| A | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.DNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.RNA |
| 3 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 4 (Data Constructor) | Biobase.Primary.IUPAC |
| 5 (Data Constructor) | Biobase.Primary.AA |
| AA | |
| 1 (Type/Class) | Biobase.Primary.AA, Biobase.Primary |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| aa | Biobase.Primary.AA, Biobase.Primary |
| aaChar | Biobase.Primary.AA, Biobase.Primary |
| aaDNAmap | Biobase.Primary.Trans, Biobase.Primary |
| aaDNAseq | Biobase.Primary.Trans, Biobase.Primary |
| aaRange | Biobase.Primary.AA, Biobase.Primary |
| AC | Biobase.Secondary.Basepair |
| acgt | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| acgu | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| AG | Biobase.Secondary.Basepair |
| AU | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| B | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| Basepair | Biobase.Secondary.Basepair |
| BasepairConvert | Biobase.Secondary.Convert |
| basepairConvert | Biobase.Secondary.Convert |
| bonusCC | Biobase.Secondary.Constraint, Biobase.Secondary |
| bonusTable | Biobase.Secondary.Constraint, Biobase.Secondary |
| BP | Biobase.Secondary.Basepair |
| C | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.DNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.RNA |
| 3 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 4 (Data Constructor) | Biobase.Primary.IUPAC |
| 5 (Data Constructor) | Biobase.Primary.AA |
| CA | Biobase.Secondary.Basepair |
| CC | Biobase.Secondary.Basepair |
| cdna | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| CG | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| cgnsP | Biobase.Secondary.Vienna |
| cguaP | Biobase.Secondary.Vienna |
| charAA | Biobase.Primary.AA, Biobase.Primary |
| charBaa | Biobase.Primary.AA, Biobase.Primary |
| charDEG | Biobase.Primary.IUPAC, Biobase.Primary |
| charDNA | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| charLetter | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| charRNA | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| charXNA | Biobase.Primary.Nuc.XNA, Biobase.Primary.Nuc, Biobase.Primary |
| CHH | Biobase.Secondary.Basepair |
| CHS | Biobase.Secondary.Basepair |
| CHW | Biobase.Secondary.Basepair |
| Cis | Biobase.Secondary.Basepair |
| codonListEmbedded | Biobase.Primary.Trans, Biobase.Primary |
| codonTable | Biobase.Primary.Trans, Biobase.Primary |
| cofoldStructure | Biobase.Secondary.Diagrams, Biobase.Secondary |
| Constraint | |
| 1 (Type/Class) | Biobase.Secondary.Constraint, Biobase.Secondary |
| 2 (Data Constructor) | Biobase.Secondary.Constraint, Biobase.Secondary |
| crna | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| CSH | Biobase.Secondary.Basepair |
| CSS | Biobase.Secondary.Basepair |
| CSW | Biobase.Secondary.Basepair |
| CT | Biobase.Secondary.Basepair |
| CTisomerism | Biobase.Secondary.Basepair |
| CU | Biobase.Secondary.Basepair |
| CWH | Biobase.Secondary.Basepair |
| CWS | Biobase.Secondary.Basepair |
| CWW | Biobase.Secondary.Basepair |
| D | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| d1Distance | Biobase.Secondary.Diagrams, Biobase.Secondary |
| D1S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| D1Secondary | Biobase.Secondary.Diagrams, Biobase.Secondary |
| d1sTree | Biobase.Secondary.Diagrams, Biobase.Secondary |
| d2Compare | Biobase.Secondary.Diagrams, Biobase.Secondary |
| d2Grouping | Biobase.Secondary.Diagrams, Biobase.Secondary |
| D2S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| D2Secondary | Biobase.Secondary.Diagrams, Biobase.Secondary |
