NCBI C++ ToolKit
Functions
blast_aux.cpp File Reference

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>
+ Include dependency graph for blast_aux.cpp:

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Functions

 USING_SCOPE (objects)
 
BlastSeqLocCSeqLoc2BlastSeqLoc (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 *, bools_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.

Modified on Wed Feb 28 07:11:55 2024 by modify_doxy.py rev. 669887