Uses of Class pl.poznan.put.structure.formats.BpSeq (BioCommons 3.0.4 API)

Packages that use BpSeq
Package	Description
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.structure.formats
pl.poznan.put.structure.pseudoknots	Package contains classes that handle pseudoknots in secondary structure.
pl.poznan.put.structure.pseudoknots.dp	A set of dynamic programming solutions to pseudoknot detection.s
pl.poznan.put.structure.pseudoknots.elimination

Uses of BpSeq in pl.poznan.put.structure

Methods in pl.poznan.put.structure that return BpSeq
Modifier and Type	Method	Description
`static BpSeq`	CanonicalStructureExtractor.`bpSeq(ResidueCollection residueCollection)`	Extracts the canonical secondary structure from the 3D data and outputs it in BPSEQ format.

Uses of BpSeq in pl.poznan.put.structure.formats

Subclasses of BpSeq in pl.poznan.put.structure.formats
Modifier and Type	Class	Description
`class`	`ImmutableBpSeq`	Immutable implementation of `BpSeq`.

Methods in pl.poznan.put.structure.formats that return BpSeq
Modifier and Type	Method	Description
`static BpSeq`	BpSeq.`fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)`	Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.
`static BpSeq`	BpSeq.`fromCt(Ct ct)`	Converts RNA secondary structure in CT format to BPSEQ format.
`static BpSeq`	BpSeq.`fromDotBracket(DotBracket db)`	Converts RNA secondary structure in dot-bracket format to BPSEQ format.
`static BpSeq`	BpSeq.`fromString(String data)`	Parses string into an instance of this class.
`BpSeq`	BpSeq.`withoutIsolatedPairs()`	Finds all isolated base pairs and creates a copy of this instance without them.
`BpSeq`	BpSeq.`withoutPair(BpSeq.Entry entry)`	Creates a copy of this instance, but with the given pair removed.

Methods in pl.poznan.put.structure.formats with parameters of type BpSeq
Modifier and Type	Method	Description
`DotBracket`	Converter.`convert(BpSeq bpSeq)`	Converts the secondary structure from BPSEQ to dot-bracket format.
`DotBracket`	DefaultConverter.`convert(BpSeq bpSeq)`	Converts the secondary structure in BPSEQ format to dot-bracket.
`static ImmutableBpSeq`	ImmutableBpSeq.`copyOf(BpSeq instance)`	Creates an immutable copy of a `BpSeq` value.
`ImmutableBpSeq.Builder`	ImmutableBpSeq.Builder.`from(BpSeq instance)`	Fill a builder with attribute values from the provided `BpSeq` instance.
`static Ct`	Ct.`fromBpSeq(BpSeq bpSeq)`	Converts RNA secondary structure in BPSEQ format to CT format.
`static Ct`	Ct.`fromBpSeqAndPdbModel(BpSeq bpSeq, PdbModel model)`	Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).

Uses of BpSeq in pl.poznan.put.structure.pseudoknots

Methods in pl.poznan.put.structure.pseudoknots that return types with arguments of type BpSeq
Modifier and Type	Method	Description
`List<BpSeq>`	PseudoknotFinder.`findPseudoknots(BpSeq bpSeq)`	Finds pseudoknots in BPSEQ data.

Methods in pl.poznan.put.structure.pseudoknots with parameters of type BpSeq
Modifier and Type	Method	Description
`static List<Region>`	Region.`createRegions(BpSeq bpSeq)`	Creates a list of regions from a secondary structure in BPSEQ format.
`List<BpSeq>`	PseudoknotFinder.`findPseudoknots(BpSeq bpSeq)`	Finds pseudoknots in BPSEQ data.

Uses of BpSeq in pl.poznan.put.structure.pseudoknots.dp

Methods in pl.poznan.put.structure.pseudoknots.dp that return types with arguments of type BpSeq
Modifier and Type	Method	Description
`List<BpSeq>`	DynamicProgrammingAll.`findPseudoknots(BpSeq bpSeq)`

Methods in pl.poznan.put.structure.pseudoknots.dp with parameters of type BpSeq
Modifier and Type	Method	Description
`List<BpSeq>`	DynamicProgrammingAll.`findPseudoknots(BpSeq bpSeq)`

Uses of BpSeq in pl.poznan.put.structure.pseudoknots.elimination

Methods in pl.poznan.put.structure.pseudoknots.elimination that return types with arguments of type BpSeq
Modifier and Type	Method	Description
`List<BpSeq>`	AbstractRegionRemover.`findPseudoknots(BpSeq bpSeq)`	Finds pseudoknots by removing one region at a time until there are any conflicts.

Methods in pl.poznan.put.structure.pseudoknots.elimination with parameters of type BpSeq
Modifier and Type	Method	Description
`List<BpSeq>`	AbstractRegionRemover.`findPseudoknots(BpSeq bpSeq)`	Finds pseudoknots by removing one region at a time until there are any conflicts.