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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/deltablast__args_8cpp_source.html below:

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

kProgram(

);

));

m_Args.push_back(arg);

kQueryIsProtein =

;

kFilterByDefault =

;

kIsDeltaBlast =

;

kIsCBS2and3Supported =

;

kDefaultTask[] =

;

SetTask(kDefaultTask);

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);

arg.

(m_DeltaBlastArgs);

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.

@ eDeltaBlast

Delta Blast.

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.

Handle command line arguments for deltablast binary.

bool GetSaveLastPssm(void) const

Should PSSM after last database search be saved.

virtual int GetQueryBatchSize(void) const

Get query batch size.

CRef< CPsiBlastArgs > m_PsiBlastArgs

Pssm search and Psi-Blast sepcific arguments.

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

Create the options handle based on the command line arguments.

Argument class to collect options specific to DELTA-BLAST.

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

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.

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

Argument class to collect options specific to PSI-BLAST.

@ eProteinDb

Traditional, iterated PSI-BLAST.

bool GetSaveLastPssm(void) const

Should the PSSM after the last database search be saved.

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 kDfltArgCompBasedStatsDelta

Main argument class for DELTA-BLAST application.

Declares the CDeltaBlastOptionsHandle class.

virtual string Print(void) const

Print version information.

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.

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