| AbstractCombinedStrand |
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| BpSeq |
RNA secondary structure in BPSEQ format.
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| BpSeq.Entry |
An entry of a BPSEQ data.
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| CombinedStrand |
A dot-bracket encoded structure made from combining one or more strands.
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| CombinedStrandFromPdb |
A dot-bracket encoded structure made from combining one or more strands.
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| Ct |
An RNA secondary structure encoded in CT (connect) format.
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| Ct.ExtendedEntry |
A single entry in the CT formatted structure.
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| DefaultConverter |
A default converter from BPSEQ to dot-bracket which iteratively (1) finds non-pseudoknots and
assigns the current lowest level, then (2) increases level and (3) treats pseudoknots as the next
input to (1) until there are base pairs without level assigned.
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| DefaultDotBracket |
A default implementation of a dot-bracket.
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| DefaultDotBracketFromPdb |
A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.
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| DefaultStrand |
A default implementation of a strand.
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| ImmutableBpSeq |
Immutable implementation of BpSeq.
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| ImmutableBpSeq.Builder |
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| ImmutableCombinedStrand |
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| ImmutableCombinedStrand.Builder |
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| ImmutableCombinedStrandFromPdb |
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| ImmutableCombinedStrandFromPdb.Builder |
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| ImmutableCt |
Immutable implementation of Ct.
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| ImmutableCt.Builder |
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| ImmutableDefaultConverter |
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| ImmutableDefaultConverter.Builder |
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| ImmutableDefaultDotBracket |
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| ImmutableDefaultDotBracket.Builder |
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| ImmutableDefaultDotBracketFromPdb |
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| ImmutableDefaultDotBracketFromPdb.Builder |
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| ImmutableDefaultStrand |
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| ImmutableDefaultStrand.Builder |
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| ImmutableEntry |
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| ImmutableEntry.Builder |
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| ImmutableExtendedEntry |
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| ImmutableExtendedEntry.Builder |
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| ImmutableMultiLineDotBracket |
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| ImmutableMultiLineDotBracket.Builder |
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| ImmutableStrandView |
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| ImmutableStrandView.Builder |
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| ImmutableTerminalMissing |
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| ImmutableTerminalMissing.Builder |
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| MultiLineDotBracket |
An extended secondary structure, which contains also non-canonical base pairs.
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| StrandView |
A strand which is defined as a fragment of a dot-bracket structure.
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| TerminalMissing |
A colecction of missing dot-bracket symbols at 5' or 3' end.
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