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NCBI C++ ToolKit: src/app/blast/rpstblastn_app.cpp Source File

(!isArchiveFormat) {

batch_size = 8000;

* mt_query_batch_env = getenv(

);

(mt_query_batch_env) {

(

<< batch_size);

(!

.AtEOF()) {

(!master_node.

()) {

num_q =

.GetQueryBatch(qb, q_index);

(chunk_num < kMaxNumOfThreads){

(

argc,

* argv[]

)

Produce formatted blast output for command line applications.

void LogCmdOptions(blast::CBlastUsageReport &report, const CBlastAppArgs &args)

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.

blast::SDataLoaderConfig InitializeQueryDataLoaderConfiguration(bool query_is_protein, CRef< blast::CLocalDbAdapter > db_adapter)

Initialize the data loader configuration for the query.

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.

void QueryBatchCleanup()

Clean up formatter scope and release.

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

Recover search strategy from input file.

void CheckMTByQueries_QuerySize(EProgram prog, int batch_size)

void PrintErrorArchive(const CArgs &a, const list< CRef< CBlast4_error > > &msg)

Function to print blast archive with only error messages (search failed) to output stream.

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.

string GetCmdlineArgs(const CNcbiArguments &a)

void BlastFormatter_PreFetchSequenceData(const blast::CSearchResultSet &results, CRef< CScope > scope, blast::CFormattingArgs::EOutputFormat format_type)

This method optimize the retrieval of sequence data to scope.

void LogBlastOptions(blast::CBlastUsageReport &report, const CBlastOptions &opt)

bool UseXInclude(const CFormattingArgs &f, const string &s)

bool IsIStreamEmpty(CNcbiIstream &in)

void LogQueryInfo(CBlastUsageReport &report, const CBlastInput &q_info)

Utility functions for BLAST command line applications.

#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.

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)

string GetClientId() const

Retrieve the client ID for remote requests.

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...

Class to capture message from diag handler.

string GetDatabaseName() const

Get the BLAST database name.

Class representing a text file containing sequences in fasta format.

This class formats the BLAST results for command line applications.

void LogBlastSearchInfo(blast::CBlastUsageReport &report)

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 SetBaseFile(string base)

For use by XML2 only.

void ResetScopeHistory()

Resets the scope history for some output formats.

void SetLineLength(size_t len)

Set Alignment Length.

void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())

Writes out the query and results as an "archive" format.

void PrintProlog()

Print the header of the blast report.

void SetQueryRange(const TSeqRange &query_range)

Set query range.

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...

CConditionVariable & GetBuzzer()

void RegisterNode(CBlastNode *node, CBlastNodeMailbox *mailbox)

Encapsulates ALL the BLAST algorithm's options.

void AddParam(EUsageParams p, int val)

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

virtual bool ArchiveFormatRequested(const CArgs &args) 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.

size_t GetLineLength() const

bool DisplayHtmlOutput() const

Display HTML output?

CRef< CSearchResultSet > Run()

Argument class to collect multi-threaded arguments.

size_t GetNumThreads() const

Get the number of threads to spawn.

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 blastx binary.

virtual CNcbiIstream & GetInputStream()

Get the input stream.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

virtual int GetQueryBatchSize() const

@inheritDoc

virtual void Init()

@inheritDoc

CBlastUsageReport m_UsageReport

CRef< CRPSTBlastnAppArgs > m_CmdLineArgs

This application's command line args.

CRPSTBlastnApp()

@inheritDoc

int x_RunMTBySplitQuery()

virtual int Run()

@inheritDoc

Search Results for All Queries.

const string kArgOutput

Output file name.

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.

void Print(const CCompactSAMApplication::AlignInfo &ai)

int GetDbGeneticCode() const

void ResetMessages(void)

Reset messgae buffer, erase all saved message.

int GetFilteringAlgorithm()

Retrieve the database filtering algorithm.

EProgram GetProgram() const

Accessors/Mutators for individual options.

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.

void DoNotSaveMessages(void)

Call to turn off saving diag message, discard all saved message.

const char * GetMatrixName() const

list< CRef< objects::CBlast4_error > > & GetMessages(void)

Return list of saved diag messages.

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.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

#define INFO_POST(message)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void SetDiagHandler(CDiagHandler *handler, bool can_delete=true)

Set the diagnostic handler using the specified diagnostic handler class.

@ eDiag_Warning

Warning message.

void Warning(CExceptionArgs_Base &args)

void Reset(void)

Reset reference object.

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

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.

Declares the CLocalRPSBlast class.

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

Main argument class for RPS TBLASTN application.

Defines BLAST database access classes.

Configuration structure for the CBlastScopeSource.

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