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NCBI C++ ToolKit: src/app/blastvdb/tblastn_vdb.cpp Source File

(

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num_threads = (

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dbInfo.is_protein =

;

dbInfo.definition = dbInfo.name;

->SetVersionInfo(

CBlastVdbVersion);

vector<string> paths;

);

vector< CBlastFormatUtil::SDbInfo > vecDbInfo(1);

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(

argc,

* argv[])

Produce formatted blast output for command line applications.

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.

string GetCmdlineArgs(const CNcbiArguments &a)

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

Interface for reading SRA sequences into blast input.

CRef< CScope > GetVDBScope(string dbAllNames)

void SortAndFetchSeqData(const blast::CSearchResultSet &results, CRef< CScope > scope, CScope::TBioseqHandles &handles)

Utility functions for BLAST VDB command line applications.

const string kArgSRASearchMode

const string kArgIncludeFilteredReads

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.

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.

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.

string GetDatabaseName() const

Get the BLAST database name.

Defines BLAST error codes (user errors included)

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.

void SetQueryLocalIdMode()

Append query-specific prefix codes to all generated local ids.

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

Encapsulates ALL the BLAST algorithm's options.

void AddParam(EUsageParams p, int val)

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?

Defines user input exceptions.

static string PreprocessDBs(CLocalVDBBlast::SLocalVDBStruct &local_vdb, const string db_names, unsigned int num_threads=kDisableThreadedSearch, ESRASearchMode seach_mode=eAligned)

CRef< CSearchResultSet > Run()

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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.

Handles command line arguments for blastx binary.

virtual int GetQueryBatchSize() const

Get the query batch size.

CRef< objects::CPssmWithParameters > GetInputPssm() const

Get the PSSM.

static void FindVDBPaths(const string &dbname, bool isProtein, vector< string > &paths, vector< string > *db_alias_list=NULL, vector< string > *vdb_alias_list=NULL, bool recursive=true, bool expand_links=true, bool verify_dbs=true)

Get the list of vdb names.

static Uint4 SetupVDBManager()

*Note* Call this in main thread first, if you are going to instantiate this object or use any of the ...

static void ReleaseVDBManager()

Call this release vdb manager if SetupManger has been explicitly called in the main thread.

void x_GetFullVDBPaths(void)

CVDBTblastnApp()

Constructor, sets up the version info.

CLocalVDBBlast::SLocalVDBStruct m_localVDBStruct

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

virtual int Run(void)

Run the application.

void x_FillVDBInfo(CBlastFormatUtil::SDbInfo &vecDbInfo)

CRef< CTblastnVdbAppArgs > m_CmdLineArgs

This application's command line arguments.

CRef< CScope > x_GetScope(void)

CBlastUsageReport m_UsageReport

void x_SetupLocalVDBSearch()

const string kArgOutput

Output file name.

const string kArgDb

BLAST database name.

const string kArgNumThreads

Argument to determine the number of threads to use when running BLAST.

void Print(const CCompactSAMApplication::AlignInfo &ai)

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

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.

CNcbiEnvironment & SetEnvironment(void)

Get a non-const copy of the application's cached environment.

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.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

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

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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...

vector< CBioseq_Handle > TBioseqHandles

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

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

bool IsEnabled(void)

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

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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.

unsigned int

A callback function used to compare two keys in a database.

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.

Configuration structure for the CBlastScopeSource.

void OptimizeForWholeLargeSequenceRetrieval(bool value=true)

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

#define BLAST_SRA_UNKNOWN_ERROR

Exit code for all other errors and unknown exceptions.

#define BLAST_SRA_EXIT_SUCCESS

Exit code for successful completion of the Blast search.

#define BLAST_SRA_ENGINE_ERROR

Exit code for a Blast engine-related error.

#define BLAST_SRA_INPUT_ERROR

Exit code for a Blast input error (in query/options).

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

Defines database alias file access classes.

Declares the CLocalVDBBlast class.

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