| d2sTree | Biobase.Secondary.Diagrams, Biobase.Secondary |
| defaultIsostericityMap | Biobase.Secondary.Isostericity, Biobase.Secondary |
| DEG | Biobase.Primary.IUPAC, Biobase.Primary |
| degChar | Biobase.Primary.IUPAC, Biobase.Primary |
| Degenerate | Biobase.Primary.IUPAC, Biobase.Primary |
| degSeq | Biobase.Primary.IUPAC, Biobase.Primary |
| detailedCSV | Biobase.Secondary.Isostericity, Biobase.Secondary |
| DNA | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| dnaAAmap | Biobase.Primary.Trans, Biobase.Primary |
| dnaAAseq | Biobase.Primary.Trans, Biobase.Primary |
| dnaChar | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| dnaGxna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| dnaSeq | Biobase.Primary.Nuc.DNA, Biobase.Primary.Nuc, Biobase.Primary |
| dnaTrna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| dotBracket2pairlist | Biobase.Secondary.Diagrams, Biobase.Secondary |
| E | Biobase.Primary.AA |
| Edge | |
| 1 (Type/Class) | Biobase.Secondary.Basepair |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| ExtPair | Biobase.Secondary.Basepair |
| ExtPairAnnotation | Biobase.Secondary.Basepair |
| ExtPairIdx | Biobase.Secondary.Basepair |
| F | Biobase.Primary.AA |
| foldStructure | Biobase.Secondary.Diagrams, Biobase.Secondary |
| fromD1S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| fromD2S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| fromDegenerate | Biobase.Primary.IUPAC, Biobase.Primary |
| FullStructure | |
| 1 (Type/Class) | Biobase.Secondary.New |
| 2 (Data Constructor) | Biobase.Secondary.New |
| fullStructure | Biobase.Secondary.New |
| G | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.DNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.RNA |
| 3 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 4 (Data Constructor) | Biobase.Primary.IUPAC |
| 5 (Data Constructor) | Biobase.Primary.AA |
| GA | Biobase.Secondary.Basepair |
| GC | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| getBP | Biobase.Secondary.Basepair |
| getClasses | Biobase.Secondary.Isostericity, Biobase.Secondary |
| getLetter | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| getPretty | Biobase.Primary.Pretty |
| GG | Biobase.Secondary.Basepair |
| GU | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| H | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| 3 (Data Constructor) | Biobase.Secondary.Basepair |
| hash2primary | Biobase.Primary.Hashed, Biobase.Primary |
| HashedPrimary | |
| 1 (Type/Class) | Biobase.Primary.Hashed, Biobase.Primary |
| 2 (Data Constructor) | Biobase.Primary.Hashed, Biobase.Primary |
| I | Biobase.Primary.AA |
| inClass | Biobase.Secondary.Isostericity, Biobase.Secondary |
| isCanonicalStructure | Biobase.Secondary.Diagrams, Biobase.Secondary |
| isConstraintStructure | Biobase.Secondary.Diagrams, Biobase.Secondary |
| IsostericityLookup | Biobase.Secondary.Isostericity, Biobase.Secondary |
| isViennaPair | Biobase.Secondary.Vienna |
| iupacNucleotides | Biobase.Primary.IUPAC, Biobase.Primary |
| iupacXDNAchars | Biobase.Primary.IUPAC, Biobase.Primary |
| K | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| L | Biobase.Primary.AA |
| label | Biobase.Secondary.New |
| Letter | |
| 1 (Type/Class) | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| 2 (Data Constructor) | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| LetterChar | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| letterChar | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| M | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| MkConstraint | Biobase.Secondary.Constraint, Biobase.Secondary |
| mkConstraint | Biobase.Secondary.Constraint, Biobase.Secondary |
| mkD1S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| MkD1Secondary | Biobase.Secondary.Diagrams, Biobase.Secondary |
| mkD2S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| MkD2Secondary | Biobase.Secondary.Diagrams, Biobase.Secondary |
| mkHashedPrimary | Biobase.Primary.Hashed, Biobase.Primary |
| mkIsostericityList | Biobase.Secondary.Isostericity, Biobase.Secondary |
| mkIsostericityMap | Biobase.Secondary.Isostericity, Biobase.Secondary |
| MkPrimary | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| MVector | Biobase.Primary.Letter, Biobase.Primary.Hashed, Biobase.Primary.Nuc, Biobase.Secondary.Vienna, Biobase.Primary, Biobase.Secondary.Basepair |
| MV_Basepair | Biobase.Secondary.Basepair |
| MV_CTisomerism | Biobase.Secondary.Basepair |
| MV_Edge | Biobase.Secondary.Basepair |
| MV_HashedPrimary | Biobase.Primary.Hashed, Biobase.Primary |
| MV_Letter | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| MV_ViennaPair | Biobase.Secondary.Vienna |
| N | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.DNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.RNA |
| 3 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 4 (Data Constructor) | Biobase.Primary.IUPAC |
| 5 (Data Constructor) | Biobase.Primary.AA |
| nobonusCC | Biobase.Secondary.Constraint, Biobase.Secondary |
| NoBP | Biobase.Secondary.Basepair |
| NP | Biobase.Secondary.Vienna |
| NS | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| P | Biobase.Primary.AA |
| Pair | Biobase.Secondary.Basepair |
| Paired | Biobase.Secondary.New |
| PairIdx | Biobase.Secondary.Basepair |
| pairToString | Biobase.Secondary.Vienna |
| parsedCSV | Biobase.Secondary.Isostericity, Biobase.Secondary |
| parseVienna | Biobase.Secondary.New |
| pFullStructure | Biobase.Secondary.New |
| pPaired | Biobase.Secondary.New |
| Pretty | |
| 1 (Type/Class) | Biobase.Primary.Pretty |
| 2 (Data Constructor) | Biobase.Primary.Pretty |
| Primary | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| primary | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| pSubStructure | Biobase.Secondary.New |
| pUnpaired | Biobase.Secondary.New |
| Q | Biobase.Primary.AA |
| R | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| removeByCounting | Biobase.Secondary.Pseudoknots, Biobase.Secondary |
| RemovePseudoKnots | Biobase.Secondary.Pseudoknots, Biobase.Secondary |
| revPair | Biobase.Secondary.Vienna |
| RNA | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| rnaChar | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| rnaGxna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| rnaSeq | Biobase.Primary.Nuc.RNA, Biobase.Primary.Nuc, Biobase.Primary |
| rnaTdna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| S | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| 3 (Data Constructor) | Biobase.Secondary.Basepair |
| SecondaryStructure | Biobase.Secondary.Structure, Biobase.Secondary |
| SS | Biobase.Secondary.Structure, Biobase.Secondary |
| SSExtern | Biobase.Secondary.Diagrams, Biobase.Secondary |
| SSTree | |
| 1 (Type/Class) | Biobase.Secondary.Diagrams, Biobase.Secondary |
| 2 (Data Constructor) | Biobase.Secondary.Diagrams, Biobase.Secondary |
| Stop | Biobase.Primary.AA |
| StructureParseError | |
| 1 (Type/Class) | Biobase.Secondary.New |
| 2 (Data Constructor) | Biobase.Secondary.New |
| structures | Biobase.Secondary.Diagrams, Biobase.Secondary |
| SubStructure | Biobase.Secondary.New |
| subStructures | Biobase.Secondary.New |
