de.jstacs.algorithms.alignment.cost
Class AffineCosts

java.lang.Object
  de.jstacs.algorithms.alignment.cost.AffineCosts

All Implemented Interfaces:

Costs

Direct Known Subclasses:

MatrixCosts, SimpleCosts

public abstract class AffineCosts
extends Object
implements Costs

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.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from interface de.jstacs.algorithms.alignment.cost.Costs

Costs.Direction

Constructor Summary

protected

AffineCosts(double start, double elong) This constructor must be used by any constructor of any subclass to define the affine gap costs of an alignment.

Method Summary

double	getElongateCosts() Returns the costs to elongate a gap by one position.
double	getGapCostsFor(int length) Returns the costs for a gap of length length.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface de.jstacs.algorithms.alignment.cost.Costs

getCostFor

Constructor Detail

AffineCosts

protected AffineCosts(double start,
                      double elong)

This constructor must be used by any constructor of any subclass to define the affine gap costs of an alignment.

Parameters:

start - the costs for starting a gap

elong - the cost for elongating a gap

Method Detail

getElongateCosts

public double getElongateCosts()

Description copied from interface: Costs

Returns the costs to elongate a gap by one position.

Specified by:

getElongateCosts in interface Costs

Returns:

the corresponding costs

getGapCostsFor

public double getGapCostsFor(int length)

Description copied from interface: Costs

Returns the costs for a gap of length length.

Specified by:

getGapCostsFor in interface Costs

Parameters:

length - the length of the gap

Returns:

the corresponding costs