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NCBI C++ ToolKit: src/algo/blast/blastinput/kblastp_args.cpp Source File

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kProgram(

);

kQueryIsProtein =

;

kFilterByDefault =

;

m_Args.push_back(arg);

m_BlastDbArgs->SetDatabaseMaskingSupport(

);

arg.

(m_BlastDbArgs);

m_Args.push_back(arg);

arg.

(m_KBlastpArgs);

m_Args.push_back(arg);

arg.

(m_StdCmdLineArgs);

m_Args.push_back(arg);

m_Args.push_back(arg);

m_Args.push_back(arg);

m_Args.push_back(arg);

m_Args.push_back(arg);

m_Args.push_back(arg);

arg.

(m_QueryOptsArgs);

m_Args.push_back(arg);

arg.

(m_FormattingArgs);

m_Args.push_back(arg);

arg.

(m_MTArgs);

m_Args.push_back(arg);

m_Args.push_back(arg);

arg.

(m_DebugArgs);

m_Args.push_back(arg);

Declares singleton objects to store the version and reference for the BLAST engine.

Declares the CBlastAdvancedProteinOptionsHandle class.

Declares the BLAST exception class.

Auxiliary classes/functions for BLAST input library.

Argument class to collect database/subject arguments.

EAPILocality

Enumerates the possible contexts in which objects of this type can be used.

Handle to the protein-protein options to the BLAST algorithm.

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

Argument class for collecting composition based statistics options.

Argument class to collect debugging options.

Argument class for collecting filtering options.

Argument class to collect formatting options, use this to create a CBlastFormat object.

Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...

Handles command line arguments for blastp binary.

virtual CRef< CBlastOptionsHandle > x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs &args)

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

Argument class to collect options specific to KBLASTP.

Argument class to collect multi-threaded arguments.

Argument class to retrieve and set the scoring matrix name BLAST algorithm option.

Argument class to populate an application's name and description.

Argument class to collect query options.

Argument class to retrieve input and output streams for a command line program.

Argument class to retrieve and set the window size BLAST algorithm option.

Argument class to retrieve and set the word threshold BLAST algorithm option.

virtual string Print(void) const

Print version information.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Main argument class for KBLASTP application.

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