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

55 if

(file_deleter.

Exists

()) {

71 bool

is_remote

bool

use_default

72 string

task_name

bool

mt_mode

)

86 char

* batch_sz_str = getenv(

"BATCH_SIZE"

);

89 _TRACE

(

"DEBUG: Using query batch size "

<< retval);

99 if

(! use_default)

return

101 if

(task_name ==

""

)

125 if

(task_name ==

"blastx-fast"

&& mt_mode ==

true

)

141 _TRACE

(

"Using query batch size "

<< retval);

147 const char

* error_prefix

)

149 static const char

* kDfltErrorPrefix =

"Failed to parse sequence range"

;

150 static const string

kDelimiters(

"-"

);

151 string

error_msg(error_prefix ? error_prefix : kDfltErrorPrefix);

153

vector<string> tokens;

155 if

(tokens.size() != 2 || tokens.front().empty() || tokens.back().empty()) {

156

error_msg +=

" (Format: start-stop)"

;

161 if

(from <= 0 || to <= 0) {

162

error_msg +=

" (range elements cannot be less than or equal to 0)"

;

166

error_msg +=

" (range cannot be empty)"

;

170

error_msg +=

" (start cannot be larger than stop)"

;

183 const char

* error_prefix

)

185 static const char

* kDfltErrorPrefix =

"Failed to parse sequence range"

;

186 static const string

kDelimiters(

"-"

);

187 string

error_msg(error_prefix ? error_prefix : kDfltErrorPrefix);

189

vector<string> tokens;

191 if

(tokens.front().empty()) {

192

error_msg +=

" (start cannot be empty)"

;

200 if

(!tokens.back().empty()) {

203 if

(from <= 0 || to <= 0) {

204

error_msg +=

" (range elements cannot be less than or equal to 0)"

;

208

error_msg +=

" (start cannot be larger than stop)"

;

226 bool

use_lcase_masking,

238 if

(!read_proteins && gaps_to_Ns) {

245

sequences =

input

->GetAllSeqs(*scope);

256 const TSeqPos

kResetSeqNumMax = 1000;

257 const TSeqPos

kResetSeqNum250 = 250;

259 if

(num_descriptions) {

260

*num_descriptions = max_target_seqs;

261

warnings +=

"Number of descriptions overridden to "

;

266

warnings += (warnings.empty() ?

"Number "

", number "

);

267

warnings +=

"of overview alignments overridden to "

;

270 if

(num_alignments) {

271 bool

overridden =

false

;

272 TSeqPos

halfHits = max_target_seqs/2;

274

*num_alignments = max_target_seqs;

277 else if

(halfHits < kResetSeqNum250) {

281 else if

(halfHits <= kResetSeqNumMax) {

282

*num_alignments = halfHits;

286

*num_alignments = kResetSeqNumMax;

290

warnings += (warnings.empty() ?

"Number "

", number "

);

291

warnings +=

"of alignments overridden to "

;

295 if

( !warnings.empty() ) {

309

bioseq.GetLength() == 0)

311 else if

(bioseq.GetInst().CanGetSeq_data() ==

true

)

313 else if

(bioseq.GetInst().IsSetExt())

319

bioseq.GetInst().GetExt().GetDelta().Get()) {

336 if

(sequences.

Empty

() || sequences->

Empty

()) {

340

vector<string> empty_sequence_ids;

341 bool

all_empty =

true

;

344 if

((*query)->GetLength() == 0) {

346

push_back((*query)->GetQuerySeqLoc()->GetId()->AsFastaString());

354 "Query contains no sequence data"

);

357 if

(!empty_sequence_ids.empty())

359

warnings.assign(

"The following sequences had no sequence data:"

);

360

warnings += empty_sequence_ids.front();

361 for

(

TSeqPos i

= 1;

< empty_sequence_ids.size();

++) {

362

warnings +=

", "

+ empty_sequence_ids[

];

372 if

(sequences.empty()) {

376

vector<string> empty_sequence_ids;

377 bool

all_empty =

true

;

382

push_back(

query

->seqloc->GetId()->AsFastaString());

390 "Query contains no sequence data"

);

393 if

(!empty_sequence_ids.empty())

395

warnings.assign(

"The following sequences had no sequence data:"

);

396

warnings += empty_sequence_ids.front();

397 for

(

TSeqPos i

= 1;

< empty_sequence_ids.size();

++) {

398

warnings +=

", "

+ empty_sequence_ids[

];

408 if

(sequences.

Empty

()) {

412

vector<string> empty_sequence_ids;

413 bool

all_empty =

true

;

417 if

(!itr->IsSetLength() || itr->GetLength() == 0) {

419

push_back(itr->GetFirstId()->AsFastaString());

427 "Query contains no sequence data"

);

430 if

(!empty_sequence_ids.empty())

432

warnings.assign(

"The following sequences had no sequence data:"

);

433

warnings += empty_sequence_ids.front();

434 for

(

TSeqPos i

= 1;

< empty_sequence_ids.size();

++) {

435

warnings +=

", "

+ empty_sequence_ids[

];

User-defined methods of the data storage class.

Declares the BLAST exception class.

Interface for reading SRA sequences into blast input.

bool HasRawSequenceData(const objects::CBioseq &bioseq)

Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field.

TSeqRange ParseSequenceRange(const string &range_str, const char *error_prefix)

Parse and extract a sequence range from argument provided to this function.

int GetQueryBatchSize(EProgram program, bool is_ungapped, bool is_remote, bool use_default, string task_name, bool mt_mode)

Retrieve the appropriate batch size for the specified task.

TSeqRange ParseSequenceRangeOpenEnd(const string &range_str, const char *error_prefix)

Parse and extract a sequence range from argument provided to this function.

void CheckForEmptySequences(CRef< CBlastQueryVector > sequences, string &warnings)

Inspect the sequences parameter for empty sequences.

string CalculateFormattingParams(TSeqPos max_target_seqs, TSeqPos *num_descriptions, TSeqPos *num_alignments, TSeqPos *num_overview)

Calculates the formatting parameters based on the maximum number of target sequences selected (a....

CRef< CScope > ReadSequencesToBlast(CNcbiIstream &in, bool read_proteins, const TSeqRange &range, bool parse_deflines, bool use_lcase_masking, CRef< CBlastQueryVector > &sequences, bool gaps_to_Ns)

Read sequence input for BLAST.

Auxiliary classes/functions for BLAST input library.

EProgram

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

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

@ eMapper

Jumper alignment for mapping.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eBlastx

Translated nucl-Protein.

CNcbiOstream * GetStream()

Retrieve the newly opened stream, caller doesn't own the return value.

unique_ptr< CNcbiOstream > m_FileStream

The output stream.

string m_FileName

The file's name.

int m_Version

File version if larger than zero.

static bool IsEmptyBioseq(const CBioseq &bioseq)

Returns true if the Bioseq contained in the seq_entry is empty (i.e.

Defines BLAST error codes (user errors included)

Class representing a text file containing sequences in fasta format.

Class that centralizes the configuration data for sequences to be converted.

void SetConvertGapsToNs(bool val)

Turn on/off converting gaps to Ns in read FASTA sequences.

void SetLowercaseMask(bool mask)

Turn lowercase masking on/off.

void SetSubjectLocalIdMode()

Append subject-specific prefix codes to all generated local ids.

void SetRange(const TSeqRange &r)

Set range for all sequences.

void SetBelieveDeflines(bool believe)

Turn parsing of sequence IDs on/off.

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

bool Empty() const

Returns true if this query vector is empty.

Defines user input exceptions.

Template class for iteration on objects of class C (non-medifiable version)

const TSeqPos kDfltArgMaxTargetSequences

Default maximum number of target sequences, to be used only on the web.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

virtual bool Exists(void) const

Check existence of file.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

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

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

bool Empty(void) const THROWS_NONE

Check if CRef is empty â not pointing to any object, which means having a null value.

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetTo(TTo value)

Assign a value to To data member.

list< CRef< CDelta_seq > > Tdata

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_virtual

no seq data

@ e_Loc

point to a sequence

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

Main argument class for PSI-BLAST application.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastinputaux_8cpp_source.html below: