biu::AllowedBasePairs Class Reference
#include <AllowedBasePairs.hh>
Detailed Description
This class handels possible base pairs of an RNA structure.
Definition at line 18 of file AllowedBasePairs.hh.
Public Member Functions | |
| bool | allowedBasePair (const Alphabet::AlphElem &first, const Alphabet::AlphElem &second) const |
| AllowedBasePairs (const Alphabet *alphabet, const std::string &bps, const bool symmetric=true) | |
| const Alphabet * | getAlphabet () const |
| bool | operator!= (const AllowedBasePairs &abp2) const |
| bool | operator== (const AllowedBasePairs &abp2) const |
| ~AllowedBasePairs () | |
Private Types | |
| typedef std::pair< Alphabet::AlphElem, Alphabet::AlphElem > | BPair |
Private Attributes | |
| biu::Matrix< bool > | allowedPairs |
| const Alphabet * | alph |
Member Typedef Documentation
typedef std::pair<Alphabet::AlphElem, Alphabet::AlphElem> biu::AllowedBasePairs::BPair [private] |
Constructor & Destructor Documentation
| biu::AllowedBasePairs::AllowedBasePairs | ( | const Alphabet * | alphabet, | |
| const std::string & | bps, | |||
| const bool | symmetric = true | |||
| ) |
Construction
- Parameters:
-
alphabet has to be a structure alphabet for a RNA bps the allowed combinations of alphabet elements as comma separated list of alphabet element, e.g. "AU,GU". symmetric when true, it builds a symmetric matrix, so supplying AU is enough for UA to be valid as well
| biu::AllowedBasePairs::~AllowedBasePairs | ( | ) |
Member Function Documentation
| bool biu::AllowedBasePairs::allowedBasePair | ( | const Alphabet::AlphElem & | first, | |
| const Alphabet::AlphElem & | second | |||
| ) | const |
Returns if two characters form a valid base pair, e.g. a Watson-Crick (AU, CG) or a non-standard (GU) pair.
| const Alphabet* biu::AllowedBasePairs::getAlphabet | ( | ) | const |
Returns the alphabet the base pairs are basing on.
| bool biu::AllowedBasePairs::operator!= | ( | const AllowedBasePairs & | abp2 | ) | const |
| bool biu::AllowedBasePairs::operator== | ( | const AllowedBasePairs & | abp2 | ) | const |
Field Documentation
biu::Matrix< bool > biu::AllowedBasePairs::allowedPairs [private] |
Matrix of the allowed combinations of base pairs.
Definition at line 27 of file AllowedBasePairs.hh.
const Alphabet* biu::AllowedBasePairs::alph [private] |
the Alphabet the allowed base pairs are basing on
Definition at line 24 of file AllowedBasePairs.hh.
The documentation for this class was generated from the following file:
- src/biu/AllowedBasePairs.hh