Uses of Interface
pl.poznan.put.structure.pseudoknots.PseudoknotFinder

Packages that use PseudoknotFinder

Package	Description
pl.poznan.put.structure.formats
pl.poznan.put.structure.pseudoknots.dp	A set of dynamic programming solutions to pseudoknot detection.s
pl.poznan.put.structure.pseudoknots.elimination

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

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

Modifier and Type	Method	Description
PseudoknotFinder	DefaultConverter.pseudoknotFinder()
PseudoknotFinder	ImmutableDefaultConverter.pseudoknotFinder()

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

Modifier and Type	Method	Description
ImmutableDefaultConverter.Builder	ImmutableDefaultConverter.Builder.pseudoknotFinder(PseudoknotFinder pseudoknotFinder)	Initializes the value for the pseudoknotFinder attribute.
ImmutableDefaultConverter	ImmutableDefaultConverter.withPseudoknotFinder(PseudoknotFinder value)	Copy the current immutable object by setting a value for the pseudoknotFinder attribute.

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

Classes in pl.poznan.put.structure.pseudoknots.dp that implement PseudoknotFinder

Modifier and Type	Class	Description
class	DynamicProgrammingAll	Java implementation of OPT ALL algorithm as presented in: Smit, S. et al., 2008.
class	ImmutableDynamicProgrammingAll	Immutable implementation of DynamicProgrammingAll.

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

Subinterfaces of PseudoknotFinder in pl.poznan.put.structure.pseudoknots.elimination

Modifier and Type	Interface	Description
interface	RegionRemover	A pseudoknot finder algorithm which works by selecting a region to remove in each iteration.

Classes in pl.poznan.put.structure.pseudoknots.elimination that implement PseudoknotFinder

Modifier and Type	Class	Description
class	AbstractRegionRemover	Java implementation of region removal algorithm as presented in: Smit, S. et al., 2008.
class	ImmutableMaxConflicts	Immutable implementation of MaxConflicts.
class	ImmutableMinGain	Immutable implementation of MinGain.
class	MaxConflicts	Java implementation of Elimination Conflicts algorithm as presented in: Smit, S. et al., 2008.
class	MinGain	Java implementation of Elimination Gain algorithm as presented in: Smit, S. et al., 2008.