| BestInteractionE typedef | IntaRNA::PredictorMfe | protected |
| BestInteractionZ typedef | IntaRNA::PredictorMfe | protected |
| E2dMatrix typedef | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| energy | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| fillHybridE(const size_t j1, const size_t j2, const size_t i1init, const size_t i2init, const bool callUpdateOptima) | IntaRNA::PredictorMfe2d | protectedvirtual |
| fillHybridE_left(const size_t j1, const size_t j2) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| fillHybridE_right(const size_t i1, const size_t i2) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| getMaxInteractionWidth(const size_t w, const size_t maxLoopSize) | IntaRNA::Predictor | inlinestatic |
| getNextBest(Interaction &curBest) | IntaRNA::PredictorMfe | protectedvirtual |
| getZall() const | IntaRNA::Predictor | inline |
| HashIdx2E typedef | IntaRNA::PredictorMfe | protected |
| hybridE_left | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| hybridE_pq | IntaRNA::PredictorMfe2d | protected |
| hybridE_right | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| incrementZall(const Z_type partZ) | IntaRNA::Predictor | inlineprotected |
| initOptima() | IntaRNA::PredictorMfe | 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 |
| mfe4leftEnd | IntaRNA::PredictorMfe | protected |
| mfeInteractions | IntaRNA::PredictorMfe | protected |
| output | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| parallelDropOutLength | IntaRNA::PredictorMfe2dSeedExtensionRIblast | |
| parallelExtension(ExtendedSeed &seed, const size_t max_extension1, size_t max_extension2) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protectedvirtual |
| predict(const IndexRange &r1=IndexRange(0, RnaSequence::lastPos), const IndexRange &r2=IndexRange(0, RnaSequence::lastPos)) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | virtual |
| Predictor(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::Predictor | inline |
| PredictorMfe(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::PredictorMfe | |
| PredictorMfe2d(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker) | IntaRNA::PredictorMfe2d | |
| PredictorMfe2dSeedExtensionRIblast(const InteractionEnergy &energy, OutputHandler &output, PredictionTracker *predTracker, SeedHandler *seedHandler) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | |
| predTracker | IntaRNA::PredictorMfe | protected |
| printMatrix(const E2dMatrix &matrix) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | inlineprotected |
| reportedInteractions | IntaRNA::PredictorMfe | protected |
| reportOptima() | IntaRNA::PredictorMfe | protectedvirtual |
| seedHandler | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protected |
| thoroughDropOutLength | IntaRNA::PredictorMfe2dSeedExtensionRIblast | |
| traceBack(Interaction &interaction) | IntaRNA::PredictorMfe2dSeedExtensionRIblast | protectedvirtual |
| 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) | IntaRNA::PredictorMfe | 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 |
| Zall | IntaRNA::Predictor | protected |
| ~Predictor() | IntaRNA::Predictor | inlinevirtual |
| ~PredictorMfe() | IntaRNA::PredictorMfe | virtual |
| ~PredictorMfe2d() | IntaRNA::PredictorMfe2d | virtual |
| ~PredictorMfe2dSeedExtensionRIblast() | IntaRNA::PredictorMfe2dSeedExtensionRIblast | virtual |
