#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:

Go to the SVN repository for this file.

Classes
class	TruncatedSequence

Typedefs
typedef vector< CRef< TruncatedSequence > >	TruncatedSequences

Functions
	USING_SCOPE (objects)

static CRef< TruncatedSequence >	CreateTruncatedSequence (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

Definition at line 76 of file cn3d_blast.cpp.

References BlockMultipleAlignment::alignDependentFrom, BlockMultipleAlignment::alignDependentTo, BlockMultipleAlignment::alignMasterFrom, BlockMultipleAlignment::alignMasterTo, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), BlockMultipleAlignment::GetMaster(), BlockMultipleAlignment::GetSequenceOfRow(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), LookupNCBIStdaaNumberFromCharacter(), CRef< C, Locker >::Reset(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), and TRACEMSG.

Referenced by BLASTer::CreateNewPairwiseAlignmentsByBlast().

◆ GetStandardProbability()

double GetStandardProbability ( char ch )

Definition at line 575 of file cn3d_blast.cpp.

References BLAST_GetStandardAaProbabilities(), BLASTAA_SIZE, ERROR_MESSAGE, ERRORMSG, f, i, LookupCharacterFromNCBIStdaaNumber(), sfree, toupper(), WARNING_MESSAGE, and WARNINGMSG.

◆ IsLocalID()

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

inlinestatic

Definition at line 154 of file cn3d_blast.cpp.

References CObject_id_Base::GetId(), CSeq_id_Base::GetLocal(), CObject_id_Base::GetStr(), NStr::IntToString(), CObject_id_Base::IsId(), CSeq_id_Base::IsLocal(), and CObject_id_Base::IsStr().

Referenced by BLASTer::CreateNewPairwiseAlignmentsByBlast(), and SeqIdMatchesMaster().

◆ MapBlockFromConsensusToMaster()

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