RetroSearch Browse

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastoptionshandle_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/blast_options_handle.cpp Source File

62

: m_DefaultsMode(

false

)

69

m_DefaultsMode(

false

)

201 "eBlastNotSet may not be used as argument"

);

216

retval.

insert

(

"blastn"

);

217

retval.

insert

(

"blastn-short"

);

218

retval.

insert

(

"megablast"

);

219

retval.

insert

(

"dc-megablast"

);

220

retval.

insert

(

"vecscreen"

);

222

retval.

insert

(

"rmblastn"

);

226

retval.

insert

(

"blastp"

);

227

retval.

insert

(

"blastp-short"

);

228

retval.

insert

(

"blastp-fast"

);

232 if

(choice ==

eAll

) {

233

retval.

insert

(

"psiblast"

);

235

retval.

insert

(

"phiblastp"

);

236

retval.

insert

(

"rpsblast"

);

237

retval.

insert

(

"rpstblastn"

);

238

retval.

insert

(

"blastx"

);

239

retval.

insert

(

"blastx-fast"

);

240

retval.

insert

(

"deltablast"

);

241

retval.

insert

(

"tblastn"

);

242

retval.

insert

(

"tblastn-fast"

);

243

retval.

insert

(

"psitblastn"

);

244

retval.

insert

(

"tblastx"

);

245

retval.

insert

(

"kblastp"

);

249

retval.

insert

(

"mapper"

);

250

retval.

insert

(

"mapr2g"

);

251

retval.

insert

(

"mapr2r"

);

252

retval.

insert

(

"mapg2g"

);

261 string

task(task_name);

265 if

(task ==

"blastn"

) {

266

retval.assign(

"Traditional BLASTN requiring an exact match of 11"

);

267

}

else if

(task ==

"blastn-short"

) {

268

retval.assign(

"BLASTN program optimized for sequences shorter than "

);

269

retval +=

"50 bases"

;

270

}

else if

(task ==

"vecscreen"

) {

271

retval.assign(

"BLASTN with several options re-set for running VecScreen"

);

272

}

else if

(task ==

"rmblastn"

) {

273

retval.assign(

"BLASTN with complexity adjusted scoring and masklevel"

);

274

retval +=

"filtering"

;

275

}

else if

(task ==

"blastp"

) {

276

retval.assign(

"Traditional BLASTP to compare a protein query to a "

);

277

retval +=

"protein database"

;

278

}

else if

(task ==

"blastp-short"

) {

279

retval.assign(

"BLASTP optimized for queries shorter than 30 residues"

);

280

}

else if

(task ==

"blastp-fast"

) {

281

retval.assign(

"BLASTP optimized for faster runtime"

);

282

}

else if

(task ==

"blastx"

) {

283

retval.assign(

"Search of a (translated) nucleotide query against a "

);

284

retval +=

"protein database"

;

285

}

else if

(task ==

"blastx-fast"

) {

286

retval.assign(

"Search of a (translated) nucleotide query against a "

);

287

retval +=

"protein database with parameters optimized for faster runtime"

;

288

}

else if

(task ==

"dc-megablast"

) {

289

retval.assign(

"Discontiguous megablast used to find more distant "

);

290

retval +=

"(e.g., interspecies) sequences"

;

291

}

else if

(task ==

"megablast"

) {

292

retval.assign(

"Traditional megablast used to find very similar "

);

293

retval +=

"(e.g., intraspecies or closely related species) sequences"

;

295

retval.assign(

"Limits BLASTP search to those subjects with a "

);

296

retval +=

"pattern matching one in the query"

;

297

}

else if

(task ==

"psiblast"

) {

298

retval.assign(

"PSIBLAST that searches a (protein) profile against "

);

299

retval +=

"a protein database"

;

300

}

else if

(task ==

"rpsblast"

) {

301

retval.assign(

"Search of a protein query against a database of motifs"

);

302

}

else if

(task ==

"rpstblastn"

) {

303

retval.assign(

"Search of a (translated) nucleotide query against "

);

304

retval.append(

"a database of motifs"

);

305

}

else if

(task ==

"tblastn"

) {

306

retval.assign(

"Search of a protein query against a (translated) "

);

307

retval +=

"nucleotide database"

;

308

}

else if

(task ==

"tblastn-fast"

) {

309

retval.assign(

"Search of a protein query against a (translated) "

);

310

retval +=

"nucleotide database with parameters optimized for faster runtime"

;

311

}

else if

(task ==

"psitblastn"

) {

312

retval.assign(

"Search of a PSSM against a (translated) "

);

313

retval +=

"nucleotide database"

;

314

}

else if

(task ==

"tblastx"

) {

315

retval.assign(

"Search of a (translated) nucleotide query against "

);

316

retval +=

"a (translated) nucleotide database"

;

317

}

else if

(task ==

"deltablast"

) {

318

retval.assign(

"DELTA-BLAST builds profile using conserved domain "

);

319

retval +=

"and uses this profile to search protein database"

;

320

}

else if

(task ==

"mapper"

) {

321

retval.assign(

"Map short reads to a genome"

);

322

}

else if

(task ==

"mapr2g"

) {

323

retval.assign(

"Map RNA-seq sequence to a genome"

);

324

}

else if

(task ==

"mapr2r"

) {

325

retval.assign(

"Map RNA-seq sequences to an mRNA database"

);

326

}

else if

(task ==

"mapg2g"

) {

327

retval.assign(

"Map genomic reads to a genome"

);

328

}

else if

(task ==

"kblastp"

) {

329

retval.assign(

"Kmer screenign followed by BLASTP"

);

331

retval.assign(

"Unknown task"

);

388 if

(task ==

"blastp-short"

) {

395

}

else if

(task ==

"blastp-fast"

) {

429 if

(task ==

"blastx-fast"

) {

442 if

(task ==

"tblastn-fast"

) {

Declares the CBlastAdvancedProteinOptionsHandle class.

