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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/table2asn_8hpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/table2asn.hpp Source File

69 void Init

()

override

;

82 void

Setup(

const CArgs

& args);

84 void

ProcessOneFile(

bool

isAlignment,

bool

manageDiagnosticStreams =

true

bool

manageDataStream=

true

);

96 bool

ProcessOneDirectory(

const CDir

& directory,

const CMask

mask

bool

recurse);

98 void

ReportUnusedSourceQuals();

100 void

xProcessSecretFiles1Phase(

bool

readModsFromTitle,

CSeq_entry

result

);

101 void

ProcessSecretFiles1Phase(

bool

readModsFromTitle,

TAsyncToken

&);

105 void

LoadPEPFile(

const string

& pathname);

106 void

LoadRNAFile(

const string

& pathname);

107 void

LoadPRTFile(

const string

& pathname);

108 void

LoadDSCFile(

const string

& pathname);

109 void

LoadAdditionalFiles();

110 void

LoadCMTFile(

const string

& pathname, unique_ptr<CTable2AsnStructuredCommentsReader>& comments);

113 void

SetupAndOpenDiagnosticStreams();

114 void

SetupAndOpenDataStreams();

115 void

CloseDiagnosticStreams();

116 void

CloseDataStreams();

118 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

ncbi::TMaskedQueryRegions mask

EFormat

The formats are checked in the same order as declared here.

list< CRef< objects::CSeq_annot > > TAnnots

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()

CMultiReader::TAnnots TAnnots

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.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

CRef< CSeq_entry > m_possible_proteins

unique_ptr< CTable2AsnStructuredCommentsReader > m_struct_comments

CRef< CSeq_entry > m_replacement_proteins

CRef< CSeq_descr > m_descriptors

unique_ptr< IIndexedFeatureReader > m_indexed_annots

unique_ptr< CMemorySrcFileMap > mp_src_qual_map

unique_ptr< CFeatureTableReader > m_feature_table_reader

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