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NCBI C++ ToolKit: src/objtools/import/ftable/gff3_line_reader.cpp Source File

mColumnDelimiter(

),

nextLine =

;

(!lineReader.

()) {

nextLine = *(++lineReader);

,

,

scoreIsValid =

;

scoreIsValid, score, seqStrand, phase,

);

errorInvalidColumnCount;

vector<string>&

,

vector<string>&

,

(std::exception&) {

errorInvalidSeqStartValue;

(std::exception&) {

errorInvalidSeqStopValue;

vector<string> strandLegals = {

,

,

};

(find(strandLegals.begin(), strandLegals.end(),

[6]) ==

strandLegals.end()) {

errorInvalidSeqStrandValue;

vector<string>&

,

vector<string>&

,

attributesStr =

[8];

vector<string> attributesVec;

(

singleAttr: attributesVec) {

errorInvalidAttributeFormat;

std::vector<std::string>& attrVec)

strCurrAttrib;

inQuotes =

;

(

curChar: attrStr) {

(curChar ==

) {

strCurrAttrib += curChar;

(curChar ==

) {

(!strCurrAttrib.empty())

attrVec.push_back(strCurrAttrib);

strCurrAttrib.clear();

(curChar ==

) {

strCurrAttrib += curChar;

(!strCurrAttrib.empty()) {

attrVec.push_back(strCurrAttrib);

virtual void xReportProgress()

virtual bool xIgnoreLine(const string &) const

CImportMessageHandler & mErrorReporter

unsigned int LineCount() const

unsigned int mRecordCount

void Initialize(const std::string &, const std::string &, const std::string &, TSeqPos, TSeqPos, bool, double, ENa_strand, const std::string &, const std::vector< std::pair< std::string, std::string >> &)

std::vector< std::string > mValidFeatureTypes

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

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

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

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

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

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

CGff3LineReader(CImportMessageHandler &)

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

std::string mColumnDelimiter

virtual bool GetNextRecord(CStreamLineReader &, CFeatImportData &) override

virtual void ReportError(const CImportError &)

static bool GetSupportedSoTerms(vector< string > &)

Simple implementation of ILineReader for i(o)streams.

static bool InitializeFrame(const std::vector< std::string > &, std::string &)

static bool InitializeScore(const std::vector< std::string > &, bool &, double &)

static const struct attribute attributes[]

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.

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 bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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

Join strings using the specified delimiter.

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.

static string & ToLower(string &str)

Convert string to lower case – string& version.

ENa_strand

strand of nucleic acid

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

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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

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