Declares the BLAST exception class.

Declares the CBlastNucleotideOptionsHandle class.

#define BLAST_WORD_THRESHOLD_BLASTP_FAST

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Declares the CBlastProteinOptionsHandle class.

Declares the CBlastRPSOptionsHandle class.

EProgram

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

@ eBlastNotSet

Not yet set.

@ eVecScreen

Vector screening.

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ ePHIBlastn

Nucleotide PHI BLAST.

@ eBlastp

Protein-Protein.

@ ePHIBlastp

Protein PHI BLAST.

@ eMapper

Jumper alignment for mapping.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDeltaBlast

Delta Blast.

@ ePSITblastn

PSI Tblastn.

@ eKBlastp

KMER screening and BLASTP.

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

Declares the CBlastpKmerOptionsHandle class.

Declares the CBlastxOptionsHandle class.

Handle to the Advanced BLASTP options.

Defines BLAST error codes (user errors included)

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

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

Enumerates the possible contexts in which objects of this type can be used.

@ eRemote

To be used when running BLAST remotely.

Handle to the rpsblast options to the BLAST algorithm.

Handle to the KMER BLASTP options.

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

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

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

Handle to the nucleotide mapping options to the BLAST algorithm.

Handle to the nuclein PHI BLAST options.

Handle to the protein PHI BLAST options.

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

Handle to the options for translated nucleotide-RPS blast.

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

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

iterator_bool insert(const value_type &val)

Declares the CDeltaBlastOptionsHandle class.

Declares the CDiscNucleotideOptionsHandle class.

void SetGapExtensionCost(int e)

Sets GapExtensionCost.

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

void SetWordThreshold(double wt)

Sets WordThreshold.

virtual void SetScoringOptionsDefaults()=0

Sets ScoringOptionsDefaults.

void SetWordSize(int ws)

Sets WordSize.

EAPILocality GetLocality() const

Return the locality used when the object was created.

virtual void SetLookupTableDefaults()=0

Sets LookupTableDefaults.

void SetMatchReward(int r)

Sets MatchReward.

virtual void SetSubjectSequenceOptionsDefaults()=0

Sets SubjectSequenceOptionsDefaults.

virtual void SetGappedExtensionDefaults()=0

Sets GappedExtensionDefaults.

static string GetDocumentation(const string &task_name)

Return the documentation for the provided task.

void SetChaining(bool ch)

Enables/disables chaining.

void SetGapOpeningCost(int g)

Sets GapOpeningCost.

virtual void SetQueryOptionDefaults()=0

Sets QueryOptionDefaults.

CBlastOptionsHandle(EAPILocality locality)

Default c-tor.

CRef< CBlastOptions > m_Opts

Data type this class controls access to.

void SetVecScreenDefaults()

Sets default options for VecScreen.

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

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

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

virtual void SetRNAToGenomeDefaults()

void SetTraditionalBlastnDefaults()

Sets TraditionalBlastnDefaults.

void SetMismatchPenalty(int p)

Sets MismatchPenalty.

virtual void SetEffectiveLengthsOptionsDefaults()=0

Sets EffectiveLengthsOptionsDefaults.

bool Validate() const

Validate the options.

virtual void SetGenomeToGenomeDefaults()

static set< string > GetTasks(ETaskSets choice=eAll)

Retrieve the set of supported tasks.

void SetTraditionalMegablastDefaults()

Sets TraditionalMegablastDefaults.

void SetMatrixName(const char *matrix)

Sets MatrixName.

char * GetFilterString() const

Return the filtering string used.

void SetFilterString(const char *f, bool clear=true)

virtual void SetInitialWordOptionsDefaults()=0

Sets InitialWordOptionsDefaults.

virtual void SetRemoteProgramAndService_Blast3()=0

Set the program and service name for remote blast.

bool Validate() const

Validate the options contained in this object.

void SetDefaultsMode(bool dmode)

If this is true, remote options will ignore "Set" calls.

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

void SetWordSize(int ws)

Sets WordSize.

virtual void SetHitSavingOptionsDefaults()=0

Sets HitSavingOptionsDefaults.

virtual void SetRNAToRNADefaults()

virtual void SetDefaults()

Resets the state of the object to all default values.

void ThrowIfInvalidTask(const string &task)

Validates that the task provided is indeed a valid task, otherwise throws a CBlastException.

ETaskSets

Sets of tasks for the command line BLAST binaries.

char * GetFilterString() const

Returns FilterString.

void ClearFilterOptions()

Clears the filtering options.

void SetLookupTableType(ELookupTableType type)

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

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

@ eProtProt

Protein-protein tasks.

@ eNuclNucl

Nucleotide-nucleotide tasks.

@ eAll

Retrieve all available tasks.

@ eMapping

Mapping tasks.

#define NCBI_THROW(exception_class, err_code, message)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string & ToLower(string &str)

Convert string to lower case â string& version.

Declares the CPHIBlastNuclOptionsHandle class.

Declares the CPHIBlastProtOptionsHandle class.

Declares the CPSIBlastOptionsHandle class.

Declares the CRPSTBlastnOptionsHandle class.

Declares the CTBlastnOptionsHandle class.

Declares the CTBlastxOptionsHandle class.

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

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__options__handle_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/blast/api/blast_options_handle.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastoptionshandle_8cpp_source.html below: