package compbio.data.sequence;

import java.util.Arrays;

public class AnnotatedSequence extends FastaSequence {

    private final float[] annotation;

    public AnnotatedSequence(String id, String sequence, float[] annotation) {
	super(id, sequence);
	this.annotation = annotation;
	if (annotation == null || annotation.length != sequence.length()) {
	    throw new IllegalArgumentException("The length of the annotation ("
		    + ((annotation != null) ? annotation.length : "0")
		    + ") does not match the length of the sequence ("
		    + sequence.length() + ")!");
	}
    }

    public AnnotatedSequence(FastaSequence fsequence, float[] annotation) {
	this(fsequence.getId(), fsequence.getSequence(), annotation);
    }

    public float[] getAnnotation() {
	return annotation;
    }

    @Override
    public int hashCode() {
	final int prime = 7;
	int result = super.hashCode();
	result = prime * result + Arrays.hashCode(annotation);
	return result;
    }

    @Override
    public boolean equals(Object obj) {
	if (this == obj)
	    return true;
	if (!super.equals(obj))
	    return false;
	if (getClass() != obj.getClass())
	    return false;
	AnnotatedSequence other = (AnnotatedSequence) obj;
	if (!Arrays.equals(annotation, other.annotation))
	    return false;
	return true;
    }

    @Override
    public String toString() {
	return super.toString() + "Annotation:\n "
		+ Arrays.toString(annotation) + "\n";
    }

}