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package org.broadinstitute.gatk.utils.variant;

import org.broadinstitute.gatk.utils.Utils;

import java.util.Arrays;

/**
 * Utility to find and quantify tandem repeat units in a byte array.
 *
 * <p>
 *     This class provide a more efficient implementation of deprecated
 *     {@link GATKVariantContextUtils#findNumberOfRepetitions(byte[], byte[], boolean)}
 *     and RepeatCovariate which are proven to be inefficient and buggy.
 * </p>
 *
 * <p>
 *     For now it does not change the logic of those methods in order to preserve current behaviour, but this
 *     needs to be revisited at some point with the proper re-evaluation.
 *
 *     Example.
 *
 *     ttcttcttCtgca
 *
 *     Where the current offset is in the capital C, will result in the STR unit returned to be TGCA with only one repeat.
 *     whereas the logical choice is TTC with 3 repeats.
 *
 *     And for further proof, a small modification and its effect:
 *
 *     ttcttcttCttca
 *
 *     Unit T, repeated 2.
 *
 *     I would say it should be 4 TTC instead.
 *
 *     I think we might well be failing to model the actual PCR artifact appropriately:
 *
 *     <a>http://nar.oxfordjournals.org/content/24/14/2807.full</a>
 *     <a>http://www.ncbi.nlm.nih.gov/pubmed/12560493</a>
 *
 * </p>
 *
 * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
 */
public final class TandemRepeatFinder {


    private final byte[] bases;
    private final int maxRepeatCount;
    private final int maxUnitLength;

    public TandemRepeatFinder(final byte[] bases, final int maxUnitLength, final int maxRepeatLength) {
        if (bases == null) throw new IllegalArgumentException();
        if (maxRepeatLength < 0) throw new IllegalArgumentException();
        if (maxUnitLength < 0) throw new IllegalArgumentException();
        this.maxRepeatCount = maxRepeatLength;
        this.maxUnitLength = maxUnitLength;
        this.bases = bases;
    }

    /**
     * Calculates the number of repeated units of certain length starting at a position.
     *
     * <p>
     * The repeat unit is determined by the original byte array passed to this tandem repeat finder and the input
     * offset and length passed to this method based on the following pseudo-code:
     *
     * <pre>
     *     if (length > 0) {
     *         unit = bytes[offset .. (offset + length - 1)]
     *     } else if (length < 0) {
     *         unit = bytes[offset + length + 1  .. offset]
     *     } else { // length == 0
     *         throw IllegalArgumentException() // not allowed.
     *     }
     * </pre>
     * </p>
     *
     * <p>
     *     0 will be returned if given the offset and length, part of the unit falls outside the byte array.
     * </p>
     * <p>
     *     Otherwise,
     *     this method will return the number of repeats (minimum 1 indicating that there is no duplicates) only looking into
     *     a single direction: if <code>length > 0</code> forward in the byte array <code>byte[offset .. END]</code>,
     *     if <code>length < 0</code> then backward in the array <code>byte[0 .. offset]</code>.
     * </p>
     *
     * @param offset the offset in the bases byte for which to start
     * @param length the unit length, a negative indicates a backward unit.
     * @return the number of repeats.
     * @throws IllegalArgumentException if {@code length} is 0 or {@code offset} is outside boundaries: (0 .. bases.length - 1)
     *  where bases is the array passed to this finder at construction.
     */
    protected int numberOfRepeats(final int offset, final int length) {
        if (length == 0) throw new IllegalArgumentException();
        if (offset < 0 || offset >= bases.length) throw new IllegalArgumentException();
        int from = offset;
        int to = offset + length;
        if (to > bases.length || to < -1) return 0;
        final int increment = length < 0 ? -1 : 1;
        final int stop = length < 0? -1 : bases.length;
        int totalLength = 0;
        while (to != stop) {
           if (bases[to] != bases[from]) break;
           to += increment;
           from += increment;
           totalLength++;
        }
        return 1 + totalLength / Math.abs(length);
    }

    public final class Result {

        private final int unitLength;
        private final int unitOffset;
        private final int repeatCount;

        private Result(final int unitOffset, final int unitLength, final int repeatCount) {
            this.unitOffset = unitOffset;
            this.unitLength = unitLength;
            this.repeatCount = repeatCount;
        }

        /**
         * Returns the repeated unit byte sequence.
         * @return never {@code null}.
         */
        public byte[] getUnit() {
            return Arrays.copyOfRange(bases,unitOffset, unitOffset + unitLength);
        }

        /**
         * Returns the original search bases.
         *
         * @return never {@code null}.
         */
        public byte[] getBases() {
            return bases;
        }

        /**
         * Returns the unit offset.
         *
         * @return 0 to {@link #getBases().length - 1}
         */
        public int getUnitOffset() {
            return unitOffset;
        }

        /**
         * Returns the unit length.
         *
         * @return 0 to {@link #getBases().length - 1}
         */
        public int getUnitLength() {
            return unitLength;
        }

        /**
         * Returns the number of repeats of the unit in the input sequence.
         * @return 0 or greater.
         */
        public int getRepeatCount() {
            return repeatCount;
        }

    }

    /**
     * Re-implements {@link RepeatCovariate#findTandemRepeatUnits(byte[], int)}.
     *
     * @param offset search offset.
     * @return never {@code null}.
     */
    public Result findMostRelevantTandemRepeatUnitAt(final int offset) {

        // Notice that this code is not very nice and is rather long but is just a copy of the existing one implemented
        // in RepeatCovariate, eventually this should be improved.

        // first we look forward for a repeat.

        // first we find the best backward
        int bestBWRepeatCount = 0;
        int bestBWOffset = offset;
        int bestBWLength = 1;
        for (int str = 1; str <= maxUnitLength; str++) {
            final int repeatCount = numberOfRepeats(offset, -str);
            if (repeatCount == 0) {
                break;
            } else if ((bestBWRepeatCount = repeatCount) > 1) {
                bestBWOffset = offset - str + 1;
                bestBWLength = str;
                break;
            }
        }

        // The best forward:
        final int bestFWOffset = offset + 1;
        int bestFWLength = 1;
        int bestFWRepeatCount = 0;
        for (int str = 1; str <= maxUnitLength; str++) {
            final int repeatCount = numberOfRepeats(bestFWOffset, str);
            if (repeatCount == 0) {
                break;
            } else if ((bestFWRepeatCount = repeatCount) > 1) {
                bestFWLength = str;
                break;
            }
        }

        // And we combine forward and backwards results; if different forward repeat has priority:
        if (bestFWLength == bestBWLength && Utils.equalRange(bases, bestFWOffset, bases, bestBWOffset, bestFWLength)) {
            return new Result(bestBWOffset, bestBWLength, Math.min(maxRepeatCount, bestBWRepeatCount + bestFWRepeatCount));
        }
          else {
            final int bestFWBackwardRepeatCount = numberOfRepeats(bestFWOffset + bestFWLength - 1, - bestFWLength) - 1;
            return new Result(bestFWOffset, bestFWLength, Math.min(maxRepeatCount, bestFWRepeatCount + bestFWBackwardRepeatCount));
        }
    }
}
