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

));

kQueryIsProtein =

;

m_Args.push_back(arg);

kDefaultTask =

;

SetTask(kDefaultTask);

m_Args.push_back(arg);

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);

m_Args.push_back(arg);

arg.

(m_HspFilteringArgs);

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);

Declares the BLAST exception class.

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.

string GetTask() const

Get the task for this object.

CRef< CBlastOptionsHandle > x_CreateOptionsHandleWithTask(CBlastOptions::EAPILocality locality, const string &task)

Creates the BLAST options handle based on the task argument.

Argument class to collect database/subject arguments.

EAPILocality

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

Argument class to collect debugging options.

Argument class to retrieve discontiguous megablast arguments.

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 retrieve options for filtering HSPs (e.g.

Argument class to collect multi-threaded arguments.

Argument class to retrieve megablast database indexing options.

Defines values for match and mismatch in nucleotide comparisons as well as non-greedy extension.

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

Argument class to collect query options.

RMH: Argument class to retrieve and set the options specific to the RMBlastN algorithm.

Handles command line arguments for blastn binary.

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

Create the options handle based on the command line arguments.

virtual int GetQueryBatchSize() const

Get the query batch size.

Argument class to collect remote vs. local execution.

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

Argument class to specify the supported tasks a given program.

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

const string kTask

Task to perform.

Declares the CDiscNucleotideOptionsHandle class.

static set< string > GetTasks(ETaskSets choice=eAll)

Retrieve the set of supported tasks.

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

@ eNuclNucl

Nucleotide-nucleotide tasks.

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 RMBLASTN application.

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