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NCBI C++ ToolKit: src/algo/blast/vdb/vdbblast_local.cpp Source File

CSeq_align_set::Tdata::const_iterator input_it = input_list.begin();

CSeq_align_set::Tdata::iterator final_it = final_list.begin();

(input_it != input_list.end())

(hit_count >= list_size)

final_list.erase(final_it, final_list.end());

(final_it == final_list.end())

(input_evalue == final_evalue)

(input_evalue < final_evalue)

CSeq_align_set::Tdata::const_iterator start_input_it = input_it;

& id_prev = (*input_it)->GetSeq_id(1);

(input_it == input_list.end())

(! id_prev.

((*input_it)->GetSeq_id(1)))

final_list.insert(final_it, start_input_it, input_it);

& id_prev = (*final_it)->GetSeq_id(1);

(final_it == final_list.end())

(! id_prev.

((*final_it)->GetSeq_id(1)))

aggregate_search_result_set->

();

(

=0;

<

[0]->GetNumQueries();

++)

vector< CRef<CSearchResults> > thread_results;

&

= *(thread_results[0]->GetSeqId());

(

d=1; d < num_of_threads; d++)

thread_results.push_back ((*(

[d]))[id]);

(

d=0; d< num_of_threads; d++)

(thread_results[d]->HasAlignments())

align_set->

().insert(align_set->

().begin(),

thread_align_set->

().begin(),

thread_align_set->

().end());

aggregate_messages.

(thread_results[d]->GetErrors());

thread_results[0]->GetMaskedQueryRegions(query_mask);

thread_results[0]->GetAncillaryData(),

aggregate_search_result_set->

(aggregate_search_results);

aggregate_search_result_set;

include_filtered_reads)

isCSRA =

;

vdbUtil(isCSRA?csras:dbs,

, isCSRA, include_filtered_reads);

lcl_blast(query_factory, opt_handle, seqSrc, seqInfoSrc);

include_filtered_reads)

isCSRA =

;

psi_blast(pssm, db_adapter, psi_opts);

vector<string> & chunks,

vector<string> & chunks,

*

(

);

vector<string> & chunks,

include_filtered_reads):

m_chunks(chunks), m_include_filtered_reads(include_filtered_reads),

m_num_extensions(0), m_pssm(pssm)

vector<string> & chunks,

include_filtered_reads):

m_query_factory(query_factory), m_chunks(chunks),

m_include_filtered_reads(include_filtered_reads), m_num_extensions(0)

num_of_chunks =

.size();

vector<CRef<CSearchResultSet> >

;

(

=0;

< num_of_chunks;

++) {

include_filtered_reads):

m_query_vector(query_vector),

m_opt_handle(options),

m_total_num_seqs(local_vdb.total_num_seqs),

m_total_length(local_vdb.total_length),

m_chunks_for_thread(local_vdb.chunks_for_thread),

m_num_threads(local_vdb.chunks_for_thread.

()),

m_include_filtered_reads(include_filtered_reads)

include_filtered_reads):

m_opt_handle(options),

m_total_num_seqs(local_vdb.total_num_seqs),

m_total_length(local_vdb.total_length),

m_chunks_for_thread(local_vdb.chunks_for_thread),

m_num_threads(local_vdb.chunks_for_thread.

()),

m_include_filtered_reads(include_filtered_reads),

(

.length >

.length);

vector<vector<SSortStruct> > & out_list, vector<Uint8> & acc_size)

(

=0;

<

.size();

++)

min_index = 0;

(

j=1; j<num_threads; j++) {

(acc_size[j] < acc_size[min_index])

acc_size[min_index] +=

[

].length;

out_list[min_index].push_back(

[

]);

vector<SSortStruct> filtered_list;

(

= 0;

<

.size();

++) {

filtered_list.push_back(

[

]);

dbs_per_chunk,

)

num_seqs_count = 0;

db_count = 0;

(

=0;

<

.size();

++) {

num_seqs_count +=

[

].num_seqs;

(num_seqs_count > (

)

|| db_count >= dbs_per_chunk) {

chunks.push_back(dbs);

(

<< dbs <<

<< num_seqs_count -

[

].num_seqs);

num_seqs_count =

[

].num_seqs;

chunks.push_back(dbs);

(

<< dbs <<

<< num_seqs_count);

max_dbs_env =

.Get(

);

(max_dbs_per_chunk && max_dbs_per_chunk < dbs_per_chunk)

dbs_per_chunk = max_dbs_per_chunk;

dbs_per_chunk;

vector<string>::iterator uq = std::unique(dbs.begin(), dbs.end());

dbs.erase(uq, dbs.end());

num_dbs = dbs.size();

num_threads = (num_dbs < threads) ? num_dbs : threads;

vector <SSortStruct> p,

;

total_length = 0;

total_num_seqs = 0;

(

=0;

< num_dbs;

++) {

p[

].db_name = dbs[

];

total_length += p[

].length;

total_num_seqs += p[

].num_seqs;

openmp_exception += e.

();

(search_mode ==

) {

(

=0;

< num_dbs;

++) {

p[

].db_name = dbs[

];

[

].db_name = dbs[

];

total_length += (p[

].length +

[

].length);

total_num_seqs += (p[

].num_seqs +

[

].num_seqs);

openmp_exception += e.

();

(search_mode ==

) {

(

=0;

< num_dbs;

++) {

[

].db_name = dbs[

];

total_length +=

[

].length;

total_num_seqs +=

[

].num_seqs;

openmp_exception += e.

();

num_dbs =

.size() + p.size();

(

.size() == 0) {

(max_csra_thread != 0 && threads > max_csra_thread) {

threads = max_csra_thread;

num_threads = (num_dbs < threads) ? num_dbs : threads;

(total_num_seqs == 0){

zero_seq_err =

+

(search_mode) +

;

vector<Uint8> acc_size(num_threads, 0);

vector<vector<SSortStruct> > list_thread(num_threads);

(

=0;

< num_threads;

++) {

((search_mode !=

) && (

.size() > 0)){

vector<vector<SSortStruct> > list_thread(num_threads);

(

=0;

< num_threads;

++) {

(

=0;

< rs.

();

++)

rs[

].TrimSeqAlign(hit_list_size);

(orig_size <= 200)

(orig_size + 100);

(orig_size < 500)

(orig_size + 75);

(orig_size + 50);

(num_chunks == 1) {

vector<CRef<CSearchResultSet> >

;

(

=0;

< num_chunks;

++)

(

=0;

<

.Size();

++)

q->SetMaskedRegions(

[

]->GetMaskedRegions());

q->SetGeneticCodeId(

[

]->GetGeneticCodeId());

vector<CRef<CSearchResultSet> >

;

vector<CRef<IQueryFactory> > query_factory;

vector<CRef<CPssmWithParameters> > pssm;

thread[

]->Join(

**

(&thread_results[

]));

(thread_results[

] ==

) {

.push_back(thread_results[

]->thread_result_set);

(thread_results[

]);

Declares the CBlastNucleotideOptionsHandle class.

Defines BLAST error codes (user errors included)

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

void push_back(const value_type &element)

Add a value to the back of this container.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

bool m_include_filtered_reads

CRef< CBlastQueryVector > m_query_vector

CRef< CBlastOptionsHandle > m_opt_handle

void x_AdjustDbSize(void)

CRef< objects::CPssmWithParameters > m_pssm

static string PreprocessDBs(CLocalVDBBlast::SLocalVDBStruct &local_vdb, const string db_names, unsigned int num_threads=kDisableThreadedSearch, ESRASearchMode seach_mode=eAligned)

void x_PrepareQuery(vector< CRef< IQueryFactory > > &qf_v)

void x_PreparePssm(vector< CRef< CPssmWithParameters > > &pssm)

CLocalVDBBlast(const CLocalVDBBlast &)

static const unsigned int kDisableThreadedSearch

CRef< CSearchResultSet > RunThreadedSearch()

CRef< CSearchResultSet > Run()

unsigned int m_num_threads

vector< vector< string > > & m_chunks_for_thread

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

Search Results for All Queries.

Search Results for One Query.

