#include <Predictor.h>
Public Member Functions | |
| Predictor (const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | |
| virtual | ~Predictor () |
| virtual void | predict (const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos))=0 |
| Z_type | getZall () const |
Static Public Member Functions | |
| static size_t | getMaxInteractionWidth (const size_t w, const size_t maxLoopSize) |
Protected Member Functions | |
| virtual void | initOptima ()=0 |
| virtual void | updateOptima (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy, const bool isHybridE, const bool incrementZall)=0 |
| virtual void | updateZall (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy, const bool isHybridE) |
| virtual void | reportOptima ()=0 |
| void | incrementZall (const Z_type partZ) |
Protected Attributes | |
| InteractionEnergyIdxOffset | energy |
| energy computation handler | |
| OutputHandler & | output |
| interaction output handler | |
| PredictionTracker * | predTracker |
| prediction tracker to be used | |
| Z_type | Zall |
Detailed Description
RNA-RNA interaction prediction handler interface.
Constructor & Destructor Documentation
◆ Predictor()
|
inline |
Constructs an RNA-RNA interaction prediction handler and sets the central data members.
- Parameters
-
energy the handler for interaction energy computation output the output handler for identified interactions predTracker the prediction tracker to be used or NULL if no tracking is to be done; if non-NULL, the tracker gets deleted on this->destruction.
◆ ~Predictor()
|
inlinevirtual |
destruction
Member Function Documentation
◆ getMaxInteractionWidth()
|
inlinestatic |
Computes the maximal width of an interaction for a given site width and maximal size of interaction loops.
- Parameters
-
w the width to compute the maximal interacting width for maxLoopSize the maximal size of loops within interactions
- Returns
- 1 + (w-1)*(maxLoopSize+1): if w>0; 0 otherwise
◆ getZall()
|
inline |
Access to the current overall partition function covering all interactions of the last predict() call.
- Returns
- the overall hybridization partition function
◆ incrementZall()
|
inlineprotected |
Increments the overall partition function Zall with the given value
- Parameters
-
partZ the increment for Zall
◆ initOptima()
|
protectedpure virtual |
Initializes the list of best solutions to be filled by updateOptima()
Implemented in IntaRNA::PredictorMfe, and IntaRNA::PredictorEvalOnly.
◆ predict()
|
pure virtual |
Computes the predictors optimization target for the given sequence ranges in the first sequence and second sequence. The according optimal interaction is given to the output handler.
- Parameters
-
r1 the index range of the first sequence interacting with r2 r2 the index range of the second sequence interacting with r1
Implemented in IntaRNA::PredictorMfe2d, IntaRNA::PredictorMfe2dHelixBlockHeuristic, IntaRNA::PredictorMfe2dHelixBlockHeuristicSeed, IntaRNA::PredictorMfe2dHeuristic, IntaRNA::PredictorMfe2dHeuristicSeed, IntaRNA::PredictorMfe2dHeuristicSeedExtension, IntaRNA::PredictorMfe2dSeed, IntaRNA::PredictorMfe2dSeedExtension, IntaRNA::PredictorMfe2dSeedExtensionRIblast, IntaRNA::PredictorMfeEns2d, IntaRNA::PredictorMfeEns2dHeuristic, IntaRNA::PredictorMfeEns2dHeuristicSeedExtension, IntaRNA::PredictorMfeEns2dSeedExtension, IntaRNA::PredictorMfeEnsSeedOnly, IntaRNA::PredictorMfeSeedOnly, IntaRNA::PredictorEvalOnly, and IntaRNA::PredictorSeedExtensionKinetic.
◆ reportOptima()
|
protectedpure virtual |
Pushes the optimal and suboptimal solutions to the output handler.
Implemented in IntaRNA::PredictorMfe, IntaRNA::PredictorMfeEns, and IntaRNA::PredictorEvalOnly.
◆ updateOptima()
|
protectedpure virtual |
Updates the global the list of best solutions found so far
- Parameters
-
i1 the index of the first sequence interacting with i2 j1 the index of the first sequence interacting with j2 i2 the index of the second sequence interacting with i1 j2 the index of the second sequence interacting with j1 energy the energy of the interaction site isHybridE whether or not the given energy is only the hybridization energy (init+loops) or the total interaction energy incrementZall whether or not Zall is to be incremented (if needed)
Implemented in IntaRNA::PredictorMfe, and IntaRNA::PredictorEvalOnly.
◆ updateZall()
|
inlineprotectedvirtual |
Updates the global Zall partition function.
Note: should not be called for interactions for which updateOptima(..,incrementZall=true) is called. Otherwise, these interactions are considered multiple times.
- Parameters
-
i1 the index of the first sequence interacting with i2 j1 the index of the first sequence interacting with j2 i2 the index of the second sequence interacting with i1 j2 the index of the second sequence interacting with j1 energy the energy of the interaction site isHybridE whether or not the given energy is only the hybridization energy (init+loops) or the total interaction energy incrementZall whether or not Zall is to be incremented (if needed)
Member Data Documentation
◆ energy
|
protected |
energy computation handler
◆ output
|
protected |
interaction output handler
◆ predTracker
|
protected |
prediction tracker to be used
◆ Zall
|
protected |
the overall partition function since initZ() was last called. its value is updated by updateZ()
The documentation for this class was generated from the following file:
- src/IntaRNA/Predictor.h
