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package org.broadinstitute.gatk.tools.walkers.diagnostics.diagnosetargets;

import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;

/**
 * Generic code for Diagnose Target Statistics
 *
 * @author Mauricio Carneiro
 * @since 4/23/13
 */
abstract class AbstractStratification {

    private long preComputedTotalCoverage = -1;
    private Map<CallableStatus, Integer> statusTally = null;
    protected ThresHolder thresholds;

    public AbstractStratification(ThresHolder thresholds) {
        this.thresholds = thresholds;
    }

    /**
     * Calculates the average "good" coverage of this sample. Good means "passes the base and
     * mapping quality requirements.
     *
     * @return the average "good" coverage
     */
    public double averageCoverage(final int size) {
        if (preComputedTotalCoverage < 0)
            preComputedTotalCoverage = calculateTotalCoverage(getElements());
        return (double) preComputedTotalCoverage / size;
    }

    /**
     * Calculates the total "good" coverage of this sample. Good means "passes the base and
     * mapping quality requirements.
     *
     * @return the total "good" coverage across the interval for this sample
     */
    public long getCoverage() {
        if (preComputedTotalCoverage < 0)
            preComputedTotalCoverage = calculateTotalCoverage(getElements());
        return preComputedTotalCoverage;
    }


    /**
     * This is how the extending class will calculate it's own total coverage
     *
     * @return the total coverage
     */
    private long calculateTotalCoverage(Iterable<AbstractStratification> elements) {
        long cov = 0;
        for (AbstractStratification element : elements) {
            cov += element.getCoverage();
        }
        return cov;
    }

    /**
     * What are the list of elements in your class? For example:
     *
     * IntervalStatistics => List<SampleStatistics>
     * SampleStatistics => List<LocusStatistics>
     *
     * @return the corresponding list of elements of the extending class
     */
    public abstract Iterable<AbstractStratification> getElements();

    /**
     * Calculates the Callable statuses for the statistic as a whole (interval, sample or locus)
     *
     * @return the callable status(es) for the whole object
     */
    public abstract List<CallableStatus> callableStatuses();


    /**
     * Tally up all the callable status of all elements of the stratification.
     *
     * @return a map of callable status and counts
     */
    public Map<CallableStatus, Integer> getStatusTally() {
        if (statusTally == null) {
            statusTally = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
            for (AbstractStratification stats : getElements()) {
                for (CallableStatus status : stats.callableStatuses()) {
                    statusTally.put(status, !statusTally.containsKey(status) ? 1 : statusTally.get(status) + 1);
                }
            }
        }
        return statusTally;
    }

    public List<CallableStatus> queryStatus(List<Metric> statList) {
        List<CallableStatus> output = new LinkedList<CallableStatus>();
        for (Metric stat : statList) {
            final CallableStatus status = stat.status(this);
            if (status != null) {
                output.add(status);
            }
        }
        return output;
    }

}
