de.jstacs.algorithms.alignment.cost

Class SimpleCosts

java.lang.Object

de.jstacs.algorithms.alignment.cost.SimpleCosts

All Implemented Interfaces:

Costs, Storable

public class SimpleCosts
extends Object
implements Costs

Class for simple costs with costs

• match for a match,
• mismatch for a mismatch, and
• gap for a gap (of length 1).

Author:

Jan Grau, Jens Keilwagen

Constructor Summary

Constructors

Constructor and Description
SimpleCosts(double match, double mismatch, double gap) Creates a new instance of simple costs with costs match for a match, mismatch for a mismatch, and gap for a gap (of length 1).
SimpleCosts(StringBuffer xml) Restores SimpleCosts 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	getGapCosts() Returns the costs for a gap.
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

SimpleCosts

public SimpleCosts(double match,
           double mismatch,
           double gap)

Creates a new instance of simple costs with costs match for a match, mismatch for a mismatch, and gap for a gap (of length 1).

Parameters:

match - the match costs

mismatch - the mismatch costs

gap - the costs for a gap

SimpleCosts

public SimpleCosts(StringBuffer xml)
            throws NonParsableException

Restores SimpleCosts 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)

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