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

BlastSeqSrc * GetSRASeqSrc()

Return the stored SRA BlastSeqSrc object.

static Uint4 GetMaxNumCSRAThread(void)

static void GetVDBStats(const string &strAllRuns, Uint8 &num_seqs, Uint8 &length, bool getRefStats=false)

Fucntion to get around the OID (blastseqsrc) limit So num of seqs > int4 can be returned.

static bool IsCSRA(const string &db_name)

CRef< blast::IBlastSeqInfoSrc > GetSRASeqInfoSrc()

Return the SRA BlastSeqInfoSrc object (create if none exists).

static void GetAllStats(const string &strAllRuns, Uint8 &num_seqs, Uint8 &length, Uint8 &ref_num_seqs, Uint8 &ref_length)

CVDBThread(const CVDBThread &)

void * Main(void)

Derived (user-created) class must provide a real thread function.

CRef< CBlastOptionsHandle > m_opt_handle

CRef< CSearchResultSet > RunTandemSearches(void)

CRef< CPssmWithParameters > m_pssm

CVDBThread & operator=(const CVDBThread &)

CRef< IQueryFactory > m_query_factory

vector< string > m_chunks

bool m_include_filtered_reads

CVDBThread(CRef< IQueryFactory > query_factory, vector< string > &chunks, CRef< CBlastOptions > options, bool include_filtered_reads)

Collection of masked regions for a single query sequence.

Class for the messages for an individual query sequence.

static bool DLIST_NAME() in_list(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

void SetHitlistSize(int s)

CRef< CSearchResultSet > Run()

Executes the search.

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

int GetHitlistSize() const

CBlastOptions & SetOptions()

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

void SetDbSeqNum(unsigned int n)

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

size_type size() const

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

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 push_back(value_type &element)

Add a value to the back of this container.

void Combine(const TQueryMessages &other)

Combine other messages with these.

void clear()

Clears the contents of this object.

Int4 GetNumExtensions()

Retrieve the number of extensions performed during the search.

Int8 GetEffectiveSearchSpace() const

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

#define MSerial_AsnBinary

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

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

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#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 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.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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

Convert string to unsigned int.

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

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

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines NCBI C++ exception handling.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Multi-threading – mutexes; rw-locks; semaphore.

Multi-threading – classes, functions, and features.

Defines: CTimeFormat - storage class for time format.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

Declares the CPSIBlastOptionsHandle class.

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Complete type definition of Blast Sequence Source ADT.

vector< vector< string > > chunks_for_thread

CRef< CSearchResultSet > thread_result_set

Declares the CTBlastnOptionsHandle class.

const string k_CSRA_CHUNK("CSRA_CHUNK: ")

CRef< CSearchResultSet > s_RunLocalVDBSearch(const string &dbs, CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opt_handle, Int4 &num_extensions, bool include_filtered_reads)

void s_TrimResults(CSearchResultSet &rs, int hit_list_size)

static CRef< CSearchResultSet > s_CombineSearchSets(vector< CRef< CSearchResultSet > > &t, unsigned int num_of_threads, const int list_size)

static void s_DivideDBsForThread(unsigned int num_threads, vector< SSortStruct > &in_list, vector< vector< SSortStruct > > &out_list, vector< Uint8 > &acc_size)

static void s_GetChunksForThread(vector< SSortStruct > &in_list, vector< string > &chunks, const unsigned int dbs_per_chunk, const string tag)

static const unsigned int DEFAULT_MAX_DBS_PER_CHUNK

static const unsigned int DEFAULT_MAX_DBS_OPEN

static void s_RemoveNonCSRAEntry(vector< SSortStruct > &in_list)

static int s_GetModifiedHitlistSize(const int orig_size)

CRef< CBlastQueryVector > s_CloneBlastQueryVector(const CBlastQueryVector &orig)

static bool s_SortDbSize(const SSortStruct &a, const SSortStruct &b)

const string k_NOT_CSRA_DB("NOT_CSRA")

static unsigned int s_GetNumDbsPerChunk(unsigned int num_threads, unsigned int num_dbs)

CRef< CSearchResultSet > s_RunPsiVDBSearch(const string &dbs, CRef< CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > opt_handle, bool include_filtered_reads)

static void s_MergeAlignSet(CSeq_align_set &final_set, const CSeq_align_set &input_set, const int list_size)

Declares the CLocalVDBBlast class.

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