Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastinput__demo_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/blastinput/demo/blastinput_demo.cpp Source File

(

);

(

);

(

);

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddKey(

,

,

,

arg_desc->SetConstraint(

,

arg_desc->AddDefaultKey(

,

,

,

(*query)->GetScope());

<<

<<

.

() <<

<< endl;

<<

<< (is_prot ?

:

) <<

collect_stats = args[

].AsBoolean();

is_prot =

(args[

].AsString() ==

);

->AddQueryBatch(*query_batch);

cerr <<

<< exptn.

() << endl;

}

(

exception& e) {

cerr <<

<< e.what() << endl;

cerr <<

<< endl;

(

argc,

* argv[])

Interface for reading SRA sequences into blast input.

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

Auxiliary classes/functions for BLAST input library.

int GetQueryBatchSize(EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)

Retrieve the appropriate batch size for the specified task.

EProgram

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

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

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

Class representing a text file containing sequences in fasta format.

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

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...

size_type size() const

Identical to Size, provided to facilitate STL-style iteration.

Class whose purpose is to create CScope objects which have data loaders added with different prioriti...

CRef< objects::CScope > NewScope()

Create a new, properly configured CScope.

unsigned int GetNumQueries() const

Uint8 GetNumLetters() const

unsigned int m_NumBatches

void PrintReport(CNcbiOstream &out, bool is_prot, CStopWatch &sw) const

void AddQueryBatch(const CBlastQueryVector &query_batch)

unsigned int GetNumBatches() const

unsigned int m_NumQueries

Constant declarations for command line arguments for BLAST programs.

const string kArgOutput

Output file name.

const string kDfltArgQuery

Default value for query sequence input.

const string kArgQuery

Query sequence(s)

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

main entry point for tests

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.

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.

@ fHideLogfile

Hide log file description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

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

Set diagnostic stream.

TErrCode GetErrCode(void) const

Get error code.

const string & GetMsg(void) const

Get message string.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

uint64_t Uint8

8-byte (64-bit) unsigned integer

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

string AsString(const CTimeFormat &fmt=kEmptyStr) const

Transform stopwatch time to string.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

Configuration structure for the CBlastScopeSource.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4