NCBI C++ ToolKit
Classes
hit.hpp File Reference

Interface for CHit class, used to encapsulate operations involving pairwise alignments. More...

#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/gapinfo.h>
#include <algo/align/nw/nw_aligner.hpp>
#include <algo/cobalt/base.hpp>
#include <algo/cobalt/seq.hpp>
#include <algo/cobalt/traceback.hpp>
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Classes

class  CHit
 A generalized representation of a pairwise alignment. More...
 

Detailed Description

Interface for CHit class, used to encapsulate operations involving pairwise alignments.

Given an alignment with its traceback, this class can
compute subsets of the alignment from subsets of the traceback.
This can sometimes be tricky; for example, given an alignment
described by

                      11111
traceback   012345678901234

query   10  AAAAA---AAAAAAA 21
subject 50  AAAAAAAAA--AAAA 62

the traceback is in the range 0 to 14, the query range is 10 to 21,
and the subject range is 50 to 62. For a subject range of [50,54] the
query range is [10,14]. However, a subject range of [50,56] still has
a query range of [10,14]. Some other examples:

 start with        of        compute        of
 -------------   -------    -------------   -----
 query range     [12,15]    subject range   [52,58]
 query range     [15,16]    subject range   [58,59]
 subject range   [55,56]    query range     [15,14] <- inverted!

In general, query ranges and subject ranges are assumed to exclude 
gaps at either end of the range. For scoring purposes, the traceback 
range is what's specified, as this is unambiguous.

Definition in file hit.hpp.

Modified on Wed Jun 12 11:12:26 2024 by modify_doxy.py rev. 669887