DNASequencing/AlgorithmComparisonManager.java at main · MetroCS/DNASequencing

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import java.util.ArrayList;

import java.util.List;

import java.util.Objects;

/**

* Run multiple sequence scoring algorithms against the same query and database.

* @author Dr. Jody Paul

* @version 2026-03-10

public class AlgorithmComparisonManager {

private final List<SequenceScoringAlgorithm> algorithms;

/**

* Create a manager for a list of algorithms.

* @param algorithms the algorithms to run

public AlgorithmComparisonManager(List<SequenceScoringAlgorithm> algorithms) {

Objects.requireNonNull(algorithms, "algorithms must not be null");

if (algorithms.isEmpty()) {

throw new IllegalArgumentException("algorithms must not be empty");

}

this.algorithms = new ArrayList<>(algorithms);

}

/**

* Run all algorithms against the given query and database.

* @param querySequence the query DNA sequence

* @param database the database of labeled DNA sequences

* @return a list of match results, one per algorithm

public List<MatchResult> compareAll(String querySequence, List<DNASequence> database) {

List<MatchResult> results = new ArrayList<>();

for (SequenceScoringAlgorithm algorithm : algorithms) {

SequenceMatcher matcher = new SequenceMatcher(algorithm);

MatchResult result = matcher.findBestMatch(querySequence, database);

results.add(result);

}

return results;

}

/**

* Return a defensive copy of the registered algorithms.

* @return the registered algorithms

public List<SequenceScoringAlgorithm> getAlgorithms() {

return new ArrayList<>(algorithms);

}