Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCEditScript.html below:
NCBI C++ ToolKit: CEditScript Class Reference
Search Toolkit Book for CEditScript
Interface for the traceback from blast hits. More...
#include <algo/cobalt/traceback.hpp>
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...
Interface for the traceback from blast hits.
Definition at line 54 of file traceback.hpp.
◆ TScriptOps ◆ CEditScript() [1/4] CEditScript::CEditScript ( ) inline ◆ CEditScript() [2/4] ◆ 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 ◆ AddOps() ◆ 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()
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()
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()
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() ◆ MakeEditScript() [1/2]
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] ◆ ReverseEditScript() void CEditScript::ReverseEditScript ( ) inline ◆ VerifyScript() void CEditScript::VerifyScript ( TRange seq1_range, TRange seq2_range ) ◆ m_Script
The documentation for this class was generated from the following files:
RetroSearch is an open source project built by @garambo
| Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4