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

Definition at line 267 of file aln_reader.cpp.

References CLineErrorEx::Create(), NCBI_THROW2, and ILineErrorListener::PutError().

Referenced by CAlnReader::x_GetSequenceMolType().

USING_SCOPE()

USING_SCOPE

(

objects

)