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## de.jstacs.algorithms.alignment.cost
Class MatrixCosts

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

All Implemented Interfaces:
  Costs

    public class MatrixCosts

extends Object
implements Costs

Class for matrix costs, i.e., the cost of any match/mismatch is stored in a matrix allowing a huge degree of freedom.

Author:
  Jens Keilwagen

Constructor Summary
`MatrixCosts(double[][] matrix, double gap)` Creates a new instance of `MatrixCosts` where the costs for mismatch and match are given in `matrix`.

Method Summary
`double` | `getCostFor(Sequence s1, Sequence s2, int i, int j)` Returns the costs for the alignment of `s1(i)` and `s2(j)`.
`double` | `getGapCosts()` Returns the costs for a gap.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### MatrixCosts

    public MatrixCosts(double[][] matrix,
                       double gap)
                throws CloneNotSupportedException

  Creates a new instance of `MatrixCosts` where the costs for mismatch and match are given in `matrix`. Additionally, the costs for a gap can be specified.

  Parameters:
    `matrix` - the match and mismatch costs
    `gap` - the cost for a gap
  Throws:
    `CloneNotSupportedException` - if `matrix` could not be cloned

Method Detail

### getCostFor

    public double getCostFor(Sequence s1,
                             Sequence s2,
                             int i,
                             int j)

  Description copied from interface: `Costs`
  Returns the costs for the alignment of `s1(i)` and `s2(j)`.

  Specified by:
    `getCostFor` in interface `Costs`
  Parameters:
    `s1` - the first sequence
    `s2` - the second sequence
    `i` - the index in the first sequence
    `j` - the index in the second sequence
  Returns:
    the costs
  See Also:
    `Sequence.discreteVal(int)`

### getGapCosts

    public double getGapCosts()

  Description copied from interface: `Costs`
  Returns the costs for a gap.

  Specified by:
    `getGapCosts` in interface `Costs`
  Returns:
    the costs for a gap

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