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NCBI C++ ToolKit: src/objtools/readers/microarray_reader.cpp Source File

columnCountUser->

().SetStr(

);

pAnnot->

().Set().push_back( userDesc );

pAnnot->

().SetFtable();

(

& lineInfo: readerData) {

& line = lineInfo.mData;

MAX_RECORDS = 100000;

line,

, tail;

COLUMNCOUNT = 15;

vector<string> fields;

(fields.size() != COLUMNCOUNT) {

);

annot.

().SetFtable().push_back(feature);

vector<string>& fields )

->SetLocal().SetStr( fields[0] );

vector<string>& fields )

display_data->

().SetStr(

);

display_data->

(

, fields[3] );

display_data->

(

, fields[10] );

display_data->

(

, fields[11] );

( fields.size() >= 13 ) {

( fields.size() >= 14 ) {

display_data->

(

, fields[13] );

( fields.size() >= 15 ) {

feature->

().SetUser( *display_data );

& strLine)

);

);

);

columnCount =

.size();

(columnCount <= 1) {

(columnCount <= 2) {

);

(columnCount <= 3) {

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< CSeq_annot > ReadSeqAnnot(ILineReader &, ILineErrorListener *=nullptr) override

Read an object from a given line reader, render it as a single Seq-annot, if possible.

CRef< CSeq_annot > xCreateSeqAnnot() override

bool xProcessFeature(const string &, CSeq_annot &)

CMicroArrayReader(int=fDefaults, CReaderListener *=nullptr)

virtual ~CMicroArrayReader()

void xSetFeatureLocation(CRef< CSeq_feat > &, const vector< string > &)

static void xCleanColumnValues(vector< string > &)

void xSetFeatureDisplayData(CRef< CSeq_feat > &, const vector< string > &)

vector< string >::size_type m_columncount

virtual bool xProcessTrackLine(const string &)

void xProcessData(const TReaderData &, CSeq_annot &) override

void xGetData(ILineReader &, TReaderData &) override

Common file reader utility functions.

Defines and provides stubs for a general interface to a variety of file readers.

virtual bool xParseBrowserLine(const CTempString &, CSeq_annot &)

unique_ptr< CReaderMessageHandler > m_pMessageHandler

virtual bool xUngetLine(ILineReader &)

virtual CRef< CSeq_annot > xCreateSeqAnnot()

unsigned int m_uLineNumber

vector< TReaderLine > TReaderData

virtual bool xGetLine(ILineReader &, string &)

virtual bool xParseTrackLine(const CTempString &)

virtual void xAssignTrackData(CSeq_annot &)

virtual CRef< CSeq_annot > ReadSeqAnnot(CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read an object from a given input stream, render it as a single Seq-annot.

std::atomic< unsigned int > m_uDataCount

virtual bool xIsTrackLine(const CTempString &)

namespace ncbi::objects::

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

Abstract base class for lightweight line-by-line reading.

static const char location[]

static const column_t columns[]

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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 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 bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

void SetType(TType &value)

Assign a value to Type data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

void ResetLocation(void)

Reset Location data member.

void SetTo(TTo value)

Assign a value to To data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TUser & SetUser(void)

Select the variant.

Lightweight interface for getting lines of data with minimal memory copying.

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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