de.jstacs.algorithms.alignment.cost

Class AffineCosts

java.lang.Object

de.jstacs.algorithms.alignment.cost.AffineCosts

All Implemented Interfaces:

Costs, Storable

public class AffineCosts
extends Object
implements Costs

This class implements affine gap costs, i.e., the costs for starting a new gap are given by start, and the costs for elongating a gap by one position are given by elong.

Author:

Jan Grau, Jens Keilwagen

Constructor Summary

Constructors

Constructor and Description
AffineCosts(double start, Costs c) This constructor creates a new instance of cost using affine gap costs.
AffineCosts(StringBuffer xml) Restores AffineCosts object from its XML representation.

Method Summary

Methods

Modifier and Type	Method and Description
double	getCostFor(Sequence s1, Sequence s2, int i, int j) Returns the costs for the alignment of s1(i) and s2(j).
double	getElongateCosts() Returns the costs to elongate a gap by one position.
double	getGapCosts() Returns the costs for a gap.
double	getGapCostsFor(int length) Returns the costs for a gap of length length.
Costs	getInternalCosts() Returns the internal costs (supplied as c to AffineCosts(double, Costs)) used for matches and mismatches.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AffineCosts

public AffineCosts(double start,
           Costs c)

This constructor creates a new instance of cost using affine gap costs. The costs for match, mismatch and gap elongation are defined by c, while the costs for a start of a gap are given by start.

Parameters:

start - the costs for starting a gap

c - the cost for match, mismatch and gap elongation

AffineCosts

public AffineCosts(StringBuffer xml)
            throws NonParsableException

Restores AffineCosts object from its XML representation.

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the XML could not be parsed

Method Detail

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation

getInternalCosts

public Costs getInternalCosts()

Returns the internal costs (supplied as c to AffineCosts(double, Costs)) used for matches and mismatches.

Returns:

the internal costs

getElongateCosts

public double getElongateCosts()

Returns the costs to elongate a gap by one position.

Returns:

the corresponding costs

getGapCostsFor

public double getGapCostsFor(int length)

Returns the costs for a gap of length length.

Parameters:

length - the length of the gap

Returns:

the corresponding costs

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