package uk.org.cinquin.mutinack;

import java.util.UUID;

import javax.jdo.annotations.PersistenceCapable;
import javax.jdo.annotations.Persistent;

import org.eclipse.jdt.annotation.NonNull;

import uk.org.cinquin.final_annotation.Final;
import uk.org.cinquin.mutinack.misc_util.Assert;
import uk.org.cinquin.mutinack.misc_util.ComparablePair;
import uk.org.cinquin.mutinack.qualities.Quality;

@PersistenceCapable
public class DuplexDisagreement extends ComparablePair<Mutation, Mutation> {

	private static final long serialVersionUID = 8966639744689364931L;

	public @Final boolean hasAWtStrand;
	public @Persistent Quality quality;
	public @Final @Persistent UUID duplexID;

	//Not taken into account for equality
	public double probCollision;

	public DuplexDisagreement(UUID duplexUUID, @NonNull Mutation first, @NonNull Mutation second,
			boolean hasAWtStrand, Quality quality) {
		super(first, second);
		this.duplexID = duplexUUID;
		this.hasAWtStrand = hasAWtStrand;
		Assert.isTrue(quality.atLeast(Quality.DUBIOUS));
		this.quality = quality;
	}

	public boolean hasAWtStrand() {
		return hasAWtStrand;
	}

	public Quality getQuality() {
		return quality;
	}

	public void setQuality(Quality quality) {
		this.quality = quality;
	}

	public UUID getDuplexID() {
		return duplexID;
	}

	public double getProbCollision() {
		return probCollision;
	}

	public void setProbCollision(double probCollision) {
		this.probCollision = probCollision;
	}

}

@@ -556,16 +556,84 @@
 4931L;%0A%0A
+%09//None of the following fields are taken into account for equality%0A
 %09public 
@@ -743,48 +743,8 @@
 xID;
-%0A%0A%09//Not taken into account for equality
 %0A%09pu

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