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 BlastSeqSrc * | s_QueryFactorySrcFree (BlastSeqSrc *seq_src) |
| Multi sequence source destructor: frees its internal data structure. More... | |
| static BlastSeqSrc * | s_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 BlastSeqSrc * | s_QueryFactorySrcNew (BlastSeqSrc *retval, void *args) |
| Multi-sequence source constructor. More... | |
| static BlastSeqSrc * | s_QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, const TSeqLocVector &subj_seqs, EBlastProgramType program) |
| BlastSeqSrc * | QueryFactoryBlastSeqSrcInit (CRef< IQueryFactory > query_factory, EBlastProgramType program) |
| Initialize the sequence source structure from a query factory. More... | |
| BlastSeqSrc * | QueryFactoryBlastSeqSrcInit (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.
