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

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Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

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

Interface for reading SRA sequences into blast input.

Interface for converting sources of sequence data into blast sequence input.

Declares the CBlastNucleotideOptionsHandle class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

Declares the CBlastProteinOptionsHandle class.

Definitions of special type used in BLAST.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ eBlastp

Protein-Protein.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

void ProcessCommandLineArgs(CRef< CBlastOptionsHandle > opts_handle)

Modify BLAST options from defaults based upon command-line args.

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

Class representing a text file containing sequences in fasta format.

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...

TSeqLocVector GetAllSeqLocs(CScope &scope)

Read and convert all the sequences from the source.

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

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

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.

Search Results for All Queries.

Class for the messages for an individual query sequence.

std::ofstream out("events_result.xml")

main entry point for tests

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

CRef< CSearchResultSet > Run()

Executes the search.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

bool Validate() const

Validate the options contained in this object.

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

@ eBlastDbIsNucleotide

nucleotide

@ eBlastDbIsProtein

protein

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

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

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define MSerial_AsnText

I/O stream manipulators –.

const string AsFastaString(void) const

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

Main class to perform a BLAST search on the local machine.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Definition of SSeqLoc structure.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

Uniform BLAST Search Interface.

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