de.jstacs.algorithms.alignment.cost

Class MatrixCosts

java.lang.Object

de.jstacs.algorithms.alignment.cost.MatrixCosts

All Implemented Interfaces:

Costs, Storable

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

Constructors

Constructor and Description
MatrixCosts(double[][] matrix, double inDel) Creates a new instance of MatrixCosts where the costs for mismatch and match are given in matrix.
MatrixCosts(double[][] matrix, double insert, double delete) Creates a new instance of MatrixCosts where the costs for mismatch and match are given in matrix.
MatrixCosts(StringBuffer xml) Restores MatrixCosts object from its XML representation.

Method Summary

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	getDeleteCosts() Returns the costs for a delete gap, i.e., a gap in the second string.
double	getInsertCosts() Returns the costs for an insert gap, i.e., a gap in the first string.
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

MatrixCosts

public MatrixCosts(double[][] matrix,
                   double insert,
                   double delete)
            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

insert - the cost for an insert gap, i.e., a gap in the first string

delete - the cost for a delete gap, i.e., a gap in the second string

Throws:

CloneNotSupportedException - if matrix could not be cloned

MatrixCosts

public MatrixCosts(double[][] matrix,
                   double inDel)
            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

inDel - the cost for a gap

Throws:

CloneNotSupportedException - if matrix could not be cloned

MatrixCosts

public MatrixCosts(StringBuffer xml)
            throws NonParsableException

Restores MatrixCosts 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

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)

getInsertCosts

public double getInsertCosts()

Description copied from interface: Costs

Returns the costs for an insert gap, i.e., a gap in the first string.

Specified by:

getInsertCosts in interface Costs

Returns:

the costs for an insert gap

getDeleteCosts

public double getDeleteCosts()

Description copied from interface: Costs

Returns the costs for a delete gap, i.e., a gap in the second string.

Specified by:

getDeleteCosts in interface Costs

Returns:

the costs for a delete gap