Implementation of Alignment.
More...
#include <alignment_impl.hh>
Implementation of Alignment.
Constructor as empty alignment of two sequences.
- Parameters
-
| self | self pointer |
| seqA | sequence A |
| seqB | sequence B |
| std::string LocARNA::AlignmentImpl::dot_bracket_structure |
( |
const std::string & |
str, |
|
|
const Alignment::edge_ends_t & |
x |
|
) |
| |
|
static |
dot bracket structure
- Parameters
-
| str | structure string |
| x | edge ends array |
- Returns
- structure string
| void LocARNA::AlignmentImpl::write_debug |
( |
std::ostream & |
out | ) |
const |
Write raw alignment information for debugging.
- Parameters
-
Write raw alignment information (one sequence) for debugging.
- Parameters
-
| out | output stream |
| ends | description of alignment edge ends |
first components of alignment edges
a_[i] is the position of the i-th alignment edge in seq A. Entries are positions of sequence A or -1 for gap.
Edges are sorted in ascending order.
- Note
- the contained positions define the aligned subsequence! Not necessarily all sequence positions are contained.
second components of alignment edges
b_[i] is the position of the i-th alignment edge in seq B. Entries are positions of sequence B or -1 for gap.
Edges are sorted in ascending order.
- Note
- the contained positions define the aligned subsequence! Not necessarily all sequence positions are contained.
The documentation for this class was generated from the following files:
1.8.11
