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

* overlap_sz_str = getenv(

);

(

<< retval);

(

<< retval);

concatenated_query_length,

concatenated_query_length,

concatenated_query_length, num_queries)) {

(

);

num_chunks = 0;

chunk_size_delta = ((*chunk_size) %

);

num_chunks = concatenated_query_length / ((*chunk_size) - overlap_size);

(num_chunks <= 1) {

*

= (concatenated_query_length + (num_chunks - 1) * overlap_size) / num_chunks;

(

<< num_chunks <<

<< target_chunk_size <<

(total_length <= 0)

num_seqs, total_length,

vector<Int8> eff_searchsp;

(

index = 0; index <= (size_t)qinfo->

; index++) {

seqsrc, num_threads);

(setup_data->m_QuerySplitter->IsQuerySplit() ==

);

setup_data->m_InternalData->m_FnInterrupt = full_data->

;

setup_data->m_InternalData;

(

= 0;

< kNumChunks;

++) {

(query_chunk_factories ==

|| options ==

) {

(

= 0;

< kNumChunks;

++) {

ctx <= chunk_qinfo->last_context;

++) {

context_in_chunk)

absolute_context)

vector<int>::const_iterator itr = find(context_indices.begin(),

context_indices.end(),

(itr == context_indices.end()) {

(itr - context_indices.begin());

context_in_chunk)

retval = curr_chunk;

(--curr_chunk;

(curr_chunk) >= 0; --curr_chunk) {

(retval);

<< endl <<

<< kNumChunks << endl;

(

= 0;

< kNumChunks;

++) {

<<

<<

<<

(

= 0;

< kNumChunks;

++) {

<<

<<

<<

(

= 0;

< kNumChunks;

++) {

(vector<size_t>, itr, query_indices) {

global_query_indices.

(*itr);

(retval);

vector<size_t>::const_iterator itr =

(

)global_query_index);

retval =

(

);

User-defined methods of the data storage class.

Auxiliary functions for BLAST.

SBlastProgress * SBlastProgressNew(void *user_data)

Allocates and initializes a new SBlastProgress structure.

#define CODON_LENGTH

Codons are always of length 3.

Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p)

Returns true if program is PHI-BLAST (i.e.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Boolean Blast_SubjectIsPssm(EBlastProgramType p)

Returns true if the subject is PSSM.

Int4 Blast_GetQueryIndexFromContext(Int4 context, EBlastProgramType program)

Given a context from BLAST engine core, return the query index.

Int8 BlastSeqSrcGetTotLenStats(const BlastSeqSrc *seq_src)

Get the total length of all sequences for calculation of expect value etc.

BlastSeqSrc * BlastSeqSrcCopy(const BlastSeqSrc *seq_src)

Copy function: needed to guarantee thread safety.

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined construct...

Int4 BlastSeqSrcGetNumSeqsStats(const BlastSeqSrc *seq_src)

Get the number of sequences used for calculation of expect values etc.

void BlastSeqSrcResetChunkIterator(BlastSeqSrc *seq_src)

Reset the internal "bookmark" of the last chunk for iteration provided by this object.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

Encapsulates ALL the BLAST algorithm's options.

Auxiliary class to provide convenient and efficient access to conversions between contexts local to q...

Auxiliary class to compute the effective search space.

Wrapper class for SBlastProgress .

Wrapper class around SSplitQueryBlk structure.

iterator_bool insert(const value_type &val)

static const int chunk_size

Declares auxiliary class to calculate the effective search space.

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

main entry point for tests

vector< vector< int > > m_StartingChunks

CQueryDataPerChunk(const CSplitQueryBlk &sqb, EBlastProgramType program, CRef< ILocalQueryData > local_query_data)

Constructor.

void SplitQuery_SetEffectiveSearchSpace(CRef< CBlastOptions > options, CRef< IQueryFactory > full_query_fact, CRef< SInternalData > full_data)

this might supercede the function below...

size_t SplitQuery_GetOverlapChunkSize(EBlastProgramType program)

Size of the region that overlaps in between each query chunk.

CRef< SBlastSetupData > BlastSetupPreliminarySearchEx(CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, size_t num_threads)

Extended interface to set up internal data structures used by the BLAST CORE engine.

vector< vector< int > > m_ContextsPerChunk

Each element in this vector represents a chunk, and it contains the contexts numbers that correspond ...

int GetLastChunk(int global_query_index)

get the last chunk where query identified with global_query_index is found

CRef< TBlastSeqSrc > m_SeqSrc

The source of subject sequence data.

size_t GetNumChunks() const

Retrieve the number of chunks.

int GetAbsoluteContext(size_t chunk_num, Int4 context_in_chunk) const

Get the context number in the absolute (i.e.

Int8 GetEffSearchSpaceForContext(size_t ctx_index) const

Retrieve the effective search space calculated for a given query context.

void SetEffectiveSearchSpace(Int8 eff)

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

CRef< SInternalData > SplitQuery_CreateChunkData(CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CRef< SInternalData > full_data, size_t num_threads)

Function used by search class to retrieve a query factory for a given chunk.

ostream & operator<<(ostream &out, const CContextTranslator &rhs)

SBlastProgress * Get() const

size_t GetQueryLength(size_t chunk_num, int context_in_chunk) const

Get the length of the query.

vector< size_t > m_QueryLengths

Lengths of the queries.

vector< int > m_LastChunkForQueryCache

Lists the last chunk where the query can be found.

CStructWrapper< BlastSeqSrc > TBlastSeqSrc

CRef< TBlastScoreBlk > m_ScoreBlk

BLAST score block structure.

CContextTranslator(const CSplitQueryBlk &sqb, vector< CRef< IQueryFactory > > *query_chunk_factories=NULL, const CBlastOptions *options=NULL)

Constructor.

TInterruptFnPtr m_FnInterrupt

The interrupt callback.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

CRef< CSBlastProgress > m_ProgressMonitor

The user data structure to aid in progress monitoring.

BlastQueryInfo * m_QueryInfo

The query information structure.

size_t x_ContextInChunkToQueryIndex(int context_in_chunk) const

Convert a context in a chunk to a query index (within the chunk)

int GetContextInChunk(size_t chunk_num, int absolute_context) const

Get the context number in the split query chunk.

vector< size_t > GetQueryIndices(size_t chunk_num) const

Get the indices of the queries contained in a given chunk.

EBlastProgramType m_Program

BLAST program type.

vector< vector< int > > m_AbsoluteContexts

int GetStartingChunk(size_t curr_chunk, Int4 context_in_chunk) const

Get the chunk number where context_in_chunk starts (i.e.

virtual size_t GetSeqLength(size_t index)=0

Get the length of the sequence indicated by index.

bool SplitQuery_ShouldSplit(EBlastProgramType program, size_t chunk_size, size_t concatenated_query_length, size_t num_queries)

Determines if the input query sequence(s) should be split because it.

vector< int > GetQueryContexts(size_t chunk_num) const

Get the contexts of the queries contained in a given chunk.

Uint4 SplitQuery_CalculateNumChunks(EBlastProgramType program, size_t *chunk_size, size_t concatenated_query_length, size_t num_queries)

Calculate the number of chunks that a query will be split into based upon query length,...

string s_PrintVector(const vector< T > &data2print)

Auxiliary function to print a vector.

Int8 GetEffectiveSearchSpace() const

vector< vector< size_t > > m_QueryIndicesPerChunk

Each element in this vector represents a chunk, and it contains the query indices that correspond in ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Reset(void)

Reset reference object.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

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

Convert string to int.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

const Int4 kInvalidContext

Value to represent an invalid context.

Auxiliary functions and classes to assist in query splitting.

The query related information.

Int4 first_context

Index of the first element of the context array.

Int4 last_context

Index of the last element of the context array.

Complete type definition of Blast Sequence Source ADT.

Progress monitoring structure.

void * user_data

Pointer to user-provided data.

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