Uses of Class
pl.poznan.put.structure.DotBracketSymbol

Packages that use DotBracketSymbol

Package	Description
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.structure.formats

Uses of DotBracketSymbol in pl.poznan.put.structure

Subclasses of DotBracketSymbol in pl.poznan.put.structure

Modifier and Type	Class	Description
final class	ImmutableDotBracketSymbol	Immutable implementation of DotBracketSymbol.

Methods in pl.poznan.put.structure with parameters of type DotBracketSymbol

Modifier and Type	Method	Description
final int	DotBracketSymbol.compareTo(DotBracketSymbol t)
static ImmutableDotBracketSymbol	ImmutableDotBracketSymbol.copyOf(DotBracketSymbol instance)	Creates an immutable copy of a DotBracketSymbol value.
final ImmutableDotBracketSymbol.Builder	ImmutableDotBracketSymbol.Builder.from(DotBracketSymbol instance)	Fill a builder with attribute values from the provided DotBracketSymbol instance.

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

Methods in pl.poznan.put.structure.formats that return DotBracketSymbol

Modifier and Type	Method	Description
final DotBracketSymbol	CombinedStrandFromPdb.symbol(PdbResidueIdentifier residueIdentifier)
final DotBracketSymbol	DefaultDotBracketFromPdb.symbol(PdbResidueIdentifier residueIdentifier)
DotBracketSymbol	DotBracketFromPdb.symbol(PdbResidueIdentifier residueIdentifier)	Maps the given residue identifier to its corresponding dot-bracket symbol.

Methods in pl.poznan.put.structure.formats that return types with arguments of type DotBracketSymbol

Modifier and Type	Method	Description
protected abstract Map<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.inputSymbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.inputSymbolToResidue()
default Set<DotBracketSymbol>	DotBracket.isolatedSymbols()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.mapping()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.mapping()
default List<DotBracketSymbol>	DotBracket.missingInternal()
Map<DotBracketSymbol,DotBracketSymbol>	CombinedStrand.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	CombinedStrand.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	CombinedStrandFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	CombinedStrandFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	DefaultDotBracket.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	DefaultDotBracket.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	DefaultDotBracketFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	DefaultDotBracketFromPdb.pairs()
default Map<DotBracketSymbol,DotBracketSymbol>	DotBracket.pairs()
default Map<DotBracketSymbol,DotBracketSymbol>	DotBracket.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableCombinedStrand.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableCombinedStrand.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableCombinedStrandFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableCombinedStrandFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableDefaultDotBracket.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableDefaultDotBracket.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableDefaultDotBracketFromPdb.pairs()
Map<DotBracketSymbol,DotBracketSymbol>	ImmutableDefaultDotBracketFromPdb.pairs()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	DefaultDotBracketFromPdb.residueToSymbol()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	ImmutableDefaultDotBracketFromPdb.residueToSymbol()
List<DotBracketSymbol>	AbstractCombinedStrand.symbols()
List<DotBracketSymbol>	CombinedStrand.symbols()
List<DotBracketSymbol>	CombinedStrandFromPdb.symbols()
abstract List<DotBracketSymbol>	DefaultStrand.symbols()
List<DotBracketSymbol>	DotBracket.symbols()
List<DotBracketSymbol>	ImmutableCombinedStrand.symbols()
List<DotBracketSymbol>	ImmutableCombinedStrandFromPdb.symbols()
List<DotBracketSymbol>	ImmutableDefaultStrand.symbols()
List<DotBracketSymbol>	ImmutableStrandView.symbols()
List<DotBracketSymbol>	ImmutableTerminalMissing.symbols()
List<DotBracketSymbol>	StrandView.symbols()
abstract List<DotBracketSymbol>	TerminalMissing.symbols()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	DefaultDotBracketFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableDefaultDotBracketFromPdb.symbolToResidue()

Methods in pl.poznan.put.structure.formats with parameters of type DotBracketSymbol

