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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/feat__import_8cpp_source.html below:

NCBI C++ ToolKit: src/app/feat_import/feat_import.cpp Source File

64  virtual void Init

(

void

);

65  virtual int Run

(

void

);

66  virtual void Exit

(

void

);

89

arg_desc->SetUsageContext

91  "CFeatureImport front end: Import feature tables"

);

96

arg_desc->AddDefaultKey(

102

arg_desc->AddAlias(

"i"

,

"input"

);

104

arg_desc->AddDefaultKey(

109

arg_desc->AddAlias(

"o"

,

"output"

);

111

arg_desc->AddDefaultKey(

114  "Input file format"

,

117

arg_desc->SetConstraint(

120  ""

,

"5col"

,

"bed"

,

"gff3"

,

"gtf"

,

"tbl"

));

122

arg_desc->AddDefaultKey(

125  "Output file format"

,

128

arg_desc->SetConstraint(

131  "asn-text"

,

"asn-binary"

,

"xml"

,

"json"

));

135  "turn all ids into local ids"

,

139  "numeric-ids-as-local"

,

140  "turn integer ids into local ids"

,

145  "periodically report line and record counts"

,

166

unique_ptr<CFeatImporter> pImporter(

nullptr

);

173  throw

errorFormatNotRecognized;

177

cerr <<

"Line "

<<

error

.LineNumber() <<

": "

<<

error

.SeverityStr()

178

<<

": "

<<

error

.Message() <<

"\n"

;

185

pImporter->ReadSeqAnnot(istr, annot);

188

cerr <<

"Line "

<<

error

.LineNumber() <<

": "

<<

error

.SeverityStr()

189

<<

": "

<<

error

.Message() <<

"\n"

;

192  const auto

& annotData = annot.

GetData

();

193  if

(!annotData.IsFtable() || annotData.GetFtable().empty()) {

198

errorHandler.

Dump

(cerr);

217  auto format

= args[

"format"

].AsString();

231  fg

.GetFormatHints().DisableAllNonpreferred();

233  switch

(

fg

.GuessFormat()) {

255  if

(args[

"all-ids-as-local"

]) {

258  if

(args[

"numeric-ids-as-local"

]) {

261  if

(args[

"show-progress"

]) {

274  auto

outFormat = args[

"out-format"

].AsString();

275  if

(outFormat ==

"asn-binary"

) {

278  if

(outFormat ==

"xml"

) {

281  if

(outFormat ==

"json"

) {

289 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

virtual void Init(void)

Initialize the application.

string xGetInputFormat(const CArgs &, CNcbiIstream &)

MSerial_Format xGetOutputFormat(const CArgs &)

unsigned int xGetImporterFlags(const CArgs &)

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

static CFeatImporter * Get(const std::string &, unsigned int, CImportMessageHandler &)

Class implements different ad-hoc unreliable file format identifications.

@ eFiveColFeatureTable

Five-column feature table.

@ eBed

UCSC BED file format, CBedReader.

@ eGtf

New GTF, CGtfReader.

@ eGff3

GFF3, CGff3Reader.

@ eGffAugustus

GFFish output of Augustus Gene Prediction.

void Dump(CNcbiOstream &out)

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

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ fBinary

Open file in binary mode.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

virtual void Reset(void)

Reset the whole object.

const TData & GetData(void) const

Get the Data member data.

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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