Implements C++ wrapper classes for structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures. More...
#include <ncbi_pch.hpp>#include <objects/seqloc/Seq_id.hpp>#include <objects/seqloc/Seq_loc.hpp>#include <objects/seqloc/Seq_interval.hpp>#include <objects/seqloc/Seq_point.hpp>#include <objects/seqloc/Packed_seqint.hpp>#include <objects/seqloc/Seq_loc_mix.hpp>#include <objects/seqset/Bioseq_set.hpp>#include <objects/seqset/Seq_entry.hpp>#include <algo/blast/core/gencode_singleton.h>#include <objects/seqfeat/Genetic_code_table.hpp>#include <objects/seq/NCBIstdaa.hpp>#include <objects/seq/seqport_util.hpp>#include <algo/blast/api/blast_aux.hpp>#include <algo/blast/api/blast_options_handle.hpp>#include <algo/blast/core/blast_seqsrc_impl.h>#include <algo/blast/api/sseqloc.hpp>#include "blast_setup.hpp"#include "blast_aux_priv.hpp"#include <objects/seq/Seq_ext.hpp>#include <objects/seq/Delta_seq.hpp>#include <objects/seq/Delta_ext.hpp>#include <objmgr/seq_map_ci.hpp>#include <algorithm>#include <sstream>
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Functions | |
| USING_SCOPE (objects) | |
| BlastSeqLoc * | CSeqLoc2BlastSeqLoc (const objects::CSeq_loc *slp) |
| Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast. More... | |
| TAutoUint1ArrayPtr | FindGeneticCode (int genetic_code) |
| Retrieves the requested genetic code in Ncbistdaa format. More... | |
| DEFINE_CLASS_STATIC_FAST_MUTEX (CAutomaticGenCodeSingleton::sm_Mutex) | |
| void | ThrowIfInvalidTask (const string &task) |
| Validates that the task provided is indeed a valid task, otherwise throws a CBlastException. More... | |
| string | EProgramToTaskName (EProgram p) |
| Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries) More... | |
| EBlastProgramType | EProgramToEBlastProgramType (EProgram p) |
| Convert EProgram to EBlastProgramType. More... | |
| EProgram | ProgramNameToEnum (const std::string &program_name) |
| Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax). More... | |
| string | Blast_ProgramNameFromType (EBlastProgramType program) |
| Returns a string program name, given a blast::EBlastProgramType enumeration. More... | |
| template<class Position > | |
| CRange< Position > | Map (const CRange< Position > &target, const CRange< Position > &range) |
| static pair< BlastSeqLoc *, bool > | s_GetBlastnMask (const BlastMaskLoc *mask, unsigned int query_index) |
| Return the masked locations for a given query as well as whether the linked list's elements should be reverted or not (true in the case of negative only strand) The first element of the returned pair is the linked list of masked locations The second element of the returned pair is true if the linked list needs to be reversed. More... | |
| static void | s_ConvertBlastnMasks (const CPacked_seqint::Tdata &query_intervals, const BlastMaskLoc *mask, TSeqLocInfoVector &retval) |
| Convert EBlastTypeBlastn CORE masks into TSeqLocInfoVector. More... | |
| void | Blast_GetSeqLocInfoVector (EBlastProgramType program, const objects::CPacked_seqint &queries, const BlastMaskLoc *mask, TSeqLocInfoVector &mask_v) |
| Converts a BlastMaskLoc internal structure into an object returned by the C++ API. More... | |
| CRef< objects::CBioseq_set > | TSeqLocVector2Bioseqs (const TSeqLocVector &input) |
| Convert a TSeqLocVector to a CBioseq_set. More... | |
| bool | IsLocalId (const objects::CSeq_id *seqid) |
| Returns true if the CSeq_id is a local id. More... | |
| void | LoadSequencesToScope (CScope::TIds &ids, vector< TSeqRange > &ranges, CRef< CScope > &scope) |
Detailed Description
Implements C++ wrapper classes for structures in algo/blast/core as well as some auxiliary functions to convert CSeq_loc to/from BlastMask structures.
Definition in file blast_aux.cpp.
