de.jstacs.algorithms.alignment.cost
Class SimpleCosts

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

All Implemented Interfaces:

Costs

public class SimpleCosts
extends AffineCosts

Class for simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of match for a match.

Nested Class Summary

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

Costs.Direction

Constructor Summary

SimpleCosts(double match, double mismatch, double start, double elong)
Creates a new instance of simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of match for a match.

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

SimpleCosts

public SimpleCosts(double match,
                   double mismatch,
                   double start,
                   double elong)

Creates a new instance of simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of match for a match.

Parameters:

match - the match costs

mismatch - the mismatch costs

start - the costs to start a gap

elong - the costs to elongate a gap

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