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NCBI C++ ToolKit: include/objtools/readers/agp_validate_reader.hpp Source File

AddCompLen(

& acc,

,

increment_count=

);

add(

& c);

{ ORI_plus, ORI_minus,

, ORI_na, ORI_count };

beg=

.component_beg;

end=

.component_end;

ori=

.orientation;

file_num = ((

*)(

.GetErrorHandler()))->GetFileNum();

s += agpErrEx->

(file_num);

AddSpan(

& span);

Reset(

for_chr_from_scaf=

);

x_PrintPatterns(

& namePatterns,

& strHeader,

fasta_count,

* count_label=

,

&

=cout,

use_xml=

);

OnScaffoldEnd();

OnObjectChange();

OnGapOrComponent();

OnError();

OnComment();

x_GetMostFreqGapsText(

gap_type,

& eol_text,

& attrs);

map< string, TAgpLen > TMapStrInt

CRangeCollection< TSeqPos > TRangeColl

map< string, TRangeColl > TMapStrRangeColl

Accession naming patterns; find ranges for consequtive digits.

vector< double > TDoubleVec

Correctly print multiple errors and warnings on consequitive lines; suppress undesired or higly repet...

const string & GetFile(int num)

Detects scaffolds, object boundaries, errors that involve 2 consecutive lines, and is intended as a s...

A container for both the original string column values (Get*() methods) and the values converted to i...

CAgpValidateReader & m_reader

CIdsNotInAgp(CAgpValidateReader &reader)

CAccPatternCounter m_patterns

bool m_last_scaf_start_is_obj

CAccPatternCounter::TDoubleVec * m_prev_id_digits

TMapIntInt m_ln_ev_flags2count

pair< TObjSet::iterator, bool > TObjSetResult

pair< string, CCompSpans > TCompIdSpansPair

int m_last_scaf_start_line

pair< TAgpPos, int > TPairIntInt

IAgpRowOutput * m_row_output

pair< TMapIntInt::iterator, bool > TMapIntIntResult

map< int, int > TMapIntInt

string m_prev_component_id

int m_SingleCompObjects_withGaps

TAgpLen m_expected_obj_len

map< string, CCompSpans > TCompId2Spans

int m_componentsInLastObject

int m_SingleCompScaffolds

int m_SingleCompScaffolds_withGaps

CAccPatternCounter m_objNamePatterns

int m_componentsInLastScaffold

TMapIntInt m_Ngap_ln2count

TCompId2Spans m_CompId2Spans

CValuesCount m_TypeCompCnt

TMapStrRangeColl * m_comp2range_coll

CAccPatternCounter::TDoubleVec * m_obj_id_digits

int m_last_scaf_start_file

TMapIntInt m_Ugap_ln2count

TAgpPos m_prev_component_end

pair< iterator, TAgpPos > TCheckSpan

CCompSpans(const CCompVal &src)

void init(CAgpRow &row, int line_num_arg)

string ToString(CAgpErrEx *agpErrEx) const

pair< TMapStrInt::iterator, bool > TMapStrIntResult

vector< value_type * > TValPtrVec

virtual void SaveRow(const string &s, CRef< CAgpRow > row, TRangeColl *runs_of_Ns)=0

Output the count as text or as xml.

void Print(const CCompactSAMApplication::AlignInfo &ai)

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

static unsigned int line_num

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

#define NCBI_XOBJREAD_EXPORT

static const char label[]

double value_type

The numeric datatype used by the parser.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

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