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NCBI C++ ToolKit: src/app/rmblastn/rmblastn_app.cpp Source File

lcl_blast(queries, opts_hndl, db_adapter);

(

argc,

* argv[]

)

Produce formatted blast output for command line applications.

CRef< blast::CRemoteBlast > InitializeRemoteBlast(CRef< blast::IQueryFactory > queries, CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool verbose_output, const string &client_id, CRef< objects::CPssmWithParameters > pssm)

Initializes a CRemoteBlast instance for usage by command line BLAST binaries.

void SaveSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)

Save the search strategy corresponding to the current command line search.

bool RecoverSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args)

Recover search strategy from input file.

void InitializeSubject(CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, bool is_remote_search, CRef< blast::CLocalDbAdapter > &db_adapter, CRef< objects::CScope > &scope)

Initializes the subject/database as well as its scope.

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

#define BLAST_EXIT_SUCCESS

Command line binary exit code: success.

Interface for reading SRA sequences into blast input.

CRef< CBlastOptionsHandle > SetOptionsForSavedStrategy(const CArgs &args)

Combine the command line arguments into a CBlastOptions object recovered from saved search strategy.

string GetTask() const

Get the task for this object.

virtual CNcbiIstream & GetInputStream()

Get the input stream.

size_t GetNumThreads() const

Get the number of threads to spawn.

CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)

Extract the command line arguments into a CBlastOptionsHandle object.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database arguments.

CArgDescriptions * SetCommandLine()

Set the command line arguments.

bool ExecuteRemotely() const

Determine whether the search should be executed remotely or not.

bool ProduceDebugRemoteOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const

Get the options for the query sequence(s)

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

bool ProduceDebugOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Class representing a text file containing sequences in fasta format.

This class formats the BLAST results for command line applications.

void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)

Print all alignment information for a single query sequence along with any errors or warnings (errors...

void PrintEpilog(const blast::CBlastOptions &options)

Print the footer of the blast report.

void ResetScopeHistory()

Resets the scope history for some output formats.

void PrintProlog()

Print the header of the blast report.

Class that centralizes the configuration data for sequences to be converted.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

Encapsulates ALL the BLAST algorithm's options.

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const

string GetCustomOutputFormatSpec() const

Retrieve for string that specifies the custom output format for tabular and comma-separated value.

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

TSeqPos GetNumAlignments() const

Number of alignments to show in traditional BLAST output.

bool ShowGis() const

Display the NCBI GIs in formatted output?

TSeqPos GetNumDescriptions() const

Number of one-line descriptions to show in traditional BLAST output.

bool DisplayHtmlOutput() const

Display HTML output?

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

objects::ENa_strand GetStrand() const

Get strand to search in query sequence(s)

bool GetParseDeflines() const

Should the defline be parsed?

bool QueryIsProtein() const

Is the query sequence protein?

TSeqRange GetRange() const

Get query sequence range restriction.

bool UseLowercaseMasks() const

Use lowercase masking in FASTA input?

Handles command line arguments for blastn binary.

virtual int GetQueryBatchSize() const

Get the query batch size.

virtual int Run()

@inheritDoc

CRMBlastnApp()

@inheritDoc

CRef< CRMBlastnAppArgs > m_CmdLineArgs

This application's command line args.

virtual void Init()

@inheritDoc

Search Results for All Queries.

int GetDbGeneticCode() const

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

CRef< CSearchResultSet > Run()

Executes the search.

static void InitializeMegablastDbIndex(CRef< CBlastOptions > options)

Initialize a megablast BLAST database index.

CBlastOptions & SetOptions()

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

int GetFilteringAlgorithm()

Retrieve the database filtering algorithm.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

int GetQueryGeneticCode() const

bool GetSumStatisticsMode() const

Sum statistics options.

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

bool GetMBIndexLoaded() const

const char * GetMatrixName() const

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eDiag_Warning

Warning message.

void Reset(void)

Reset reference object.

Main class to perform a BLAST search on the local machine.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declares the CRemoteBlast class.

int main(int argc, const char *argv[])

Main argument class for RMBLASTN application.

Configuration structure for the CBlastScopeSource.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

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