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## 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

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