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 * Copyright (c) 2007-2015 Broad Institute
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 * of this software and associated documentation files (the "Software"), to deal
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 * copies of the Software, and to permit persons to whom the Software is
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 * all copies or substantial portions of the Software.
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 *
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package org.broad.igv.feature;

import java.util.List;

/**
 * Represents an amino acid sequence for an exon
 *
 * @author jrobinso
 */
public class AminoAcidSequence {

    private final Strand strand;
    private final int start;                // Genomic position for start of sequence.
    private final List<AminoAcid> sequence;

    private boolean nonNullSequence;

    /**
     * If the sequence was computed from a nucleotide sequence,
     * we store how the calculation was performed
     */
    private final AminoAcidManager.CodonTableKey codonTableKey;

    public AminoAcidSequence(Strand strand, int startPosition, List<AminoAcid> sequence, AminoAcidManager.CodonTableKey codonTableKey) {
        this.strand = strand;
        this.start = startPosition;
        this.sequence = sequence;
        this.codonTableKey = codonTableKey;

        // Look for a non null sequence.  Sequences are null if the sequence
        // directory is undefined or unreachable.  
        nonNullSequence = false;
        for (AminoAcid aa : sequence) {
            if (aa != null) {
                nonNullSequence = true;
                break;
            }
        }

    }

    public Strand getStrand() {
        return strand;
    }

    public int getStart() {
        return start;
    }

    public List<AminoAcid> getSequence() {
        return sequence;
    }

    public boolean hasNonNullSequence() {
        return nonNullSequence;
    }

    public AminoAcidManager.CodonTableKey getCodonTableKey() {
        return codonTableKey;
    }
}