue.

= (rgbInt & 0x0000ff);

473

rgbValue.

= rgbValue.

= 0;

477 if

(rgbValue.

< 0 || 255 < rgbValue.

) {

478

rgbValue.

= rgbValue.

= 0;

482 if

(rgbValue.

< 0 || 255 < rgbValue.

) {

483

rgbValue.

= rgbValue.

= 0;

487 if

(rgbValue.

< 0 || 255 < rgbValue.

) {

488

rgbValue.

= rgbValue.

= 0;

497 const

vector<string>&

columns

516 throw

errorInvalidThickStartValue;

523 throw

errorInvalidThickEndValue;

530 const

vector<string>&

columns

544 const

vector<string>&

columns

545 unsigned int

& blockCount,

546

vector<int>& blockStarts,

547

vector<int>& blockSizes)

570 catch

(std::exception&) {

571 throw

errorInvalidBlockCountValue;

577

vector<string> blockSizesSplits;

579 if

(blockSizesSplits.back().empty()) {

580

blockSizesSplits.pop_back();

582 for

(

auto

blockSize: blockSizesSplits) {

586 catch

(std::exception&) {

587 throw

errorInvalidBlockSizesValue;

589 if

(blockCount != blockSizes.size()) {

590 throw

errorInconsistentBlocksInformation;

594

vector<string> blockStartsSplits;

596 if

(blockStartsSplits.back().empty()) {

597

blockStartsSplits.pop_back();

599 for

(

auto

blockStart: blockStartsSplits) {

603 catch

(std::exception&) {

604 throw

errorInvalidBlockStartsValue;

606 if

(blockCount != blockStarts.size()) {

607 throw

errorInconsistentBlocksInformation;

614 const

vector<string>&

columns

638 TSeqPos

thickStart = chromStart, thickEnd = chromStart;

640 if

(thickStart < chromStart || thickEnd > chromEnd) {

641 throw

errorInvalidThickInterval;

647 unsigned int

blockCount;

648

vector<int> blockStarts, blockSizes;

651

record.

Initialize

(chromId, chromStart, chromEnd, name, score, chromStrand,

652

thickStart, thickEnd, rgbValue, blockCount, blockStarts, blockSizes);

std::string ValueOf(const std::string &) const

void SetValue(const std::string &, const std::string &)

void Initialize(const std::string &, TSeqPos, TSeqPos, const std::string &, double, ENa_strand, TSeqPos, TSeqPos, const RgbValue &, unsigned int, const std::vector< int > &, const std::vector< int > &)

void xInitializeRgb(const std::vector< string > &, CBedImportData::RgbValue &)

void xInitializeThickInterval(const std::vector< std::string > &, TSeqPos &, TSeqPos &)

void xInitializeRgbFromScoreColumn(const std::vector< string > &, CBedImportData::RgbValue &)

void xInitializeRgbFromRgbColumn(const std::vector< string > &, CBedImportData::RgbValue &)

CBedImportData::RgbValue mRgbStrandMinus

void xInitializeRgbFromStrandColumn(const std::vector< string > &, CBedImportData::RgbValue &)

void SetInputStream(CNcbiIstream &, bool=false) override

void xInitializeScore(const std::vector< string > &, double &)

bool xProcessTrackLine(const string &)

std::string mColumnDelimiter

CBedLineReader(CImportMessageHandler &)

void xInitializeBlocks(const std::vector< string > &, unsigned int &blockCount, std::vector< int > &blockStarts, std::vector< int > &blockSizes)

void xSplitLine(const std::string &, std::vector< std::string > &)

void xInitializeChromInterval(const std::vector< std::string > &, std::string &, TSeqPos &, TSeqPos &, ENa_strand &)

CBedImportData::RgbValue mRgbStrandPlus

void xInitializeRecord(const std::vector< std::string > &, CFeatImportData &) override

void xInitializeChromName(const std::vector< std::string > &, std::string &)

bool GetNextRecord(CStreamLineReader &, CFeatImportData &) override

bool xIgnoreLine(const string &) const override

virtual void xReportProgress()

virtual bool xIgnoreLine(const string &) const

CAnnotImportData mAnnotInfo

CImportMessageHandler & mErrorReporter

unsigned int LineCount() const

virtual void SetInputStream(CNcbiIstream &, bool=false)

unsigned int mRecordCount

void AmendMessage(const std::string &amend)

virtual void ReportError(const CImportError &)

Simple implementation of ILineReader for i(o)streams.

static const column_t columns[]

unsigned int TSeqPos

Type for sequence locations and lengths.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static unsigned long StringToULong(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned long.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

ENa_strand

strand of nucleic acid

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

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

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NCBI C++ ToolKit: src/objtools/import/ftable/bed_line_reader.cpp Source File

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