package compbio.data.sequence;

import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.util.HashSet;
import java.util.List;

public class ScoreManager {

	private List<ScoreHolder> seqScores;

	private ScoreManager() {
		// Default JAXB constructor
	}

	public int getNumberOfSeq() {
		return seqScores.size();
	}

	public ScoreHolder getFirstSequenceScores() {
		if (seqScores.isEmpty())
			return null;
		return seqScores.get(0);
	}

	public ScoreHolder getAnnotationForSequence(String seqId) {
		for (ScoreHolder sch : seqScores) {
			if (sch.id.equals(seqId)) {
				return sch;
			}
		}
		return null;
	}

	public void writeOut(OutputStream outStream) throws IOException {
		BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
				outStream));
		for (ScoreHolder oneSeqScores : seqScores) {
			oneSeqScores.writeOut(outStream);
		}
		writer.flush();
	}

	public static class ScoreHolder {

		public String id;
		public HashSet<Score> scores;

		public void writeOut(OutputStream outStream) throws IOException {
			BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
					outStream));
			writer.write(">" + id + "\n");
			Score.write(scores, outStream);
		}

		public Score getFirstScore() {
			if (scores.isEmpty())
				return null;
			return scores.iterator().next();
		}

		public Score getScoreByMethod(Enum<?> method) {
			for (Score sc : scores) {
				if (method == sc.getMethod()) {
					return sc;
				}
			}
			return null;
		}

		public int getNumberOfScores() {
			return scores.size();
		}
	}
}