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

kProgram[] =

;

));

kQueryIsProtein =

;

m_Args.push_back(arg);

kDefaultTask[] =

;

SetTask(kDefaultTask);

tasks.

(

);

m_Args.push_back(arg);

m_BlastDbArgs->SetDatabaseMaskingSupport(

);

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_HspFilteringArgs);

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);

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

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.

Main argument class for BLASTN application.

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

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.

bool m_IsUngapped

Is this application being run ungapped.

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.

Handles command line arguments for blastn binary.

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

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiIstream & GetInputStream()

Get the input stream.

virtual int GetQueryBatchSize() const

@inheritDoc

CNcbiIstrstream * m_InputStream

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

CBlastnNodeArgs(const string &input)

Constructor.

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

@inheritDoc

CNcbiStrstream m_OutputStream

virtual ~CBlastnNodeArgs()

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 retrieve and set the off-diagonal range used in 2-hit algorithm.

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

Argument class to collect query options.

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 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).

virtual string Print(void) const

Print version information.

@ eNuclNucl

Nucleotide-nucleotide tasks.

bool Exist(const string &name) const

Check existence of argument description.

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.

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