A row in a multiple alignment.
More...
#include <multiple_alignment.hh>
A row in a multiple alignment.
pair of a name string and a sequence string; support projections
- See also
- MultipleAlignment
LocARNA::MultipleAlignment::SeqEntry::SeqEntry |
( |
const std::string & |
name, |
|
|
const std::string & |
seq |
|
) |
| |
|
inline |
Construct from strings name and seq.
- Parameters
-
- Note
- empty description
LocARNA::MultipleAlignment::SeqEntry::SeqEntry |
( |
const std::string & |
name, |
|
|
const string1 & |
seq |
|
) |
| |
|
inline |
Construct from strings name and 1-based string seq.
- Parameters
-
- Note
- empty description
LocARNA::MultipleAlignment::SeqEntry::SeqEntry |
( |
const std::string & |
name, |
|
|
const std::string & |
description, |
|
|
const std::string & |
seq |
|
) |
| |
|
inline |
Construct from strings name, description and seq.
- Parameters
-
LocARNA::MultipleAlignment::SeqEntry::SeqEntry |
( |
const std::string & |
name, |
|
|
const std::string & |
description, |
|
|
const string1 & |
seq |
|
) |
| |
|
inline |
Construct from strings name, description and 1-based string seq.
- Parameters
-
map alignment column -> sequence positions
- Note
- time O(len)
- Parameters
-
col | column index in aligmnent |
- Returns
- pair of positions (pos1,pos2) if column col contains a non-gap, then pos1=pos2 is the position of the gap if column col contains a gap, then pos1 is the sequence position left of the gap or 0 and pos2 the position right of the gap or sequence length+1
map sequence position -> alignment column.
- Note
- time O(len)
- Parameters
-
pos | position in sequence (without gaps) as marginal cases: pos 0 maps to 0 and a too large position maps to length+1 |
void LocARNA::MultipleAlignment::SeqEntry::push_back |
( |
char |
c | ) |
|
|
inline |
append character to sequence
- Parameters
-
The documentation for this class was generated from the following files: