Uses of Interface
de.jstacs.algorithms.alignment.cost.Costs

Packages that use Costs

Package	Description
de.jstacs.algorithms.alignment	Provides classes for alignments.
de.jstacs.algorithms.alignment.cost	Provides classes for cost functions used in alignments.

Uses of Costs in de.jstacs.algorithms.alignment

Fields in de.jstacs.algorithms.alignment declared as Costs

Modifier and Type	Field and Description
protected Costs	Alignment.costs The alignment costs

Constructors in de.jstacs.algorithms.alignment with parameters of type Costs

Constructor and Description
Alignment(Costs costs) Creates a new Alignment instance that aligns the sequences s1 and s2 using the costs defined in costs.
Alignment(Costs costs, int offDiagonal) Creates a new Alignment instance that aligns the sequences s1 and s2 using the costs defined in costs and a banded version of the alignment algorithm.

Uses of Costs in de.jstacs.algorithms.alignment.cost

Classes in de.jstacs.algorithms.alignment.cost that implement Costs

Modifier and Type	Class and Description
class	AffineCosts This class implements affine gap costs, i.e., the costs for starting a new gap are given by start, and the costs for elongating a gap by one position are given by elong.
class	MatrixCosts Class for matrix costs, i.e., the cost of any match/mismatch is stored in a matrix allowing a huge degree of freedom.
class	SimpleCosts Class for simple costs with costs match for a match, mismatch for a mismatch, and gap for a gap (of length 1).

Methods in de.jstacs.algorithms.alignment.cost that return Costs

Modifier and Type	Method and Description
Costs	AffineCosts.getInternalCosts() Returns the internal costs (supplied as c to AffineCosts.AffineCosts(double, Costs)) used for matches and mismatches.

Constructors in de.jstacs.algorithms.alignment.cost with parameters of type Costs

Constructor and Description
AffineCosts(double start, Costs c) This constructor creates a new instance of cost using affine gap costs.