81 void Setup(
const CArgs& args);
83 void ProcessOneFile(
bool isAlignment,
bool manageDiagnosticStreams =
true,
bool manageDataStream=
true);
95 bool ProcessOneDirectory(
const CDir& directory,
const CMask&
mask,
bool recurse);
97 void ReportUnusedSourceQuals();
100 void ProcessSecretFiles1Phase(
bool readModsFromTitle,
TAsyncToken&);
104 void LoadPEPFile(
const string& pathname);
105 void LoadRNAFile(
const string& pathname);
106 void LoadPRTFile(
const string& pathname);
107 void LoadDSCFile(
const string& pathname);
108 void LoadAdditionalFiles();
109 void LoadCMTFile(
const string& pathname, unique_ptr<CTable2AsnStructuredCommentsReader>& comments);
110 void LoadAnnotMap(
const string& pathname,
TAnnotMap& annotMap);
112 void SetupAndOpenDiagnosticStreams();
113 void SetupAndOpenDataStreams();
114 void CloseDiagnosticStreams();
115 void CloseDataStreams();
117 size_t xGetNumThreads()
const;
141 static const Int8 TBL2ASN_MAX_ALLOWED_FASTA_SIZE =
INT8_C(0x7FFFFFFF);
152 const string& sMessage,
153 const Uint8 iNumDone = 0,
154 const Uint8 iNumTotal = 0)
override;
static const CDataLoadersUtil::TLoaders default_loaders
map< string, list< CRef< CSeq_annot > >> TAnnotMap
Base class for all serializable objects.
CRef< CTable2AsnValidator > m_validator
CTable2AsnContext m_context
int DryRun() override
Test run the application.
TAdditionalFiles m_global_files
void xProcessHugeEntries()
unique_ptr< CMultiReader > m_reader
CRef< CTable2AsnLogger > m_logger
unique_ptr< TAdditionalFiles > m_secret_files
static SQLCHAR output[256]
int64_t Int8
8-byte (64-bit) signed integer
uint64_t Uint8
8-byte (64-bit) unsigned integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
void Run(void)
Enter the main loop.
set< string > m_MatchedAnnots
CRef< CSeq_entry > m_possible_proteins
unique_ptr< CTable2AsnStructuredCommentsReader > m_struct_comments
CRef< CSeq_entry > m_replacement_proteins
CRef< CSeq_descr > m_descriptors
CMultiReader::TAnnotMap m_AnnotMap
unique_ptr< CMemorySrcFileMap > mp_src_qual_map
unique_ptr< CFeatureTableReader > m_feature_table_reader