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