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NCBI C++ ToolKit: src/app/igblast/igblastp_app.cpp Source File

db_is_remote =

;

blastdb.

(&(*(ig_opts->

[0])));

db_is_remote =

;

blastdb_full.

(&(*blastdb));

blastdb_full.

(&(*blastdb));

vector<CBlastFormatUtil::SDbInfo> db_info;

CBlastFormatUtil::GetBlastDbInfo(db_info, blastdb_full->

(),

lcl_blast(

, blastdb, opts_hndl, ig_opts, scope);

(

argc,

* argv[]

)

Produce formatted blast output for command line applications.

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.

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.

#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.

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.

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

CRef< IQueryFactory > GetSubjects(objects::CScope *scope=NULL)

Retrieve subject sequences, if provided.

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 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.

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

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.

@ eFlatQueryAnchoredNoIdentities

@ eFlatQueryAnchoredIdentities

Flat query anchored no identities.

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?

void AddIgSequenceScope(CRef< objects::CScope > scope)

CRef< CIgBlastOptions > GetIgBlastOptions()

Keeps track of the version of IgBLAST in the NCBI C++ toolkit.

Handles command line arguments for igblastp binary.

CRef< CIgBlastArgs > GetIgBlastArgs() const

virtual int GetQueryBatchSize() const

@inheritDoc

virtual int Run()

@inheritDoc

CRef< CIgBlastpAppArgs > m_CmdLineArgs

This application's command line args.

virtual void Init()

@inheritDoc

CBlastUsageReport m_UsageReport

CIgBlastpApp()

@inheritDoc

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

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.

void Print(const CCompactSAMApplication::AlignInfo &ai)

int GetDbGeneticCode() const

string GetDatabaseName() const

Returns the database name if appropriate, else kEmptyStr for subject sequences.

CRef< CSearchResultSet > Run()

Run the Ig-BLAST engine.

CRef< CLocalDbAdapter > m_Db[5]

void SetNumberOfThreads(size_t nthreads)

Set MT mode.

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.

const char * GetMatrixName() const

@ eBlastDbIsProtein

protein

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.

@ 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.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

int32_t Int4

4-byte (32-bit) signed integer

bool IsEnabled(void)

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

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

Main argument class for IGBLASTP application.

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.

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