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

& program_desc)

kProgram(

);

));

kQueryIsProtein =

;

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.

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

string GetTask() const

Get the task for this object.

CRef< CQueryOptionsArgs > m_QueryOptsArgs

query options object

CRef< CBlastDatabaseArgs > m_BlastDbArgs

database/subject object

CRef< CSearchStrategyArgs > m_SearchStrategyArgs

arguments for dealing with search strategies

CRef< CDebugArgs > m_DebugArgs

Debugging arguments.

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

Creates the BLAST options handle based on the task argument.

CRef< CMTArgs > m_MTArgs

multi-threaded options

CRef< CFormattingArgs > m_FormattingArgs

formatting options

bool m_IsUngapped

Is this application being run ungapped.

TBlastCmdLineArgs m_Args

Set of command line argument objects.

CRef< CStdCmdLineArgs > m_StdCmdLineArgs

standard command line arguments class

string m_ClientId

Client ID used for remote BLAST submissions, must be populated by subclasses.

Argument class to collect database/subject arguments.

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

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

Argument class to collect debugging 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 options specific to igBLAST.

Program description without BLAST+ version.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CIgBlastProgramDescriptionArgs(const string &program_name, const string &program_desc)

CRef< CIgBlastArgs > m_IgBlastArgs

CIgBlastnAppArgs()

Constructor.

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

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

Argument class to collect multi-threaded arguments.

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

Argument class to collect query options.

Argument class to collect remote vs. local execution.

Argument class to import/export the search strategy.

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

void SetSRAaccessionEnabled(bool g)

enables sra accession flag

const size_t kDfltIgBlastNumThreads

Default number of threads for IgBLAST command line tools.

Declares the CDiscNucleotideOptionsHandle class.

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

void SetGapOpeningCost(int g)

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

void SetGapExtensionCost(int e)

void SetMismatchPenalty(int p)

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

EProgram ProgramNameToEnum(const std::string &program_name)

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

void SetMatchReward(int r)

void SetUsageContext(const string &usage_name, const string &usage_description, bool usage_sort_args=false, SIZE_TYPE usage_width=78)

Set extra info to be used by PrintUsage().

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.

Main argument class for IGBLASTN application.

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