NCBI C++ ToolKit
Classes | Macros | Functions
aln_reader.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/readers/aln_reader.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <objtools/error_codes.hpp>
#include <util/format_guess.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/IUPACna.hpp>
#include <objects/seq/IUPACaa.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objtools/readers/fasta.hpp>
#include <objtools/readers/mod_reader.hpp>
#include <objtools/logging/listener.hpp>
#include <objtools/readers/reader_error_codes.hpp>
#include <objtools/readers/seqid_validate.hpp>
#include "aln_errors.hpp"
#include <cassert>
+ Include dependency graph for aln_reader.cpp:

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Classes

class  CDefaultIdErrorReporter
 
class  CDefaultIdValidate
 

Macros

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Align
 

Functions

 USING_SCOPE (objects)
 
string sAlnErrorToString (const CAlnError &error)
 
static CAlnReader::FValidateIds s_GetMultiIdValidate (CAlnReader::FIdValidate fSingleIdValidate)
 
static void sReportError (ILineErrorListener *pEC, EDiagSev severity, int code, int subcode, const string &seqId, int lineNumber, const string &message, ILineError::EProblem problemType=ILineError::eProblem_GeneralParsingError)
 
static void s_AppendMods (const CModHandler::TModList &mods, string &title)
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Align

Definition at line 57 of file aln_reader.cpp.

Function Documentation

◆ s_AppendMods()

static void s_AppendMods ( const CModHandler::TModList mods,
string title 
)
static

Definition at line 793 of file aln_reader.cpp.

References mod().

Referenced by CAlnReader::x_AddMods().

◆ s_GetMultiIdValidate()

static CAlnReader::FValidateIds s_GetMultiIdValidate ( CAlnReader::FIdValidate  fSingleIdValidate)
static

Definition at line 186 of file aln_reader.cpp.

◆ sAlnErrorToString()

string sAlnErrorToString ( const CAlnError error)

Definition at line 63 of file aln_reader.cpp.

References FORMAT.

◆ sReportError()

static void sReportError ( ILineErrorListener pEC,
EDiagSev  severity,
int  code,
int  subcode,
const string seqId,
int  lineNumber,
const string message,
ILineError::EProblem  problemType = ILineError::eProblem_GeneralParsingError 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Fri Mar 01 10:06:46 2024 by modify_doxy.py rev. 669887