Interface for the traceback from blast hits. More...

#include <algo/cobalt/traceback.hpp>

Classes
struct	STracebackOp
	Runlength-encoded representation of a traceback operation. More...

Public Member Functions
	CEditScript ()
	Generate empty traceback. More...

	CEditScript (GapEditScript *blast_tback)
	Generate traceback from a blast alignment. More...

	CEditScript (const objects::CDense_seg &denseg)
	Generate traceback from a Dense_seg. More...

	CEditScript (const objects::CDense_diag &dendiag)
	Generate traceback from a Dense_diag. More...

	~CEditScript ()
	Destructor. More...

bool	Empty ()
	Test whether edit script is empty. More...

void	ReverseEditScript ()
	Reverse an edit script; insertions become deletions and vice versa. More...

CEditScript	MakeEditScript (TRange tback_range)
	Return an edit script corresponding to a subset of the complete traceback available. More...

void	FindOffsetFromSeq2 (TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq2_target, TOffset &new_tback, bool go_past_seq1_gap)
	Given a subject offset, find the corresponding query offset. More...

void	FindOffsetFromSeq1 (TOffsetPair start_offsets, TOffsetPair &new_offsets, TOffset seq1_target, TOffset &new_tback, bool go_past_seq2_gap)
	Given a query offset, find the corresponding subject offset. More...

int	GetScore (TRange tback_range, TOffsetPair start_offsets, CSequence &seq1, int **seq2_pssm, int gap_open, int gap_extend)
	Compute the score associated with (a portion of) an alignment Assumes that seq1 is a sequence and that seq2 is a PSSM. More...

vector< TOffsetPair >	ListMatchRegions (TOffsetPair start_offsets)
	Compile a list of regions in the current edit script that contain substitutions. More...

void	VerifyScript (TRange seq1_range, TRange seq2_range)
	Validate that the alignment described by the CEditScript has the same size for each sequence as the input ranges. More...

Static Public Member Functions
static CEditScript	MakeEditScript (const CNWAligner::TTranscript &tback, TRange tback_range)
	Convert a CNWAligner edit script to a CEditScript. More...

Private Types
typedef vector< STracebackOp >	TScriptOps
	Edit script type. More...

Private Member Functions
void	AddOps (EGapAlignOpType op_type, int num_ops)
	Add a new edit operation to the current list. More...

Private Attributes
TScriptOps	m_Script
	The list of edit operations in the current edit script. More...

Detailed Description

Interface for the traceback from blast hits.

Definition at line 54 of file traceback.hpp.

Member Typedef Documentation

◆ TScriptOps

typedef vector<STracebackOp> CEditScript::TScriptOps

private

Edit script type.

Definition at line 205 of file traceback.hpp.

Constructor & Destructor Documentation

◆ CEditScript() [1/4]

CEditScript::CEditScript ( )

inline

Generate empty traceback.

Definition at line 59 of file traceback.hpp.

◆ CEditScript() [2/4]

CEditScript::CEditScript ( GapEditScript * blast_tback )

Generate traceback from a blast alignment.

Parameters

blast_tback Edit script for the alignment, computed by the blast engine [in]

Definition at line 68 of file traceback.cpp.

References _ASSERT, AddOps(), i, GapEditScript::num, GapEditScript::op_type, and GapEditScript::size.

◆ CEditScript() [3/4]

CEditScript::CEditScript ( const objects::CDense_seg & denseg )

Generate traceback from a Dense_seg.

Parameters

denseg Dense_seg representing a single pairwise alignment [in]

◆ CEditScript() [4/4]

CEditScript::CEditScript ( const objects::CDense_diag & dendiag )

Generate traceback from a Dense_diag.

Parameters

dendiag Dense_diag representing a single ungapped pairwise alignment [in]

◆ ~CEditScript()

CEditScript::~CEditScript ( )

inline

Destructor.

Definition at line 80 of file traceback.hpp.

Member Function Documentation

◆ AddOps()

void CEditScript::AddOps	(	EGapAlignOpType	op_type,
		int	num_ops
	)

private

Add a new edit operation to the current list.

Parameters

op_type	Type of new operation [in]
num_ops	The number of such operations [in]

Definition at line 47 of file traceback.cpp.

References CEditScript::STracebackOp::num_ops, and CEditScript::STracebackOp::op_type.

Referenced by CEditScript(), and MakeEditScript().

◆ Empty()

bool CEditScript::Empty ( )

inline

Test whether edit script is empty.

Returns: true if there are no edit operations in the script

Definition at line 85 of file traceback.hpp.

◆ FindOffsetFromSeq1()

void CEditScript::FindOffsetFromSeq1	(	TOffsetPair	start_offsets,
		TOffsetPair &	new_offsets,
		TOffset	seq1_target,
		TOffset &	new_tback,
		bool	go_past_seq2_gap
	)

Given a query offset, find the corresponding subject offset.

Parameters

start_offsets	The sequence offsets corresponding to the start of the edit script [in]
new_offsets	The offsets into the unaligned sequences where the specified query offset occurs [out]
seq1_target	The query offset to find [in]
new_tback	The offset of the traceback operation where where seq1_target was found [out]
go_past_seq2_gap	If seq1_target aligns with a gap in seq2, include the gap if true [in]

Definition at line 270 of file traceback.cpp.

References _ASSERT, eGapAlignDel, eGapAlignSub, and m_Script.

Referenced by CHit::GetRangeFromSeq1().

◆ FindOffsetFromSeq2()

void CEditScript::FindOffsetFromSeq2	(	TOffsetPair	start_offsets,
		TOffsetPair &	new_offsets,
		TOffset	seq2_target,
		TOffset &	new_tback,
		bool	go_past_seq1_gap
	)

Given a subject offset, find the corresponding query offset.

Parameters

start_offsets	The sequence offsets corresponding to the start of the edit script [in]
new_offsets	The offsets into the unaligned sequences where the specified subject offset occurs [out]
seq2_target	The subject offset to find [in]
new_tback	The offset of the traceback operation where where seq2_target was found [out]
go_past_seq1_gap	If seq2_target aligns with a gap in seq1, include the gap if true [in]

Definition at line 196 of file traceback.cpp.

References _ASSERT, eGapAlignDel, eGapAlignSub, and m_Script.

Referenced by CHit::GetRangeFromSeq2().

◆ GetScore()

int CEditScript::GetScore	(	TRange	tback_range,
		TOffsetPair	start_offsets,
		CSequence &	seq1,
		int **	seq2_pssm,
		int	gap_open,
		int	gap_extend
	)

Compute the score associated with (a portion of) an alignment Assumes that seq1 is a sequence and that seq2 is a PSSM.

Parameters

tback_range	The starting and ending traceback operation of the sub-alignment to score [in]
start_offsets	The sequence offsets of the beginning of the region described by the CEditScript [in]
seq1	The complete first sequence [in]
seq2_pssm	PSSM representing the second sequence [in]
gap_open	Penalty for opening a gap [in]
gap_extend	Penalty for extending a gap [in]

Returns: The score of the (sub-)alignment given by tback_range

Definition at line 343 of file traceback.cpp.

References _ASSERT, eGapAlignDel, eGapAlignIns, eGapAlignSub, COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CSequence::GetLetter(), CRange_Base::GetTo(), i, m_Script, and min().

Referenced by CHit::ResolveSubHitConflicts(), and CMultiAligner::x_RealignBlocks().

◆ ListMatchRegions()

vector< TOffsetPair > CEditScript::ListMatchRegions ( TOffsetPair start_offsets )

Compile a list of regions in the current edit script that contain substitutions.

Parameters

start_offsets The sequence offsets corresponding to the start of the range described by the CEditScript [in]

Returns: List of regions within the CEditScript that contain substitutions

Definition at line 444 of file traceback.cpp.

References eGapAlignDel, eGapAlignIns, eGapAlignSub, and m_Script.

Referenced by CMultiAligner::x_AssignRPSResFreqs(), and CMultiAligner::x_FindInClusterConstraints().

◆ MakeEditScript() [1/2]

CEditScript CEditScript::MakeEditScript	(	const CNWAligner::TTranscript &	tback,
		TRange	tback_range
	)

static

Convert a CNWAligner edit script to a CEditScript.

Parameters

tback	The edit script generated by CNWAligner [in]
tback_range	The portion of the traceback desired. The starting and ending offsets in this range will also be included in the traceback structure returned [in]

Returns: The subset of the traceback

Definition at line 111 of file traceback.cpp.

References _ASSERT, AddOps(), eGapAlignDel, eGapAlignIns, eGapAlignSub, COpenRange< Position >::Empty(), CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CRange_Base::GetFrom(), CRange_Base::GetTo(), and i.

◆ MakeEditScript() [2/2]

CEditScript CEditScript::MakeEditScript ( TRange tback_range )

Return an edit script corresponding to a subset of the complete traceback available.

Parameters

tback_range The portion of the traceback desired. The starting and ending offsets in this range will also be included in the traceback structure returned [in]

Returns: The subset of the traceback

Definition at line 153 of file traceback.cpp.

References _ASSERT, AddOps(), COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), m_Script, and min().

Referenced by CHit::ResolveSubHitConflicts(), and CMultiAligner::x_RealignBlocks().

◆ ReverseEditScript()

void CEditScript::ReverseEditScript ( )

inline

Reverse an edit script; insertions become deletions and vice versa.

Definition at line 90 of file traceback.hpp.

References eGapAlignDel, eGapAlignIns, and i.

Referenced by CHitList::MakeCanonical().

◆ VerifyScript()

void CEditScript::VerifyScript	(	TRange	seq1_range,
		TRange	seq2_range
	)

Validate that the alignment described by the CEditScript has the same size for each sequence as the input ranges.

Parameters

seq1_range	Start/stop offsets of the first sequence [in]
seq2_range	Start/stop offsets of the second sequence [in]

Definition at line 475 of file traceback.cpp.

References _ASSERT, eGapAlignDel, eGapAlignIns, eGapAlignSub, COpenRange< Position >::GetLength(), i, int, and m_Script.

Referenced by CHit::VerifyHit().

Member Data Documentation

◆ m_Script

TScriptOps CEditScript::m_Script

private

The list of edit operations in the current edit script.

Definition at line 208 of file traceback.hpp.

Referenced by FindOffsetFromSeq1(), FindOffsetFromSeq2(), GetScore(), ListMatchRegions(), MakeEditScript(), and VerifyScript().

The documentation for this class was generated from the following files:

include/algo/cobalt/traceback.hpp
src/algo/cobalt/traceback.cpp

Classes

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ TScriptOps

Constructor & Destructor Documentation

◆ CEditScript() [1/4]

◆ CEditScript() [2/4]

◆ CEditScript() [3/4]

◆ CEditScript() [4/4]

◆ ~CEditScript()

Member Function Documentation

◆ AddOps()

◆ Empty()

◆ FindOffsetFromSeq1()

◆ FindOffsetFromSeq2()

◆ GetScore()

◆ ListMatchRegions()

◆ MakeEditScript() [1/2]

◆ MakeEditScript() [2/2]

◆ ReverseEditScript()

◆ VerifyScript()

Member Data Documentation

◆ m_Script