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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/streamtest_8cpp_source.html below:

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

107 virtual void Init

(

void

);

108 virtual int Run

(

void

);

109 virtual void Exit

(

void

);

124

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

125 "Object Manager Stream Test"

);

138

arg_desc->AddDefaultKey(

"i"

140 "Bioseq-set to test"

145

arg_desc->AddDefaultKey(

"o"

151

arg_desc->AddFlag(

"binary"

152 "Input is binary ASN"

);

154

arg_desc->AddFlag(

"compressed"

155 "Input is compressed"

);

157

arg_desc->AddFlag(

"cleanup"

158 "BasicCleanup each record"

);

160

arg_desc->AddFlag(

"extended"

161 "ExtendedCleanup each record"

);

163

arg_desc->AddDefaultKey(

"skip"

165 "Skip certain record types"

169

arg_desc->AddKey(

"test"

171 "Mode for generation"

190 "unindexed-defline"

194

arg_desc->AddDefaultKey(

"options"

196 "Test-specific options. E.g. 'map' for agpwrite tests " 197 "the comp id mapper "

201

arg_desc->AddFlag(

"batch"

202 "Process genbank release file"

);

204

arg_desc->AddFlag(

"catenated"

205 "Process concatenated Seq-entry"

);

207

arg_desc->AddFlag(

"gbload"

208 "Use GenBank data loader"

);

210

arg_desc->AddDefaultKey(

"accn"

212 "Accession to match"

216

arg_desc->AddOptionalKey(

"from"

218 "Begining of shown range"

221

arg_desc->AddOptionalKey(

"to"

223 "End of shown range"

226

arg_desc->AddFlag(

"revcomp"

227 "Reverse complement"

);

229

arg_desc->AddOptionalKey(

"policy"

234

arg_desc->AddOptionalKey(

"flags"

239

arg_desc->AddOptionalKey(

"depth"

245

arg_desc->AddFlag(

"wgsload"

246 "Use WGS data loader"

);

249

arg_desc->AddFlag(

"rf"

250 "Generate final report"

);

252

arg_desc->AddDefaultKey(

"ri"

254 "Generate report after every N objects processed"

258

arg_desc->AddDefaultKey(

"count"

260 "Repeat process N times"

264

arg_desc->AddDefaultKey(

"journal"

266 "Test Journal Lookup"

270

arg_desc->AddDefaultKey(

"gap-mode"

281

arg_desc->AddFlag(

"show-mods"

282 "Show FASTA header mods (e.g. [strain=abc])"

);

284

arg_desc->AddFlag(

"flat-set"

285 "Generate flatfile for each component"

);

287

arg_desc->AddFlag(

"debug"

288 "Show debugging information"

);

292 GetRWConfig

().

Set

(

"SERIAL"

"DISABLE_DELAY_BUFFERS"

"yes"

);

307 if

( pProcess == 0 || pPresenter == 0 ) {

315

pPresenter->

Run

( pProcess );

339 string

testcase = args[

"test"

].AsString();

342 if

( testcase ==

"null"

) {

345 if

( testcase ==

"copy"

) {

348 if

( testcase ==

"agpwrite"

) {

351 if

( testcase ==

"cleanup"

) {

354 if

( testcase ==

"defline"

) {

357 if

( testcase ==

"deprecated-title"

) {

360 if

( testcase ==

"eutils"

) {

363 if

( testcase ==

"explore"

) {

366 if

( testcase ==

"fasta"

) {

369 if

( testcase ==

"flatfile"

) {

372 if

( testcase ==

"gene-overlap"

) {

375 if

( testcase ==

"gene-feattree"

) {

378 if

( testcase ==

"gpipe-defline"

) {

381 if

( testcase ==

"invert"

) {

384 if

( testcase ==

"prosplign"

) {

387 if

( testcase ==

"seqvector"

) {

390 if

( testcase ==

"unindexed-defline"

) {

393 if

( testcase ==

"validate"

) {

396 if

( testcase ==

"word-pair"

) {

409 if

( args[

"batch"

] ) {

412 else if

( args[

"catenated"

] ) {

423 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

virtual void Run(CSeqEntryProcess *process)

virtual void Initialize(const CArgs &args)

virtual void Finalize(const CArgs &args)

virtual void ProcessFinalize()

virtual void ProcessInitialize(const CArgs &args)

CSeqEntryPresenter * GetPresenter(const CArgs &)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

CSeqEntryProcess * GetProcess(const CArgs &)

virtual void Exit(void)

Cleanup on application exit.

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.

CNcbiRegistry & GetRWConfig(void)

Get the application's cached configuration parameters, accessible for read-write for an application's...

const CNcbiArguments & GetArguments(void) const

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

@ fBinary

Open as binary file; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

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.

void Error(CExceptionArgs_Base &args)

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines: CTimeFormat - storage class for time format.

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

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