Uses of Class
pl.poznan.put.structure.pseudoknots.Region

Packages that use Region

Package	Description
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 Region in pl.poznan.put.structure.pseudoknots

Subclasses of Region in pl.poznan.put.structure.pseudoknots

Modifier and Type	Class	Description
class	ImmutableRegion	Immutable implementation of Region.

Methods in pl.poznan.put.structure.pseudoknots that return Region

Modifier and Type	Method	Description
static Region	Region.merge(Region... regions)	Merges many regions into a new one.

Methods in pl.poznan.put.structure.pseudoknots that return types with arguments of type Region

Modifier and Type	Method	Description
protected Map<Region,Set<Region>>	ConflictGraph.conflicts()
protected Map<Region,Set<Region>>	ConflictGraph.conflicts()
protected Map<Region,Set<Region>>	ImmutableConflictGraph.conflicts()
protected Map<Region,Set<Region>>	ImmutableConflictGraph.conflicts()
Set<Region>	ConflictGraph.conflictsWith(Region region)	Returns all regions that conflict with a given one.
static List<Region>	Region.createRegions(BpSeq bpSeq)	Creates a list of regions from a secondary structure in BPSEQ format.
protected abstract List<Region>	ConflictGraph.regions()
protected List<Region>	ImmutableConflictGraph.regions()
Set<Region>	ConflictGraph.regionsWithConflicts()	Returns all regions that are in conflict with at least one other region.

Methods in pl.poznan.put.structure.pseudoknots with parameters of type Region

Modifier and Type	Method	Description
ImmutableConflictGraph.Builder	ImmutableConflictGraph.Builder.addRegions(Region element)	Adds one element to regions list.
ImmutableConflictGraph.Builder	ImmutableConflictGraph.Builder.addRegions(Region... elements)	Adds elements to regions list.
int	Region.compareTo(Region t)
Set<Region>	ConflictGraph.conflictsWith(Region region)	Returns all regions that conflict with a given one.
static ImmutableRegion	ImmutableRegion.copyOf(Region instance)	Creates an immutable copy of a Region value.
ImmutableRegion.Builder	ImmutableRegion.Builder.from(Region instance)	Fill a builder with attribute values from the provided Region instance.
boolean	ConflictGraph.hasConflicts(Region region)	Checks if a given region has any conflicts.
static boolean	ConflictGraph.isConflicting(Region first, Region second)	Checks if given regions are conflicting.
static Region	Region.merge(Region... regions)	Merges many regions into a new one.
void	ConflictGraph.removeRegion(Region region)	Removes region and all associated conflicts with it from the graph.
ImmutableConflictGraph	ImmutableConflictGraph.withRegions(Region... elements)	Copy the current immutable object with elements that replace the content of regions.

Method parameters in pl.poznan.put.structure.pseudoknots with type arguments of type Region

Modifier and Type	Method	Description
ImmutableConflictGraph.Builder	ImmutableConflictGraph.Builder.addAllRegions(Iterable<? extends Region> elements)	Adds elements to regions list.
static ImmutableConflictGraph	ImmutableConflictGraph.of(Iterable<? extends Region> regions)	Construct a new immutable ConflictGraph instance.
static ImmutableConflictGraph	ImmutableConflictGraph.of(List<Region> regions)	Construct a new immutable ConflictGraph instance.
ImmutableConflictGraph.Builder	ImmutableConflictGraph.Builder.regions(Iterable<? extends Region> elements)	Sets or replaces all elements for regions list.
ImmutableConflictGraph	ImmutableConflictGraph.withRegions(Iterable<? extends Region> elements)	Copy the current immutable object with elements that replace the content of regions.

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

Methods in pl.poznan.put.structure.pseudoknots.dp that return types with arguments of type Region

Modifier and Type	Method	Description
Optional<Region>	ConflictClique.findRegion(int begin, int end)	Searches for a region given its begin and end indices.
abstract Set<Region>	ConflictClique.regions()
Set<Region>	ImmutableConflictClique.regions()

Methods in pl.poznan.put.structure.pseudoknots.dp with parameters of type Region

Modifier and Type	Method	Description
ImmutableConflictClique.Builder	ImmutableConflictClique.Builder.addRegions(Region element)	Adds one element to regions set.
ImmutableConflictClique.Builder	ImmutableConflictClique.Builder.addRegions(Region... elements)	Adds elements to regions set.
ImmutableConflictClique	ImmutableConflictClique.withRegions(Region... elements)	Copy the current immutable object with elements that replace the content of regions.

Method parameters in pl.poznan.put.structure.pseudoknots.dp with type arguments of type Region

Modifier and Type	Method	Description
ImmutableConflictClique.Builder	ImmutableConflictClique.Builder.addAllRegions(Iterable<? extends Region> elements)	Adds elements to regions set.
static ImmutableConflictClique	ImmutableConflictClique.of(Iterable<? extends Region> regions)	Construct a new immutable ConflictClique instance.
static ImmutableConflictClique	ImmutableConflictClique.of(Set<Region> regions)	Construct a new immutable ConflictClique instance.
ImmutableConflictClique.Builder	ImmutableConflictClique.Builder.regions(Iterable<? extends Region> elements)	Sets or replaces all elements for regions set.
ImmutableConflictClique	ImmutableConflictClique.withRegions(Iterable<? extends Region> elements)	Copy the current immutable object with elements that replace the content of regions.

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

Methods in pl.poznan.put.structure.pseudoknots.elimination that return Region

Modifier and Type	Method	Description
Region	MaxConflicts.selectRegionToRemove(ConflictGraph conflictGraph)	Selects a region which has the most conflicts with other regions.
Region	MinGain.selectRegionToRemove(ConflictGraph conflictGraph)	Selects a region which has the least gain (sum of length of all regions in conflict).
Region	RegionRemover.selectRegionToRemove(ConflictGraph conflictGraph)	Uses data in the conflict graph to select one region to be removed.