Modifier and Type	Method	Description
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addSymbols(DotBracketSymbol element)	Adds one element to symbols list.
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addSymbols(DotBracketSymbol... elements)	Adds elements to symbols list.
final ImmutableTerminalMissing.Builder	ImmutableTerminalMissing.Builder.addSymbols(DotBracketSymbol element)	Adds one element to symbols list.
final ImmutableTerminalMissing.Builder	ImmutableTerminalMissing.Builder.addSymbols(DotBracketSymbol... elements)	Adds elements to symbols list.
default Strand	DotBracket.findStrand(DotBracketSymbol symbol)	Finds a strand which contains the given symbol.
final PdbResidueIdentifier	CombinedStrandFromPdb.identifier(DotBracketSymbol symbol)
final PdbResidueIdentifier	DefaultDotBracketFromPdb.identifier(DotBracketSymbol symbol)
PdbResidueIdentifier	DotBracketFromPdb.identifier(DotBracketSymbol symbol)	Maps the given dot-bracket symbol to its corresponding residue identifier.
default boolean	DotBracket.isIsolated(DotBracketSymbol symbol)	Checks if a symbol is isolated, i.e., if it is a pairing symbol and both it and its pair are surrounded by unpaired residues.
final int	CombinedStrandFromPdb.originalIndex(DotBracketSymbol symbol)
final int	DefaultDotBracketFromPdb.originalIndex(DotBracketSymbol symbol)
default int	DotBracket.originalIndex(DotBracketSymbol symbol)	Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putInputSymbolToResidue(DotBracketSymbol key, PdbResidueIdentifier value)	Put one entry to the inputSymbolToResidue map.
final ImmutableDefaultStrand	ImmutableDefaultStrand.withSymbols(DotBracketSymbol... elements)	Copy the current immutable object with elements that replace the content of symbols.
final ImmutableTerminalMissing	ImmutableTerminalMissing.withSymbols(DotBracketSymbol... elements)	Copy the current immutable object with elements that replace the content of symbols.

Method parameters in pl.poznan.put.structure.formats with type arguments of type DotBracketSymbol

Modifier and Type	Method	Description
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.addAllSymbols(Iterable<? extends DotBracketSymbol> elements)	Adds elements to symbols list.
final ImmutableTerminalMissing.Builder	ImmutableTerminalMissing.Builder.addAllSymbols(Iterable<? extends DotBracketSymbol> elements)	Adds elements to symbols list.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.inputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Sets or replaces all mappings from the specified map as entries for the inputSymbolToResidue map.
static ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.of(Iterable<? extends Strand> inputStrands, Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
static ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.of(List<Strand> inputStrands, Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
static ImmutableDefaultStrand	ImmutableDefaultStrand.of(String name, Iterable<? extends DotBracketSymbol> symbols)	Construct a new immutable DefaultStrand instance.
static ImmutableDefaultStrand	ImmutableDefaultStrand.of(String name, List<DotBracketSymbol> symbols)	Construct a new immutable DefaultStrand instance.
static ImmutableTerminalMissing	ImmutableTerminalMissing.of(Iterable<? extends DotBracketSymbol> symbols)	Construct a new immutable TerminalMissing instance.
static ImmutableTerminalMissing	ImmutableTerminalMissing.of(List<DotBracketSymbol> symbols)	Construct a new immutable TerminalMissing instance.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putAllInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Put all mappings from the specified map as entries to inputSymbolToResidue map.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putInputSymbolToResidue(Map.Entry<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entry)	Put one entry to the inputSymbolToResidue map.
final ImmutableDefaultStrand.Builder	ImmutableDefaultStrand.Builder.symbols(Iterable<? extends DotBracketSymbol> elements)	Sets or replaces all elements for symbols list.
final ImmutableTerminalMissing.Builder	ImmutableTerminalMissing.Builder.symbols(Iterable<? extends DotBracketSymbol> elements)	Sets or replaces all elements for symbols list.
final ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.withInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Copy the current immutable object by replacing the inputSymbolToResidue map with the specified map.
final ImmutableDefaultStrand	ImmutableDefaultStrand.withSymbols(Iterable<? extends DotBracketSymbol> elements)	Copy the current immutable object with elements that replace the content of symbols.
final ImmutableTerminalMissing	ImmutableTerminalMissing.withSymbols(Iterable<? extends DotBracketSymbol> elements)	Copy the current immutable object with elements that replace the content of symbols.