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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/idfetch_8cpp_source.html below:

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

92

unique_ptr<CObjectOStream>

m_Os

;

113

unique_ptr<CFastaOstream>

m_Os

;

125 virtual void Init

(

void

);

126 virtual int Run

(

void

);

127 virtual void Exit

(

void

);

161

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

162 "Retrieve sequences in a varietu of formats"

);

164

arg_desc->AddDefaultKey(

"o"

"Output"

165 "Filename for output"

169

arg_desc->AddDefaultKey(

"t"

"Type"

170 "Output type. Options are:\n" 176 "6 = quality scores\n" 177 "7 = Entrez DocSums\n" 178 "8 = FASTA reverse complement\n"

181

arg_desc->SetConstraint(

"t"

184

arg_desc->AddKey(

"g"

"GI"

185 "GI to for single entry to process"

187

arg_desc->AddOptionalKey(

"s"

"SeqId"

188 "Fasta style SeqId to process"

190

arg_desc->SetDependency(

"s"

194

arg_desc->AddOptionalKey(

"q"

"Query"

195 "Use an entrez query to generate the input list"

197

arg_desc->SetDependency(

"q"

201

arg_desc->AddFlag(

"dp"

"Query is for protein database"

);

202

arg_desc->AddFlag(

"dn"

"Query is for nucleotide database"

);

217 int type

= args[

"t"

].AsInteger();

251

unique_ptr<IOutputFormatter> formatter(

x_GetFormatter

(ostr, args));

254 if

(args[

"g"

] || args[

"s"

]) {

255 if

( !formatter.get() ) {

257 "formatter type not understood or not handled"

);

266 else if

(args[

"s"

]) {

273 "failed to retrieve sequence: "

+ idh.

AsString

());

276

formatter->Format(bsh);

278 else if

(args[

"q"

]) {

279 if

( !formatter.get() ) {

281 "formatter type not understood or not handled"

);

284 string query

= args[

"q"

].AsString();

286

vector<TEntrezId> uids;

291 else if

(args[

"dn"

]) {

296 "one of -dp or -dn must be provided to " 297 "indicate the database of interest"

);

300 ITERATE

(vector<TEntrezId>, it, uids) {

305 "failed to retrieve sequence: "

+ idh.

AsString

());

308

formatter->Format(bsh);

316 "input options not yet supported"

);

338 int main

(

int

argc,

const char

* argv[])

static void SetupObjectManager(const CArgs &args, objects::CObjectManager &obj_mgr, TLoaders loaders=fDefault)

Set up the standard object manager data loaders according to the arguments provided above.

static void AddArgumentDescriptions(CArgDescriptions &arg_desc, TLoaders loaders=fDefault)

Add a standard set of arguments used to configure the object manager.

Class for querying via E-Utils.

Uint8 Search(const string &db, const string &term, vector< objects::CSeq_id_Handle > &uids, const string &xml_path=kEmptyStr)

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

static IOutputFormatter * x_GetFormatter(CNcbiOstream &ostr, const CArgs &args)

virtual int Run(void)

Run the application.

COutput_Fasta(CNcbiOstream &ostr)

unique_ptr< CFastaOstream > m_Os

virtual void Format(const CBioseq_Handle &bsh)

COutput_SerialFormat(CNcbiOstream &ostr, ESerialDataFormat fmt)

unique_ptr< CObjectOStream > m_Os

virtual void Format(const CBioseq_Handle &bsh)

virtual void Format(const CBioseq_Handle &)=0

virtual ~IOutputFormatter()

IOutputFormatter(CNcbiOstream &ostr)

#define ENTREZ_ID_TO(T, entrez_id)

#define GI_FROM(T, value)

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

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

@ eExcludes

One argument excludes another.

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string AsString(void) const

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

CRef< objects::CObjectManager > om

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