// *********************************************************

// 

//     Copyright (c) Microsoft. All rights reserved.

//     This code is licensed under the Apache License, Version 2.0.

//     THIS CODE IS PROVIDED *AS IS* WITHOUT WARRANTY OF

//     ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING ANY

//     IMPLIED WARRANTIES OF FITNESS FOR A PARTICULAR

//     PURPOSE, MERCHANTABILITY, OR NON-INFRINGEMENT.

// 

// *********************************************************

using System;

using System.Collections.Generic;

using Bio.Algorithms.Kmer;

using System.Linq;



namespace Bio

{

    /// <summary>

    /// WordMatch stores the region of similarity between two sequences.

    /// </summary>

    public class WordMatch : IComparable, IComparable<WordMatch>, IEquatable<WordMatch>

    {

        /// <summary>

        /// Length of the match.

        /// </summary>

        private int length;



        /// <summary>

        /// Start index of the first sequence.

        /// </summary>

        private int sequence1Start;



        /// <summary>

        /// Start index of the second sequence.

        /// </summary>

        private int sequence2Start;



        /// <summary>

        /// Initializes a new instance of the WordMatch class.

        /// </summary>

        /// <param name="length">Length of the match</param>

        /// <param name="sequence1Start">Start index of the first sequence.</param>

        /// <param name="sequence2Start"> Start index of the second sequence.</param>

        public WordMatch(int length, int sequence1Start, int sequence2Start)

        {

            this.length = length;

            this.sequence1Start = sequence1Start;

            this.sequence2Start = sequence2Start;

        }



        /// <summary>

        /// Gets or sets the length of the match

        /// </summary>

        public int Length

        {

            get { return length; }

            set { length = value; }

        }



        /// <summary>

        /// Gets or sets the start index of the first sequence.

        /// </summary>

        public int Sequence1Start

        {

            get { return sequence1Start; }

            set { sequence1Start = value; }

        }



        /// <summary>

        /// Gets or sets the start index of the second sequence.

        /// </summary>

        public int Sequence2Start

        {

            get { return sequence2Start; }

            set { sequence2Start = value; }

        }



        /// <summary>

        /// Gets or sets a value indicating whether this word match should be considered or not.

        /// </summary>

        public bool Deleted

        {

            get;

            set;

        }



        /// <summary>

        /// Given a list of matches, reduce it to the minimal set of best

        /// non-overlapping matches.

        /// </summary>

        /// <param name="completeList">List of matches to reduce to non-overlapping set.</param>

        /// <param name="wordLength">Wordlength entered by the user.</param>

        /// <returns>Minimal set of best non-overlapping matches.</returns>

        public static List<WordMatch> GetMinimalList(List<WordMatch> completeList, int wordLength)

        {

            List<WordMatch> minimalList = new List<WordMatch>();



            completeList.Sort();



            foreach (WordMatch wordMatch in completeList)

            {

                int deadx1 = 0;

                int deady1 = 0;

                int deadx2 = 0;

                int deady2 = 0;



                if (!wordMatch.Deleted)

                {

                    // First pos of match

                    deadx1 = wordMatch.sequence1Start;



                    // First pos of match

                    deady1 = wordMatch.sequence2Start;



                    // Last pos of match

                    deadx2 = wordMatch.sequence1Start + wordMatch.length - 1;



                    // Last pos of match

                    deady2 = wordMatch.sequence2Start + wordMatch.length - 1;



                    foreach (WordMatch innerWordMatch in completeList)

                    {

                        if (wordMatch != innerWordMatch && !innerWordMatch.Deleted)

                        {

                            // Want to remove this match if it is in the dead zone

                            bool result = WordDeadZone(innerWordMatch, deadx1, deady1, deadx2, deady2, wordLength);



                            if (result)

                            {

                                // It is in the dead zone - remove it

                                // Need to free up the match structure and remove the

                                // current node of the list                                

                                innerWordMatch.Deleted = true;

                            }

                        }

                    }

                }

            }



            foreach (WordMatch wordMatch in completeList)

            {

                if (!wordMatch.Deleted)

                {

                    minimalList.Add(wordMatch);

                }

            }



            return minimalList;

        }



        /// <summary>

        ///  Create a list of all the matches and order them by the

        /// second sequence.

        /// </summary>

        /// <param name="kmerList">List of kmer's.</param>

        /// <param name="seq2">Second sequence.</param>

        /// <param name="wordLength">Wordlength entered by the user</param>

        /// <returns>List of all the matches.</returns>

        public static List<WordMatch> BuildMatchTable(KmersOfSequence kmerList, ISequence seq2, int wordLength)

        {

            if (seq2 == null)

            {

                throw new ArgumentNullException("seq2");

            }



            int i = 0;

            int ilast = (int)seq2.Count - wordLength;

            List<WordMatch> wordCurList = new List<WordMatch>();

            List<WordMatch> hitList = new List<WordMatch>();

            bool matched = false;



            while (i < (ilast + 1))

