NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
cn3d_blast.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <objmgr/object_manager.hpp>
#include <algo/blast/api/psibl2seq.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Score.hpp>
#include <objects/general/Object_id.hpp>
#include "remove_header_conflicts.hpp"
#include "cn3d_blast.hpp"
#include "block_multiple_alignment.hpp"
#include "cn3d_pssm.hpp"
#include "sequence_set.hpp"
#include "cn3d_tools.hpp"
#include "structure_set.hpp"
#include "molecule_identifier.hpp"
#include "asn_reader.hpp"
+ Include dependency graph for cn3d_blast.cpp:

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Classes

class  TruncatedSequence
 

Typedefs

typedef vector< CRef< TruncatedSequence > > TruncatedSequences
 

Functions

 USING_SCOPE (objects)
 
static CRef< TruncatedSequenceCreateTruncatedSequence (const BlockMultipleAlignment *multiple, const BlockMultipleAlignment *pair, int alnNum, bool isMaster, int extension)
 
static bool IsLocalID (const CSeq_id &sid, int localID)
 
static bool SeqIdMatchesMaster (const CSeq_id &sid, bool usePSSM)
 
static void MapBlockFromConsensusToMaster (int consensusStart, int dependentStart, int length, BlockMultipleAlignment *newAlignment, const BlockMultipleAlignment *multiple)
 
static void RemoveAllDataLoaders ()
 
static bool SimpleSeqLocFromBioseq (const CRef< CBioseq > &bs, CSeq_loc &seqLoc)
 
double GetStandardProbability (char ch)
 

Variables

 USING_NCBI_SCOPE
 

Typedef Documentation

◆ TruncatedSequences

typedef vector< CRef < TruncatedSequence > > TruncatedSequences

Definition at line 74 of file cn3d_blast.cpp.

Function Documentation

◆ CreateTruncatedSequence()

static CRef< TruncatedSequence > CreateTruncatedSequence ( const BlockMultipleAlignment multiple,
const BlockMultipleAlignment pair,
int  alnNum,
bool  isMaster,
int  extension 
)
static

◆ GetStandardProbability()

double GetStandardProbability ( char  ch)

◆ IsLocalID()

static bool IsLocalID ( const CSeq_id sid,
int  localID 
)
inlinestatic

◆ MapBlockFromConsensusToMaster()

static void MapBlockFromConsensusToMaster ( int  consensusStart,
int  dependentStart,
int  length,
BlockMultipleAlignment newAlignment,
const BlockMultipleAlignment multiple 
)
static

◆ RemoveAllDataLoaders()

static void RemoveAllDataLoaders ( )
static

Definition at line 236 of file cn3d_blast.cpp.

References CObjectManager::GetInstance(), ITERATE, and om.

Referenced by BLASTer::CreateNewPairwiseAlignmentsByBlast().

◆ SeqIdMatchesMaster()

static bool SeqIdMatchesMaster ( const CSeq_id sid,
bool  usePSSM 
)
inlinestatic

◆ SimpleSeqLocFromBioseq()

static bool SimpleSeqLocFromBioseq ( const CRef< CBioseq > &  bs,
CSeq_loc seqLoc 
)
static

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 60 of file cn3d_blast.cpp.

Modified on Tue May 28 05:49:56 2024 by modify_doxy.py rev. 669887