Implementation of Alignment. More...
#include <alignment_impl.hh>
Public Member Functions | |
AlignmentImpl (Alignment *self, const Sequence &seqA, const Sequence &seqB) | |
Constructor as empty alignment of two sequences. | |
void | write_debug (std::ostream &out) const |
Write raw alignment information for debugging. | |
Static Public Member Functions | |
static void | write_debug (std::ostream &out, const Alignment::edge_ends_t &ends) |
Write raw alignment information (one sequence) for debugging. | |
static std::string | dot_bracket_structure (const std::string &str, const Alignment::edge_ends_t &x) |
dot bracket structure | |
Public Attributes | |
Alignment * | self_ |
self pointer | |
const Sequence & | seqA_ |
sequence A | |
const Sequence & | seqB_ |
sequence B | |
Alignment::edge_ends_t | a_ |
first components of alignment edges | |
Alignment::edge_ends_t | b_ |
second components of alignment edges | |
std::string | strA_ |
structure of A as dot-bracket string | |
std::string | strB_ |
structure of B as dot-bracket string |
Implementation of Alignment.
LocARNA::AlignmentImpl::AlignmentImpl | ( | Alignment * | self, |
const Sequence & | seqA, | ||
const Sequence & | seqB | ||
) | [inline] |
Constructor as empty alignment of two sequences.
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
str | structure string |
x | edge ends array |
void LocARNA::AlignmentImpl::write_debug | ( | std::ostream & | out | ) | const |
Write raw alignment information for debugging.
out | output stream |
void LocARNA::AlignmentImpl::write_debug | ( | std::ostream & | out, |
const Alignment::edge_ends_t & | ends | ||
) | [static] |
Write raw alignment information (one sequence) for debugging.
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.
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.