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

(node_num, ncbi_args, args, bah, query_index, num_queries, mailbox), m_Input(

)

(pssm.

()) {

(!isArchiveFormat) {

(pssm.

()) {

lcl_blast(query_factory, opts_hndl, db_adapter);

(isArchiveFormat) {

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.

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.

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.

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

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.

CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)

Extract the command line arguments into a CBlastOptionsHandle object.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database 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.

Class representing a text file containing sequences in fasta format.

This class formats the BLAST results for command line applications.

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...

void SendMsg(CBlastNodeMsg::EMsgType msg_type, void *ptr=NULL)

CBlastAppDiagHandler & GetDiagHandler()

void SetDataLoaderPrefix()

const CNcbiArguments & GetArguments()

void SetState(EState state)

void SetQueriesLength(int l)

void SetStatus(int status)

Encapsulates ALL the BLAST algorithm's options.

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.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

virtual int GetQueryBatchSize() const

@inheritDoc

virtual CNcbiIstream & GetInputStream()

Get the input stream.

CNcbiStrstream & GetOutputStrStream()

virtual int GetBlastResults(CNcbiOstream &os)

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CTblastnNode(int check_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, string &input, int query_index, int num_queries, CBlastNodeMailbox *mailbox=NULL)

CRef< CTblastnNodeArgs > m_CmdLineArgs

virtual ~CTblastnNode(void)

const string kArgOutput

Output file name.

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< CSearchResultSet > Run()

Executes the search.

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.

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

#define ERR_POST(message)

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

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

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.

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