| addExtensionProbabilityRoot(size_t i1, size_t j1, size_t i2, size_t j2, Z_type partZ, bool left, bool right) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| addSeedPartition(Interaction::BasePair seed, Interaction::BasePair left, Interaction::BasePair right, Z_type hybridZ) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| beginExtensionProbabilitySeed(size_t i1, size_t i2) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| BestInteractionE typedef | IntaRNA::PredictorMfe | protected |
| BestInteractionZ typedef | IntaRNA::PredictorMfe | protected |
| commitExtensionProbabilities() | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| E_right_opt | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| energy | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| exactBoundaryWeight(size_t i1, size_t j1, size_t i2, size_t j2) const | IntaRNA::PredictorMfeEns2dSeedExtension | protectedvirtual |
| exactContribution | IntaRNA::PredictorMfeEns | protected |
| extensionProbabilityTrace | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| extensionSeedPrefix(size_t i1, size_t i2, size_t before) const | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| fillHybridZ_left(const size_t j1, const size_t j2) override | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protectedvirtual |
| fillHybridZ_right(const size_t i1, const size_t i2, const size_t si1, const size_t si2) | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protectedvirtual |
| IntaRNA::PredictorMfeEns2dSeedExtension::fillHybridZ_right(const size_t i1, const size_t i2) | IntaRNA::PredictorMfeEns2dSeedExtension | protectedvirtual |
| finishExtensionProbabilitySeed() | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| getMaxInteractionWidth(const size_t w, const size_t maxLoopSize) | IntaRNA::Predictor | inlinestatic |
| getNextBest(Interaction &curBest) | IntaRNA::PredictorMfe | protectedvirtual |
| getNonOverlappingEnergy(const size_t si1, const size_t si2, const size_t sj1, const size_t sj2) | IntaRNA::PredictorMfeEns2dSeedExtension | protectedvirtual |
| getZall() const | IntaRNA::Predictor | inline |
| HashIdx2E typedef | IntaRNA::PredictorMfe | protected |
| hybridZ_left | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| hybridZ_right | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| incrementZall(const Z_type partZ) | IntaRNA::Predictor | inlineprotected |
| initExtensionProbabilities(size_t n, size_t m) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| initOptima() override | IntaRNA::PredictorMfe | protectedvirtual |
| initSeedCandidates() | IntaRNA::PredictorMfe | protected |
| initZ() | IntaRNA::PredictorMfeEns | protectedvirtual |
| InteractionList typedef | IntaRNA::PredictorMfe | protected |
| isValidOutputSite(const size_t i1, const size_t j1, const size_t i2, const size_t j2) const | IntaRNA::PredictorMfe | protected |
| j1opt | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| j2opt | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| mfe4leftEnd | IntaRNA::PredictorMfe | protected |
| mfeInteractions | IntaRNA::PredictorMfe | protected |
| output | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| ownedSeedCandidates | IntaRNA::PredictorMfe | protected |
| pairProbabilities | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| perSeedPass | IntaRNA::PredictorMfe | protected |
| predict(const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos)) override | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | virtual |
| Predictor(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::Predictor | inline |
| PredictorMfe(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::PredictorMfe | |
| PredictorMfeEns(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::PredictorMfeEns | |
| PredictorMfeEns2dHeuristicSeedExtension(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker, SeedHandler *seedHandler, BasePairProbabilities *pairProbabilities=nullptr) | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | |
| PredictorMfeEns2dSeedExtension(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker, SeedHandler *seedHandler, BasePairProbabilities *pairProbabilities=nullptr) | IntaRNA::PredictorMfeEns2dSeedExtension | |
| predictPerSeed(const IndexRange &r1, const IndexRange &r2, SeedHandlerIdxOffset &seeds, const std::function< Predictor *(OutputHandler &, PredictionTracker *, SeedHandler *)> &factory) | IntaRNA::PredictorMfe | protectedvirtual |
| predictStackSeeds(const IndexRange &r1, const IndexRange &r2) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| predTracker | IntaRNA::PredictorMfeEns | protected |
| prepareStackSeedExtensions(size_t n, size_t m, const StackSeedDomain &seeds) override | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protectedvirtual |
| printMatrix(const Z2dMatrix &matrix) | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| reportedInteractions | IntaRNA::PredictorMfe | protected |
| reportOptima() override | IntaRNA::PredictorMfeEns | protectedvirtual |
| seedCandidates | IntaRNA::PredictorMfe | protected |
| seedHandler | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| selectingStackSeedRight | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| stackSeedRight | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protected |
| stackSeedRightSelector() const override | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | protectedvirtual |
| traceBack(Interaction &interaction) override | IntaRNA::PredictorMfeEns2dSeedExtension | protectedvirtual |
| updateCompleteZ(const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Z_type partFunct, const bool isHybridZ) | IntaRNA::PredictorMfeEns | protected |
| updateExactCompleteZ(size_t i1, size_t j1, size_t i2, size_t j2, Z_type hybrid, Z_type coefficient) | IntaRNA::PredictorMfeEns | protected |
| updateMfe4leftEnd(const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Interaction &curInteraction) | IntaRNA::PredictorMfe | protectedvirtual |
| 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) override | IntaRNA::PredictorMfe | protectedvirtual |
| updateOptRightZ(const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type hybridE) | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | inlineprotectedvirtual |
| updateZ(const size_t i1, const size_t j1, const size_t i2, const size_t j2, const Z_type partFunct, const bool isHybridZ) | IntaRNA::PredictorMfeEns | protectedvirtual |
| updateZall(const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type energy, const bool isHybridE) | IntaRNA::Predictor | inlineprotectedvirtual |
| updateZisComplete | IntaRNA::PredictorMfeEns | protected |
| Z2dMatrix typedef | IntaRNA::PredictorMfeEns2dSeedExtension | protected |
| Z_partition | IntaRNA::PredictorMfeEns | protected |
| Zall | IntaRNA::Predictor | protected |
| ~Predictor() | IntaRNA::Predictor | inlinevirtual |
| ~PredictorMfe() override | IntaRNA::PredictorMfe | virtual |
| ~PredictorMfeEns() override | IntaRNA::PredictorMfeEns | virtual |
| ~PredictorMfeEns2dHeuristicSeedExtension() override | IntaRNA::PredictorMfeEns2dHeuristicSeedExtension | virtual |
| ~PredictorMfeEns2dSeedExtension() override | IntaRNA::PredictorMfeEns2dSeedExtension | virtual |
