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.
