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NCBI C++ ToolKit: src/algo/align/util/demo/demo_score_builder.cpp Source File

(

);

(

);

(

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

ostr <<

<< sb.

(align) << endl;

ostr <<

<< identities <<

<< mismatches << endl;

(

argc,

* argv[])

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

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

TSeqPos GetAlignLength(const CSeq_align &align, bool ungapped=false)

Compute the length of the alignment (= length of all segments, gaps + aligned)

int GetIdentityCount(CScope &scope, const CSeq_align &align)

Compute the number of identities in the alignment.

int GetMismatchCount(CScope &scope, const CSeq_align &align)

Compute the number of mismatches in the alignment.

int ComputeTieBreaker(const CSeq_align &align)

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.

@ eInputFile

Name of file (must exist and be readable)

@ eOutputFile

Name of file (must be writable)

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

Set diagnostic stream.

#define MSerial_AsnText

I/O stream manipulators –.

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.

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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