biu::IntervalEnergyFunction Class Reference
#include <DistanceEnergyFunction.hh>
Inheritance diagram for biu::IntervalEnergyFunction:
Detailed Description
An distance based energy function that does a discretised energy evaluation. For each distance interval a fixed energy table is used.
Definition at line 210 of file DistanceEnergyFunction.hh.
Public Member Functions | |
| virtual size_t | addInterval (const biu::EnergyMatrix &energies, const double upperBound) |
| virtual const Alphabet *const | getAlphabet () const |
| virtual double | getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const DblPoint &cor_i, const DblPoint &cor_j) const |
| virtual double | getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const IntPoint &cor_i, const IntPoint &cor_j) const |
| virtual double | getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const double &distance) const |
| virtual size_t | getInterval (double distance) const |
| virtual const biu::EnergyMatrix *const | getIntervalMatrix (const size_t index) const |
| virtual double | getIntervalMax (const size_t index) const |
| virtual size_t | getIntervalNum (void) const |
| IntervalEnergyFunction (const IntervalEnergyFunction &toCopy) | |
| IntervalEnergyFunction (const Alphabet *const alphabet) | |
| bool | operator!= (const DistanceEnergyFunction &cef2) const |
| bool | operator== (const DistanceEnergyFunction &cef2) const |
| virtual | ~IntervalEnergyFunction () |
Protected Attributes | |
| const Alphabet *const | alphabet |
| std::vector< const biu::EnergyMatrix * > | energyMat |
| std::vector< double > | intervalMax |
Constructor & Destructor Documentation
| biu::IntervalEnergyFunction::IntervalEnergyFunction | ( | const Alphabet *const | alphabet | ) |
Creates and initialises a new distance interval energy function.
- Parameters:
-
alphabet the alphabet the energy function supports
Definition at line 107 of file DistanceEnergyFunction.cc.
| biu::IntervalEnergyFunction::IntervalEnergyFunction | ( | const IntervalEnergyFunction & | toCopy | ) |
Copy construction
- Parameters:
-
toCopy the object to copy
Definition at line 116 of file DistanceEnergyFunction.cc.
| biu::IntervalEnergyFunction::~IntervalEnergyFunction | ( | ) | [virtual] |
Definition at line 130 of file DistanceEnergyFunction.cc.
Member Function Documentation
| size_t biu::IntervalEnergyFunction::addInterval | ( | const biu::EnergyMatrix & | energies, | |
| const double | upperBound | |||
| ) | [virtual] |
Adds a contact energy matrix to the energy function that is used for distance values that are greater than the upper bound of the last added interval and smaller or equal to the given upperBound.
- Parameters:
-
energies the contact energy matrices to use for this interval NOTE: has to have the same dimensions as the used alphabet has elements! upperBound the upper distance bound of this interval. NOTE: Has to be at higher than last upper bound so far!
- Returns:
- the index of this interval, i.e. the last interval index
Definition at line 208 of file DistanceEnergyFunction.cc.
| const Alphabet *const biu::IntervalEnergyFunction::getAlphabet | ( | ) | const [virtual] |
Access to the alphabet this energy function is based on.
- Returns:
- the alphabet in use
Implements biu::DistanceEnergyFunction.
Definition at line 142 of file DistanceEnergyFunction.cc.
| double biu::IntervalEnergyFunction::getEnergy | ( | const Alphabet::AlphElem & | seq_i, | |
| const Alphabet::AlphElem & | seq_j, | |||
| const DblPoint & | cor_i, | |||
| const DblPoint & | cor_j | |||
| ) | const [virtual] |
Returns the energy contribution of two elements of the alphabet with given coordinates.
- Parameters:
-
seq_i,seq_j have to be elements of the specified alphabet. cor_i,cor_j the corresponding coordinates of the two monomers to evaluate
- Returns:
- the energy contribution
Implements biu::DistanceEnergyFunction.
Definition at line 168 of file DistanceEnergyFunction.cc.
| double biu::IntervalEnergyFunction::getEnergy | ( | const Alphabet::AlphElem & | seq_i, | |
| const Alphabet::AlphElem & | seq_j, | |||
| const IntPoint & | cor_i, | |||
| const IntPoint & | cor_j | |||
| ) | const [virtual] |
Returns the energy contribution of two elements of the alphabet with given coordinates.
- Parameters:
-
seq_i,seq_j have to be elements of the specified alphabet. cor_i,cor_j the corresponding coordinates of the two monomers to evaluate
- Returns:
- the energy contribution
Implements biu::DistanceEnergyFunction.
Definition at line 158 of file DistanceEnergyFunction.cc.
| double biu::IntervalEnergyFunction::getEnergy | ( | const Alphabet::AlphElem & | seq_i, | |
| const Alphabet::AlphElem & | seq_j, | |||
| const double & | distance | |||
| ) | const [virtual] |
Returns the energy contribution of two elements of the alphabet that are in a certain distance.
- Parameters:
-
seq_i,seq_j have to be elements of the specified alphabet. distance the distance of the two monomers to evaluate
- Returns:
- the energy contribution
Implements biu::DistanceEnergyFunction.
Definition at line 148 of file DistanceEnergyFunction.cc.
| size_t biu::IntervalEnergyFunction::getInterval | ( | double | distance | ) | const [virtual] |
Access to the interval index of a given distance.
- Parameters:
-
distance the distance to check the interval for
- Returns:
- the interval index the distance falls into OR UINT_MAX if the distance is higher than the highest distance handled
Definition at line 243 of file DistanceEnergyFunction.cc.
| const biu::EnergyMatrix *const biu::IntervalEnergyFunction::getIntervalMatrix | ( | const size_t | index | ) | const [virtual] |
Access to the energy table used for the given interval.
- Parameters:
-
index the index of the interval of intrest (has to be less than getIntervalNum())
- Returns:
- the energy table of the specified interval
Definition at line 237 of file DistanceEnergyFunction.cc.
| double biu::IntervalEnergyFunction::getIntervalMax | ( | const size_t | index | ) | const [virtual] |
Access to the upper interval bound.
- Parameters:
-
index the index of the interval of intrest (has to be less than getIntervalNum())
- Returns:
- the upper bound of the specified interval
Definition at line 231 of file DistanceEnergyFunction.cc.
| size_t biu::IntervalEnergyFunction::getIntervalNum | ( | void | ) | const [virtual] |
Access to the number of intervals in use.
- Returns:
- the number of intervals
Definition at line 226 of file DistanceEnergyFunction.cc.
| bool biu::IntervalEnergyFunction::operator!= | ( | const DistanceEnergyFunction & | cef2 | ) | const [virtual] |
| bool biu::IntervalEnergyFunction::operator== | ( | const DistanceEnergyFunction & | cef2 | ) | const [virtual] |
Field Documentation
const Alphabet* const biu::IntervalEnergyFunction::alphabet [protected] |
the alphabet that stores all allowed sequence elements
Definition at line 216 of file DistanceEnergyFunction.hh.
std::vector<const biu::EnergyMatrix*> biu::IntervalEnergyFunction::energyMat [protected] |
Contains the energy matrices in use for each interval.
Definition at line 219 of file DistanceEnergyFunction.hh.
std::vector< double > biu::IntervalEnergyFunction::intervalMax [protected] |
The documentation for this class was generated from the following files:
- src/biu/DistanceEnergyFunction.hh
- src/biu/DistanceEnergyFunction.cc