NCBI C++ ToolKit
Classes | Functions
seqsrc_query_factory.cpp File Reference

Implementation of the BlastSeqSrc interface for a query factory. More...

#include <ncbi_pch.hpp>
#include "seqsrc_query_factory.hpp"
#include <objects/seqloc/Seq_id.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/core/blast_seqsrc_impl.h>
#include "bioseq_extract_data_priv.hpp"
#include "blast_objmgr_priv.hpp"
+ Include dependency graph for seqsrc_query_factory.cpp:

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Classes

class  CQueryFactoryInfo
 Contains information about all sequences in a set. More...
 
struct  SQueryFactorySrcNewArgs
 Encapsulates the arguments needed to initialize multi-sequence source. More...
 

Functions

 USING_SCOPE (objects)
 
static Int4 s_QueryFactoryGetMaxLength (void *multiseq_handle, void *)
 The following functions interact with the C API, and have to be declared extern "C". More...
 
static Int4 s_QueryFactoryGetMinLength (void *multiseq_handle, void *)
 Retrieves the length of the longest sequence in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetAvgLength (void *multiseq_handle, void *)
 Retrieves the average length of the sequence in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetNumSeqs (void *multiseq_handle, void *)
 Retrieves the number of sequences in the BlastSeqSrc. More...
 
static Int4 s_QueryFactoryGetNumSeqsStats (void *, void *)
 Returns zero as this implementation does not use an alias file. More...
 
static Int8 s_QueryFactoryGetTotLen (void *, void *)
 Returns 0 as total length, indicating that this is NOT a database! More...
 
static Int8 s_QueryFactoryGetTotLenStats (void *, void *)
 Returns 0 as total statistic length, as this implementation does not use alias files. More...
 
static const char * s_QueryFactoryGetName (void *, void *)
 Always returns NcbiEmptyCStr. More...
 
static Boolean s_QueryFactoryGetIsProt (void *multiseq_handle, void *)
 Answers whether this object is for protein or nucleotide sequences. More...
 
static Int2 s_QueryFactoryGetSequence (void *multiseq_handle, BlastSeqSrcGetSeqArg *args)
 Retrieves the sequence for a given index, in a given encoding. More...
 
static void s_QueryFactoryReleaseSequence (void *, BlastSeqSrcGetSeqArg *args)
 Deallocates the uncompressed sequence buffer if necessary. More...
 
static Int4 s_QueryFactoryGetSeqLen (void *multiseq_handle, void *args)
 Retrieve length of a given sequence. More...
 
static Int2 s_QueryFactoryGetNextChunk (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Mirrors the database iteration interface. More...
 
static void s_QueryFactoryResetChunkIter (void *)
 Resets the internal bookmark iterator (N/A in this case) More...
 
static Int4 s_QueryFactoryIteratorNext (void *multiseq_handle, BlastSeqSrcIterator *itr)
 Gets the next sequence index, given a BlastSeqSrc pointer. More...
 
static BlastSeqSrcs_QueryFactorySrcFree (BlastSeqSrc *seq_src)
 Multi sequence source destructor: frees its internal data structure. More...
 
static BlastSeqSrcs_QueryFactorySrcCopy (BlastSeqSrc *seq_src)
 Multi-sequence sequence source copier: creates a new reference to the CQueryFactoryInfo object and copies the rest of the BlastSeqSrc structure. More...
 
static BlastSeqSrcs_QueryFactorySrcNew (BlastSeqSrc *retval, void *args)
 Multi-sequence source constructor. More...
 
static BlastSeqSrcs_QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, const TSeqLocVector &subj_seqs, EBlastProgramType program)
 
BlastSeqSrcQueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, EBlastProgramType program)
 Initialize the sequence source structure from a query factory. More...
 
BlastSeqSrcQueryFactoryBlastSeqSrcInit (const TSeqLocVector &subj_seqs, EBlastProgramType program)
 Initialize the sequence source structure from a TSeqLocVector. More...
 

Detailed Description

Implementation of the BlastSeqSrc interface for a query factory.

Definition in file seqsrc_query_factory.cpp.

Modified on Sun Apr 14 05:26:14 2024 by modify_doxy.py rev. 669887