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

kMT1MaxDbSz_Tblastn = 280000000;

kMT1MinQSz_Tblastn = 200000;

kMT1MaxDbSz_TblastnFast = 350000000;

kMT1MinQSz_TblastnFast = 200000;

max_db_size = kMT1MaxDbSz_TblastnFast;

min_q_size = kMT1MinQSz_TblastnFast;

max_db_size = kMT1MaxDbSz_Tblastn;

min_q_size = kMT1MinQSz_Tblastn;

max_db_size = 0;

(total_length < max_db_size) {

(

.GetLength() > min_q_size) {

(total_length > max_db_size) {

(pssm.

()) {

(!isArchiveFormat) {

(pssm.

()) {

(

<< batch_size);

(!

.AtEOF()) {

(!master_node.

()) {

num_q =

.GetQueryBatch(qb, q_index);

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.

string GetSubjectFile(const CArgs &args)

Get name of subject file @parameter args arguments class [in].

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

Recover search strategy from input file.

int GetMTByQueriesBatchSize(EProgram p, int num_threads, const string &task)

void MTByQueries_DBSize_Warning(const Int8 length_limit, bool is_db_protein)

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.

const CSeq_id * GetFirstId() const

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)

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...

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Class to capture message from diag handler.

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

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 SetHitsSortOption(int hitsSortOption)

void SetHspsSortOption(int hspsSortOption)

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 SetCustomDelimiter(string customDelim)

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

int GetHitsSortOption() 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.

int GetHspsSortOption() const

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?

string GetCustomDelimiter()

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.

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

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

CSeq_entry & SetQuery()

Retrieve the query sequence.

bool HasQuery() const

Has this PSSM a query in it?

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?

Search Results for All Queries.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

Handles command line arguments for Tblastn binary.

virtual int GetQueryBatchSize() const

Get the query batch size.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM.

CBlastUsageReport m_UsageReport

int x_RunMTBySplitQuery()

virtual int Run()

@inheritDoc

CRef< CTblastnAppArgs > m_CmdLineArgs

This application's command line args.

CRef< CBlastOptionsHandle > m_OptsHndl

virtual void Init()

@inheritDoc

CBlastAppDiagHandler m_Bah

const string kArgOutput

Output file name.

const string kArgQuery

Query sequence(s)

void Print(const CCompactSAMApplication::AlignInfo &ai)

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

int GetDbGeneticCode() const

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

void ResetMessages(void)

Reset messgae buffer, erase all saved message.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

CRef< CSearchResultSet > Run()

Executes the search.

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.

bool Exist(const string &name) const

Check existence of argument 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)

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

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.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsEnabled(void)

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

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

double Elapsed(void) const

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

void Start(void)

Start the timer.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

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 CPsiBlast, the C++ API for the PSI-BLAST engine.

Declares the CRemoteBlast class.

Configuration structure for the CBlastScopeSource.

static void s_GetMT1Cutoffs(const int word_size, Int8 &max_db_size, Int8 &min_q_size)

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

Main argument class for TBLASTN application.

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