NCBI C++ ToolKit
Classes | Macros | Functions
table2asn.cpp File Reference
#include <ncbi_pch.hpp>
#include <common/ncbi_source_ver.h>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistre.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbi_mask.hpp>
#include <connect/ncbi_core_cxx.hpp>
#include <connect/ncbi_util.h>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <util/line_reader.hpp>
#include <objtools/edit/remote_updater.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include "multireader.hpp"
#include "table2asn_context.hpp"
#include "struc_cmt_reader.hpp"
#include "feature_table_reader.hpp"
#include "fcs_reader.hpp"
#include "src_quals.hpp"
#include <objects/seq/Seq_descr.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/general/Date.hpp>
#include <objects/seq/Linkage_evidence.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objtools/edit/seq_entry_edit.hpp>
#include <objects/valerr/ValidError.hpp>
#include <objtools/validator/validator.hpp>
#include <objtools/readers/message_listener.hpp>
#include "table2asn_validator.hpp"
#include <objmgr/feat_ci.hpp>
#include "visitors.hpp"
#include <objtools/readers/fasta_exception.hpp>
#include <misc/data_loaders_util/data_loaders_util.hpp>
#include <objtools/format/flat_file_generator.hpp>
#include <objtools/logging/listener.hpp>
#include <objtools/writers/async_writers.hpp>
#include <objtools/cleanup/cleanup_pub.hpp>
#include "table2asn.hpp"
#include "suspect_feat.hpp"
#include "utils.hpp"
#include <common/ncbi_revision.h>
#include <common/test_assert.h>
+ Include dependency graph for table2asn.cpp:

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Classes

class  CObjtoolsDiagMessage
 

Macros

#define THIS_IS_TRUNK_BUILD
 

Functions

static void s_FailOnBadInput (const string &specifics, IObjtoolsListener &listener)
 
void g_LogDiagMessage (ILineErrorListener *logger, EDiagSev sev, const string &msg)
 
static void s_PubCleanup (CRef< CPub > &pub)
 
static bool s_UseHugeFileMode (const CTable2AsnContext &context, CFormatGuess::EFormat format)
 
int main (int argc, const char *argv[])
 

Macro Definition Documentation

◆ THIS_IS_TRUNK_BUILD

#define THIS_IS_TRUNK_BUILD

Definition at line 96 of file table2asn.cpp.

Function Documentation

◆ g_LogDiagMessage()

void g_LogDiagMessage ( ILineErrorListener logger,
EDiagSev  sev,
const string msg 
)

◆ main()

int main ( int  argc,
const char *  argv[] 
)

Definition at line 1623 of file table2asn.cpp.

References CNcbiApplicationAPI::AppMain(), eDS_Default, next(), and NStr::Split().

◆ s_FailOnBadInput()

static void s_FailOnBadInput ( const string specifics,
IObjtoolsListener listener 
)
static

Definition at line 113 of file table2asn.cpp.

References eDiag_Fatal, and IObjtoolsListener::PutMessage().

Referenced by CTbl2AsnApp::Run().

◆ s_PubCleanup()

static void s_PubCleanup ( CRef< CPub > &  pub)
static

◆ s_UseHugeFileMode()

static bool s_UseHugeFileMode ( const CTable2AsnContext context,
CFormatGuess::EFormat  format 
)
static

Definition at line 1147 of file table2asn.cpp.

References context, CFormatGuess::eFasta, CFormatGuess::eGff3, and format.

Referenced by CTbl2AsnApp::ProcessOneFile().

Modified on Mon May 27 04:38:56 2024 by modify_doxy.py rev. 669887