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

kFilterByDefault =

;

kProgram(

);

));

kQueryIsProtein =

;

kIsRpsBlast =

;

kIsCBS2and3Supported =

;

m_Args.push_back(arg);

kDefaultTask[] =

;

SetTask(kDefaultTask);

arg.

(m_BlastDbArgs);

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);

arg.

(m_RemoteArgs);

m_Args.push_back(arg);

arg.

(m_DebugArgs);

m_Args.push_back(arg);

m_Args.push_back(arg);

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

Auxiliary classes/functions for BLAST input library.

int GetQueryBatchSize(EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)

Retrieve the appropriate batch size for the specified task.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

virtual CNcbiIstream & GetInputStream()

Get the input stream.

bool m_IsUngapped

Is this application being run ungapped.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Argument class to collect database/subject arguments.

EAPILocality

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

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 collecting gapped options.

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

Argument class to collect the genetic code for all queries/subjects.

@ eQuery

Query genetic code.

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

Argument class to collect query options.

Handles command line arguments for blastx binary.

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

@inheritDoc

virtual CNcbiIstream & GetInputStream()

Get the input stream.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

CNcbiStrstream m_OutputStream

CNcbiIstrstream * m_InputStream

virtual CNcbiIstream & GetInputStream()

Get the input stream.

virtual ~CRPSTBlastnNodeArgs()

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

@inheritDoc

CRPSTBlastnNodeArgs(const string &input)

Constructor.

virtual int GetQueryBatchSize() const

@inheritDoc

Handle to the options for translated nucleotide-RPS blast.

Argument class to collect remote vs. local execution.

bool ExecuteRemotely() const

Return whether the search should be executed remotely or not.

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.

const string kDfltArgCompBasedStatsRPS

virtual string Print(void) const

Print version information.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

Main argument class for RPSBLAST application.

Main argument class for RPS TBLASTN application.

Declares the CRPSTBlastnOptionsHandle class.

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