de.jstacs.algorithms.alignment.cost
Class MatrixCosts

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

All Implemented Interfaces:

Costs

public class MatrixCosts
extends AffineCosts

Class for matrix costs, i.e., the cost of any match/mismatch is stored in a matrix allowing a huge degree of freedom. Additionally, the class used affine gap costs. The costs start to start a new gap, and the costs elong to elongate a gap by one position.

Author:

Jens Keilwagen

Nested Class Summary

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

Costs.Direction

Constructor Summary

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

Method Summary

double

getCostFor(Sequence s1, Sequence s2, int i, int j, Costs.Direction from) Returns the costs for the alignment if s1(i) and s2(j) coming from from.

Methods inherited from class de.jstacs.algorithms.alignment.cost.AffineCosts

getElongateCosts, getGapCostsFor

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 start,
                   double elong)
            throws CloneNotSupportedException

Creates a new instance of matrix costs where the costs for mismatch and match are given in matrix. Additionally, costs start to start a new gap, and costs elong to elongate a gap by one position.

Parameters:

matrix - the match and mismatch costs

start - the costs to start a gap

elong - the costs to elongate a gap

Throws:

CloneNotSupportedException - if matrix could not be cloned

Method Detail

getCostFor

public double getCostFor(Sequence s1,
                         Sequence s2,
                         int i,
                         int j,
                         Costs.Direction from)

Description copied from interface: Costs

Returns the costs for the alignment if s1(i) and s2(j) coming from from.

Parameters:

s1 - the first sequence

s2 - the second sequence

i - the index in the first sequence

j - the index in the second sequence

from - the direction within the DP-matrix

Returns:

the costs