DNASearchDemo.java

import java.util.ArrayList;
import java.util.List;

/**
 * Demonstrate searching a DNA database with multiple scoring algorithms.
 * @author Dr. Jody Paul
 * @version 2026-03-10a
 */
public class DNASearchDemo {
    static final SequenceScoringAlgorithm EXAMPLE_ALGORITHM = new ExamplePositionMatchAlgorithm();
    /**
     * Runs the example program.
     *
     * @param args command-line arguments; not used in this demo
     */
    public static void main(String[] args) {
        List<DNASequence> database = new ArrayList<>();
        database.add(new DNASequence("Human_Example", "ACGTACGT"));
        database.add(new DNASequence("Mouse_Example", "ACGTTCGT"));
        database.add(new DNASequence("Fish_Example", "TTTTACGA"));

        String query = "ACGTACGA";

        List<SequenceScoringAlgorithm> algorithms = new ArrayList<>();
        algorithms.add(EXAMPLE_ALGORITHM);

        AlgorithmComparisonManager manager = new AlgorithmComparisonManager(algorithms);
        List<MatchResult> results = manager.compareAll(query, database);

        System.out.println("Query sequence: " + query);
        System.out.println();

        for (MatchResult result : results) {
            System.out.println("Algorithm: " + result.getAlgorithmName());
            System.out.println("Best match label: " + result.getBestSequence().getLabel());
            System.out.println("Best match sequence: " + result.getBestSequence().getSequence());
            System.out.println("Score: " + result.getScore());
            System.out.println();
        }
    }
}