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NCBI C++ ToolKit: src/algo/blast/proteinkmer/demo/kblastp_app.cpp Source File

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kBatchSize=10000;

CBlastKmerThreadPtr *

=

CBlastKmerThreadPtr[numThreads];

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=0;

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formatThr,

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].AsBoolean());

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(

argc,

* argv[])

Produce formatted blast output for command line applications.

Interface for converting blast-related command line arguments into blast options.

Interface for reading SRA sequences into blast input.

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

Declares the CBlastProteinOptionsHandle class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

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.

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Run as separate thread and format results.

void Join()

Calls Finalize (if not already called) then CThread::Join(); Should only be called if QueueResults wi...

string GetDatabaseName() const

Get the BLAST database name.

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...

virtual void Exit(void)

Cleanup on application exit.

CRef< CKBlastpAppArgs > m_CmdLineArgs

Get the command-line arguments.

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

Class of optiosn for the KMEr search.

Threading class for BlastKmer searches.

Handle to the KMER BLASTP options.

Handles command line arguments for blastp binary.

int GetMinHits()

Number of matches in LSH phase.

int GetCandidateSeqs()

Number of sequences to attempt BLASTP on.

double GetJaccardDistance()

Obtain Jaccard distance.

Operators to edit gaps in sequences.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

CRef< CBlastOptions > Clone() const

Explicit deep copy of the Blast options object.

void SetMinHits(int minhits=1)

Sets the number of hits ot initiate calculation of Jaccard distance.

void SetCandidateSeqs(int candidates=1000)

Sets the max number of candidate matches to process with BLAST @candidates max number of target seque...

void SetThresh(double thresh=0.1)

Sets Threshold for Jaccard distance.

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.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

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

Set diagnostic stream.

void Reset(void)

Reset reference object.

bool Run(TRunMode flags=fRunDefault)

Run the thread.

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

Main argument class for KBLASTP application.

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...

Defines BLAST database access classes.

Configuration structure for the CBlastScopeSource.

CRef< CTestThread > thr[k_NumThreadsMax]

Uniform BLAST Search Interface.

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