| addSeeds(Interaction &i) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| areLoopOverlapping(const size_t i1, const size_t i2, const size_t k1, const size_t k2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| deleteOnDestruction | IntaRNA::SeedHandlerIdxOffset | protected |
| energy | IntaRNA::SeedHandler | protected |
| energyIdxOffset | IntaRNA::SeedHandlerIdxOffset | protected |
| fillSeed(const size_t i1, const size_t j1, const size_t i2, const size_t j2) | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getConstraint() const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getInteractionEnergy() const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getOffset1() const | IntaRNA::SeedHandlerIdxOffset | inline |
| getOffset2() const | IntaRNA::SeedHandlerIdxOffset | inline |
| getOriginalSeedHandler() | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getSeedE(const size_t i1, const size_t i2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getSeedLength1(const size_t i1, const size_t i2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| getSeedLength2(const size_t i1, const size_t i2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| idxOffset1 | IntaRNA::SeedHandlerIdxOffset | protected |
| idxOffset2 | IntaRNA::SeedHandlerIdxOffset | protected |
| isFeasibleSeedBasePair(const size_t i1, const size_t i2, const bool atEndOfSeed=false) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| isSeedBound(const size_t i1, const size_t i2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| seedConstraint | IntaRNA::SeedHandler | protected |
| seedConstraintOffset | IntaRNA::SeedHandlerIdxOffset | protected |
| SeedHandler(const InteractionEnergy &energy, const SeedConstraint &seedConstraint) | IntaRNA::SeedHandler | inline |
| SeedHandlerIdxOffset(SeedHandler *seedHandler, const bool deleteOnDestruction=true) | IntaRNA::SeedHandlerIdxOffset | inline |
| seedHandlerOriginal | IntaRNA::SeedHandlerIdxOffset | protected |
| setOffset1(size_t offset1) | IntaRNA::SeedHandlerIdxOffset | inline |
| setOffset2(size_t offset2) | IntaRNA::SeedHandlerIdxOffset | inline |
| traceBackSeed(Interaction &interaction, const size_t i1, const size_t i2) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| updateToNextSeed(size_t &i1, size_t &i2, const size_t i1min=0, const size_t i1max=RnaSequence::lastPos, const size_t i2min=0, const size_t i2max=RnaSequence::lastPos) const | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
| ~SeedHandler() | IntaRNA::SeedHandler | inlinevirtual |
| ~SeedHandlerIdxOffset() | IntaRNA::SeedHandlerIdxOffset | inlinevirtual |
