de.jstacs.algorithms
Class Alignment.SimpleCosts

java.lang.Object
  de.jstacs.algorithms.Alignment.SimpleCosts

All Implemented Interfaces:

Alignment.Costs

Enclosing class:

Alignment

public static class Alignment.SimpleCosts
extends Object
implements Alignment.Costs

Class for simple costs with costs mismatch for a mismatch, costs start to start a new gap, elong to elongate a gap by one position, and costs of 0 for a match

Nested Class Summary

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

Alignment.Costs.Direction

Constructor Summary

Alignment.SimpleCosts(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, elong to elongate a gap by one position, and costs of 0 for a match

Method Summary

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

Constructor Detail

Alignment.SimpleCosts

public Alignment.SimpleCosts(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, elong to elongate a gap by one position, and costs of 0 for a match

Parameters:

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,
                         Alignment.Costs.Direction from)

Description copied from interface: Alignment.Costs

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

Specified by:

getCostFor in interface Alignment.Costs

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

getElongateCosts

public double getElongateCosts()

Description copied from interface: Alignment.Costs

Returns the costs to elongate a gap by one position

Specified by:

getElongateCosts in interface Alignment.Costs

Returns:

the costs

getGapCostsFor

public double getGapCostsFor(int length)

Description copied from interface: Alignment.Costs

Returns the costs for a gap of length length.

Specified by:

getGapCostsFor in interface Alignment.Costs

Parameters:

length - the length of the gap

Returns:

the corresponding costs