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NCBI C++ ToolKit: src/sample/app/alnmgr/alnmgr_sample.cpp Source File

(

);

(

);

arg_desc->SetUsageContext

);

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

asn_out->SetSeparator(

);

*asn_out << Separator;

(

= 0;

< chunk_vec->size();

++) {

(!chunk->IsGap()) {

<< chunk->GetRange().GetFrom() <<

<< chunk->GetRange().GetTo();

cout <<

;

cout <<

;

cout <<

;

cout <<

;

cout <<

;

cout <<

;

cout <<

;

int NcbiSys_main(int argc, TXChar *argv[])

@ fNotAlignedToSeqOnAnchor

void SetAnchor(TNumrow anchor)

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

void Add(const CDense_seg &ds, TAddFlags flags=0)

void Merge(TMergeFlags flags=0)

const CDense_seg & GetDenseg(void) const

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

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

Template class for iteration on objects of class C.

std::ofstream out("events_result.xml")

main entry point for tests

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

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.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

@ 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 CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

std::istream & in(std::istream &in_, double &x_)

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