edu.uci.iotproject.comparison.seqalignment

Class AlignmentPricer<T>

java.lang.Object

edu.uci.iotproject.comparison.seqalignment.AlignmentPricer<T>

Type Parameters:

T - The type of the elements that are being aligned.

Direct Known Subclasses:

SampleIntegerAlignmentPricer

public class AlignmentPricer<T>
extends java.lang.Object

Provides a generic implementation for the calculation of the cost of aligning two elements of a sequence as part of the sequence alignment algorithm (the algorithm is implemented in SequenceAlignment).

Constructor Summary

Constructors

Constructor and Description
AlignmentPricer(java.util.function.ToIntBiFunction<T,T> alignmentCostFunction, java.util.function.ToIntFunction<T> gapCostFunction) Constructs a new AlignmentPricer.

Method Summary

Modifier and Type	Method and Description
int	alignmentCost(T item1, T item2) Calculate the cost of aligning item1 with item2.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentPricer

public AlignmentPricer(java.util.function.ToIntBiFunction<T,T> alignmentCostFunction,
                       java.util.function.ToIntFunction<T> gapCostFunction)

Constructs a new AlignmentPricer.

Parameters:

alignmentCostFunction - A function that specifies the cost of aligning a T with some other T (e.g., based on the values of the properties of the two instances).

gapCostFunction - A function that specifies the cost of aligning a T with a gap. Note that the function is free to specify different gap costs for different Ts.

Method Detail

alignmentCost

public int alignmentCost(T item1,
                         T item2)

Calculate the cost of aligning item1 with item2. If either of the two arguments is set to null, the cost of aligning the other argument with a gap will be returned. Note that both arguments cannot be null at the same time as that translates to aligning a gap with a gap, which is pointless.

Parameters:

item1 - The first of the two aligned objects. Set to null to calculate the cost of aligning item2 with a gap.

item2 - The second of the two aligned objects. Set to null to calculate the cost of aligning item2 with a gap.

Returns:

The cost of aligning item1 with item2.