Uses of Interface
org.strbio.mol.lib.GapModel

Packages that use GapModel

org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.raf	These classes are related to the RAF file format used by the ASTRAL database.

Uses of GapModel in org.strbio.mol

Methods in org.strbio.mol with parameters of type GapModel

double	Polymer.globalAlign(Polymer y, GapModel gm, ScoreList sl, int[] nail) Deprecated. use AlignmentParameters
double	Polymer.globalCompare(Polymer y, GapModel gm, ScoreList sl) Deprecated. use AlignmentParameters

Uses of GapModel in org.strbio.mol.lib

Classes in org.strbio.mol.lib that implement GapModel

class	GapAffine Affine gap penalties.
class	GapConstant Constant gap penalties.
class	GapDistanceDependent Distance dependent gap penalties.
class	GapModelAdapter Default implementation of GapModel.

Fields in org.strbio.mol.lib declared as GapModel

GapModel

AlignmentParameters.gapModel The gap model used.

Constructors in org.strbio.mol.lib with parameters of type GapModel

AlignmentParameters(GapModel gm, ScoreList sl)
Provide an initial gap model and score list.

AlignmentParametersEA(GapModel gm, ScoreList sl)

Uses of GapModel in org.strbio.raf

Classes in org.strbio.raf that implement GapModel

class

GapRAF Gap penalties for RAF.