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NCBI C++ ToolKit: src/algo/sequence/demo/regexplocdemo.cpp Source File

(

);

(

);

argDescr->AddKey(

,

,

argDescr->AddKey(

,

,

,

argDescr->SetUsageContext(

().GetProgramBasename(),

,

);

cerr <<

<< acc <<

<< e.

() << endl;

seq.reserve(sv.

());

cout <<

<< seq << endl;

cerr <<

<< endl;

retCode =

(args[

].AsString(),

args[

].AsString(),

(

argc,

** argv)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

Class used to convert a PCRE match to a char* sequence into a CSeq_loc.

TSeqPos GetLoc(const char *seq, CSeq_loc *loc, TSeqPos offset=0, CRegexp::TMatch flags=0)

Gets a CSeq_loc for PCRE match to char* sequence.

Template class for iteration on objects of class C.

unsigned int TSeqPos

Type for sequence locations and lengths.

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.

void DisableArgDescriptions(TDisableArgDesc disable=fDisableStdArgs)

const CNcbiArguments & GetArguments(void) const

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

@ eString

An arbitrary string.

@ eDS_Default

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

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

@ eSerial_AsnText

ASN.1 text.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

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.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

header file for creating CSeq_locs from CRegexps.

int main(int argc, char **argv)

int GetLoc(const string &acc, const string &pat, CSeq_loc &loc, CScope &scope)

CNcbiOstream & operator<<(CNcbiOstream &os, const CSeq_loc &loc)

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