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

kQueryIsProtein =

;

kFilterByDefault =

;

kProgram(

);

));

m_Args.push_back(arg);

kDefaultTask[] =

;

SetTask(kDefaultTask);

m_BlastDbArgs->SetIPGFilteringSupport(

);

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);

arg.

(m_HspFilteringArgs);

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);

m_Args.push_back(arg);

m_Args.push_back(arg);

arg.

(m_PsiBlastArgs);

m_Args.push_back(arg);

m_Args.push_back(arg);

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.

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

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.

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 to retrieve the gap trigger option.

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 and set the scoring matrix name BLAST algorithm option.

Handle to the protein PHI BLAST options.

Handle to the protein-protein options to the BLAST algorithm.

Argument class to collect options specific to PHI-BLAST.

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

Handle command line arguments for psiblast binary Programs supported: psiblast, phi-blastn,...

CNcbiOstream * GetCheckpointStream()

Retrieve the stream to write the checkpoint file.

CRef< CPsiBlastArgs > m_PsiBlastArgs

PSI-BLAST specific argument class.

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

Create the options handle based on the command line arguments.

bool GetSaveLastPssm() const

Should the PSSM after the last database search be saved.

size_t GetNumberOfIterations() const

Get the number of iterations to perform.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM specified as input from the command line.

virtual int GetQueryBatchSize() const

Get the query batch size.

bool SaveAsciiPssm() const

Should a PSSM be saved as ASCII in a file?

CNcbiOstream * GetAsciiPssmStream()

Retrieve the stream to write the ASCII PSSM.

void SetNumberOfIterations(unsigned int num_iters)

Set number of iterations from the saved search strategy.

bool SaveCheckpoint() const

Should a PSSM be saved in a checkpoint file?

void SetInputPssm(CRef< objects::CPssmWithParameters > pssm)

Set the PSSM from the saved search strategy.

Argument class to collect options specific to PSI-BLAST.

size_t GetNumberOfIterations() const

Retrieve the number of iterations to perform.

bool RequiresAsciiPssmOutput() const

Returns true if ASCII PSSM is required to be printed.

CNcbiOstream * GetCheckPointOutputStream()

Get the checkpoint file output stream.

@ eProteinDb

Traditional, iterated PSI-BLAST.

void SetNumberOfIterations(unsigned int num_iters)

Retrieve the number of iterations to perform.

CNcbiOstream * GetAsciiMatrixOutputStream()

Get the ASCII matrix output stream.

bool RequiresCheckPointOutput() const

Returns true if checkpoint PSSM is required to be printed.

bool GetSaveLastPssm(void) const

Should the PSSM after the last database search be saved.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM read from checkpoint file.

void SetInputPssm(CRef< objects::CPssmWithParameters > pssm)

Set the PSSM read from saved search strategy.

Argument class to collect PSSM engine options.

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 retrieve and set the window size BLAST algorithm option.

Argument class to retrieve and set the word threshold BLAST algorithm option.

const string kArgPHIPatternFile

Argument to specify a PHI-BLAST pattern file.

virtual string Print(void) const

Print version information.

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.

Declares the CPHIBlastProtOptionsHandle class.

Main argument class for PSI-BLAST application.

Declares the CPSIBlastOptionsHandle class.

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