import java.time.Duration;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

public class MatchingResult {

    private final Map<String, String> metadata;
    private final List<String> comments;
    private final List<String> headers;
    private final List<List<String>> allResults;
    private final Map<String, String> matchMap;

    public MatchingResult(Map<String, String> metadata, List<String> headers,
                          List<List<String>> allResults, Map<String, String>matchMap){
        /*
         * POSSIBLE KEYS FOR METADATA MAP ARE:
         * sample plate filename *
         * graph filename *
         * matching weight *
         * well populations *
         * sequence read depth *
         * sequence read error rate *
         * read error collision rate *
         * total alphas read from plate *
         * total betas read from plate *
         * alphas in graph (after pre-filtering) *
         * betas in graph (after pre-filtering) *
         * high overlap threshold for pairing *
         * low overlap threshold for pairing *
         * maximum occupancy difference for pairing *
         * minimum overlap percent for pairing *
         * pairing attempt rate *
         * correct pairing count *
         * incorrect pairing count *
         * pairing error rate *
         * time to generate graph (seconds) *
         * time to pair sequences (seconds) *
         * total simulation time (seconds) *
         */
        this.metadata = metadata;
        this.comments = new ArrayList<>();
        for (String key : metadata.keySet()) {
            comments.add(key +": " + metadata.get(key));
        }
        this.headers = headers;
        this.allResults = allResults;
        this.matchMap = matchMap;
    }

    public Map<String, String> getMetadata() {return metadata;}

    public List<String> getComments() {
        return comments;
    }

    public List<List<String>> getAllResults() {
        return allResults;
    }

    public List<String> getHeaders() {
        return headers;
    }

    public Map<String, String> getMatchMap() {
        return matchMap;
    }

//    public Duration getTime() {
//        return time;
//    }

    public String getPlateFilename() {
        return metadata.get("sample plate filename");
    }

    public String getGraphFilename() {
        return metadata.get("graph filename");
    }

    public Integer[] getWellPopulations() {
        List<Integer> wellPopulations = new ArrayList<>();
        String popString = metadata.get("well populations");
        for (String p : popString.split(", ")) {
            wellPopulations.add(Integer.parseInt(p));
        }
        Integer[] popArray = new Integer[wellPopulations.size()];
        return wellPopulations.toArray(popArray);
    }

    public Integer getAlphaCount() {
        return Integer.parseInt(metadata.get("total alphas read from plate"));
    }

    public Integer getBetaCount() {
        return Integer.parseInt(metadata.get("total betas read from plate"));
    }

    public Integer getHighOverlapThreshold() { return Integer.parseInt(metadata.get("high overlap threshold for pairing"));}

    public Integer getLowOverlapThreshold() { return Integer.parseInt(metadata.get("low overlap threshold for pairing"));}

    public Integer getMaxOccupancyDifference() { return Integer.parseInt(metadata.get("maximum occupancy difference for pairing"));}

    public Integer getMinOverlapPercent() { return Integer.parseInt(metadata.get("minimum overlap percent for pairing"));}

    public Double getPairingAttemptRate() { return Double.parseDouble(metadata.get("pairing attempt rate"));}

    public Integer getCorrectPairingCount() { return Integer.parseInt(metadata.get("correct pairing count"));}

    public Integer getIncorrectPairingCount() { return Integer.parseInt(metadata.get("incorrect pairing count"));}

    public Double getPairingErrorRate() { return Double.parseDouble(metadata.get("pairing error rate"));}

    public String getSimulationTime() { return metadata.get("total simulation time (seconds)"); }

}