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

arg_desc.SetCurrentGroup(

);

kDfltRpsThreadingMode = 1;

,

arg_desc.AddDefaultKey(

,

,

,

arg_desc.SetCurrentGroup(

);

kQueryIsProtein =

;

kIsRpsBlast =

;

kIsCBS2and3Supported =

;

kFilterByDefault =

;

kProgram(

);

));

kDefaultTask[] =

;

cbs_opt_zero_descr =

;

cbs_opt_zero_descr));

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.

Declares the CBlastRPSOptionsHandle class.

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

Class to constrain the values of an argument to those in between the values specified in the construc...

Class to constrain the values of an argument to those greater than or equal to the value specified in...

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

virtual CNcbiIstream & GetInputStream()

Get the input stream.

CRef< CQueryOptionsArgs > m_QueryOptsArgs

query options object

CRef< CBlastDatabaseArgs > m_BlastDbArgs

database/subject object

CRef< CDebugArgs > m_DebugArgs

Debugging arguments.

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.

void SetTask(const string &task)

Set the task for this object.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

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.

EAPILocality

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

Handle to the rpsblast 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...

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

Argument class to collect query options.

CRPSBlastAppArgs()

Constructor.

virtual CNcbiIstream & GetInputStream()

Get the input stream.

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

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

CNcbiStrstream m_OutputStream

CNcbiIstrstream * m_InputStream

virtual ~CRPSBlastNodeArgs()

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

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

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiIstream & GetInputStream()

Get the input stream.

CRPSBlastNodeArgs(const string &input)

Constructor.

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

const string kArgMTMode

Argument to specify mt mode (split by db or split by queries)

const string kArgNumThreads

Argument to determine the number of threads to use when running BLAST.

virtual string Print(void) const

Print version information.

@ eInteger

Convertible into an integer number (int or Int8)

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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

Main argument class for RPSBLAST application.

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