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

kProgram(

);

));

kQueryIsProtein =

;

m_Args.push_back(arg);

kDefaultTask[] =

;

SetTask(kDefaultTask);

tasks.

(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);

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);

arg.

(m_PsiBlastArgs);

m_Args.push_back(arg);

arg.

(m_DebugArgs);

m_Args.push_back(arg);

(args[

].AsString() ==

) {

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.

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

@ eTblastn

Protein-Translated nucl.

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

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.

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 collecting gapped options.

Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...

Argument class to collect the genetic code for all queries/subjects.

@ eDatabase

Database genetic code.

Argument class to retrieve options for filtering HSPs (e.g.

Argument class for collecting the largest intron size.

Argument class to collect multi-threaded arguments.

Argument class to retrieve and set the scoring matrix name BLAST algorithm option.

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

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

Argument class to collect options specific to PSI-BLAST.

@ eNucleotideDb

PSI-Tblastn, non-iterated.

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 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.

Handles command line arguments for Tblastn binary.

virtual int GetQueryBatchSize() const

Get the query batch size.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM.

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

Set the PSSM from the saved search strategy.

CRef< CPsiBlastArgs > m_PsiBlastArgs

PSI-BLAST specific argument class (for psi-tblastn)

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

Create the options handle based on the command line arguments.

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

@inheritDoc

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

CNcbiStrstream m_OutputStream

CNcbiIstrstream * m_InputStream

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiIstream & GetInputStream()

Get the input stream.

CTblastnNodeArgs(const string &input)

Constructor.

virtual ~CTblastnNodeArgs()

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

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

iterator_bool insert(const value_type &val)

const string kArgPSIInputChkPntFile

Argument to specify a 'checkpoint' file to recover the PSSM from.

const string kTask

Task to perform.

void SetWordThreshold(double wt)

Sets WordThreshold.

void SetWordSize(int ws)

Sets WordSize.

CBlastOptions & SetOptions()

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

void SetPSITblastnDefaults()

Sets default options for psi tblastn search.

virtual string Print(void) const

Print version information.

void SetLookupTableType(ELookupTableType type)

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.

Declares the CPSIBlastOptionsHandle class.

Main argument class for TBLASTN application.

Declares the CTBlastnOptionsHandle class.

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