| T | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.DNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 3 (Data Constructor) | Biobase.Primary.IUPAC |
| 4 (Data Constructor) | Biobase.Primary.AA |
| THH | Biobase.Secondary.Basepair |
| THS | Biobase.Secondary.Basepair |
| THW | Biobase.Secondary.Basepair |
| toDegenerate | Biobase.Primary.IUPAC, Biobase.Primary |
| toTree | Biobase.Secondary.New |
| Trn | Biobase.Secondary.Basepair |
| TSH | Biobase.Secondary.Basepair |
| TSS | Biobase.Secondary.Basepair |
| TSW | Biobase.Secondary.Basepair |
| TWH | Biobase.Secondary.Basepair |
| TWS | Biobase.Secondary.Basepair |
| TWW | Biobase.Secondary.Basepair |
| U | |
| 1 (Data Constructor) | Biobase.Primary.Nuc.RNA |
| 2 (Data Constructor) | Biobase.Primary.Nuc.XNA |
| 3 (Data Constructor) | Biobase.Primary.IUPAC |
| UA | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| UC | Biobase.Secondary.Basepair |
| UG | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Basepair |
| unConstraint | Biobase.Secondary.Constraint, Biobase.Secondary |
| unCT | Biobase.Secondary.Basepair |
| unD1S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| unD2S | Biobase.Secondary.Diagrams, Biobase.Secondary |
| Undef | |
| 1 (Data Constructor) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Primary.AA |
| unEdge | Biobase.Secondary.Basepair |
| unHashedPrimary | Biobase.Primary.Hashed, Biobase.Primary |
| unk | Biobase.Primary.Unknown, Biobase.Primary |
| Unknown | Biobase.Primary.Unknown, Biobase.Primary |
| Unpaired | Biobase.Secondary.New |
| unsafeDotBracket2pairlist | Biobase.Secondary.Diagrams, Biobase.Secondary |
| unViennaPair | Biobase.Secondary.Vienna |
| UU | Biobase.Secondary.Basepair |
| V | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| Vector | Biobase.Primary.Letter, Biobase.Primary.Hashed, Biobase.Primary.Nuc, Biobase.Secondary.Vienna, Biobase.Primary, Biobase.Secondary.Basepair |
| ViennaPair | |
| 1 (Type/Class) | Biobase.Secondary.Vienna |
| 2 (Data Constructor) | Biobase.Secondary.Vienna |
| viennaPairTable | Biobase.Secondary.Vienna |
| viennaStringDistance | Biobase.Secondary.Diagrams, Biobase.Secondary |
| V_Basepair | Biobase.Secondary.Basepair |
| V_CTisomerism | Biobase.Secondary.Basepair |
| V_Edge | Biobase.Secondary.Basepair |
| V_HashedPrimary | Biobase.Primary.Hashed, Biobase.Primary |
| V_Letter | Biobase.Primary.Letter, Biobase.Primary.Nuc, Biobase.Primary |
| V_ViennaPair | Biobase.Secondary.Vienna |
| W | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| 3 (Data Constructor) | Biobase.Secondary.Basepair |
| X | Biobase.Primary.AA |
| XNA | Biobase.Primary.Nuc.XNA, Biobase.Primary.Nuc, Biobase.Primary |
| xnaChar | Biobase.Primary.Nuc.XNA, Biobase.Primary.Nuc, Biobase.Primary |
| xnaSdna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| xnaSeq | Biobase.Primary.Nuc.XNA, Biobase.Primary.Nuc, Biobase.Primary |
| xnaSrna | Biobase.Primary.Nuc.Conversion, Biobase.Primary.Nuc, Biobase.Primary |
| Y | |
| 1 (Data Constructor) | Biobase.Primary.IUPAC |
| 2 (Data Constructor) | Biobase.Primary.AA |
| Z | Biobase.Primary.AA |
| _fullStructure | Biobase.Secondary.New |
| _label | Biobase.Secondary.New |
| _Paired | Biobase.Secondary.New |
| _ssAux | Biobase.Secondary.Structure, Biobase.Secondary |
| _ssExt | Biobase.Secondary.Structure, Biobase.Secondary |
| _ssSeq | Biobase.Secondary.Structure, Biobase.Secondary |
| _ssVienna | Biobase.Secondary.Structure, Biobase.Secondary |
| _ssViennaE | Biobase.Secondary.Structure, Biobase.Secondary |
| _subStructures | Biobase.Secondary.New |
| _Unpaired | Biobase.Secondary.New |