            {

                IList<long> positions = FindCorrespondingMatch(new string(seq2.Skip(i).Take(wordLength).Select(a => (char)a).ToArray()), kmerList);



                if (positions != null)

                {

                    int kcur = 0;

                    int kcur2 = 0;

                    int knew = 0;



                    if (wordCurList.Count > 0)

                    {

                        WordMatch curmatch = wordCurList[0];

                        kcur = curmatch.sequence1Start + curmatch.length - wordLength + 1;

                        kcur2 = curmatch.sequence2Start + curmatch.length - wordLength + 1;

                    }



                    foreach (int position in positions)

                    {

                        knew = position;



                        matched = false;



                        foreach (WordMatch curmatch in wordCurList)

                        {

                            if (!curmatch.Deleted)

                            {

                                kcur = curmatch.sequence1Start + curmatch.length -

                                    wordLength + 1;

                                kcur2 = curmatch.sequence2Start + curmatch.length -

                                    wordLength + 1;



                                // When we test, we may have already incremented

                                // one of the matches - so test old and new kcur2

                                if (kcur2 != i && kcur2 != i + 1)

                                {

                                    curmatch.Deleted = true;

                                    continue;

                                }



                                if (kcur == knew && kcur2 == i)

                                {

                                    curmatch.length++;

                                    matched = true;

                                    continue;

                                }

                            }

                        }



                        if (!matched)

                        {

                            // New current match

                            WordMatch match2 = new WordMatch(wordLength, knew, i);

                            hitList.Add(match2);

                            wordCurList.Add(match2);

                        }

                    }

                }



                i++;

            }



            wordCurList.Sort();



            foreach (WordMatch curmatch in wordCurList)

            {

                curmatch.Deleted = false;

            }



            return wordCurList;

        }



        #region IComparable Members



        /// <summary>

        /// CompareTo method is used while sorting WordMatch objects. 

        /// </summary>

        /// <param name="obj">WordMatch object</param>

        /// <returns>

        /// Returns zero if the objects are equal, 

        /// Else, returns zero if the objects have the same length, sequence1start and sequence2Start 

        /// If lengths are equal, then the objects are ordered by sequence1start

        /// If lengths are equal and sequence1Start are equal, then the objects are ordered by 

        /// </returns>

        public int CompareTo(object obj)

        {

            WordMatch other = obj as WordMatch;

            if (other == null)

            {

                return -1;

            }

            else

            {

                return CompareTo(other);

            }

        }



        #endregion



        #region IComparable<WordMatch> Members



        /// <summary>

        ///  Compares two sequence matches so the result can be used in sorting.

        /// The comparison is done by size and if the size is equal, by seq1

        /// start position.  If the sequence1 start positions are equal they are

        /// sorted by sequence2 start position.

        /// </summary>

        /// <param name="other">WordMatch object</param>

        /// <returns>

        /// Returns zero if the objects have the same length, sequence1start and sequence2Start 

        /// If lengths are equal, then the objects are ordered by sequence1start

        /// If lengths are equal and sequence1Start are equal, then the objects are ordered by sequence2start

        /// </returns>

        public int CompareTo(WordMatch other)

        {

            if (other != null)

            {

                if (other.length == length)

                {

                    if (other.sequence1Start == sequence1Start)

                    {

                        if (other.sequence2Start == sequence2Start)

                        {

                            return 0;

                        }

                        else

                        {

                            return sequence2Start - other.sequence2Start;

                        }

                    }

                    else

                    {

                        return sequence1Start - other.sequence1Start;

                    }

                }

                else

                {

                    return other.length - length;

                }

            }



            return -1;

        }



        #endregion



        #region IEquatable<WordMatch> Members



        /// <summary>

        /// Checks if another WordMatch object is equal to the current

        /// object.

        /// </summary>

        /// <param name="other">WordMatch object to be compared.</param>

        /// <returns>

        /// true: if the objects are equal else false.

        /// </returns>

        public bool Equals(WordMatch other)

        {

            return length == other.length

                && sequence1Start == other.sequence1Start

                && sequence2Start == other.sequence2Start;

        }

        #endregion



        /// <summary>

        /// Determines if a match is within the region which is not overlapped by the

        /// match starting at position (deadx1, deady1) or ending at position

        /// (deadx2, deady2). If it is in this region

        /// (the 'live zone') then true is returned, else false is returned.

        /// </summary>

        /// <param name="wordMatch">Word Match object which holds the similarity of the two sequences.</param>

        /// <param name="deadx1">starting x-position of the region for which overlapped has to be checked.</param>

        /// <param name="deady1">starting y-position of the region for which overlapped has to be checked.</param>

        /// <param name="deadx2">ending x-position of the region for which overlapped has to be checked.</param>

        /// <param name="deady2">ending y-position of the region for which overlapped has to be checked.</param>

        /// <param name="wordLength">Wordlength entered by the user</param>

        /// <returns>

        /// true: if the wordMatch is in the overlapped region, else false.

        /// </returns>

        private static bool WordDeadZone(WordMatch wordMatch, int deadx1, int deady1, int deadx2, int deady2, int wordLength)

        {

            int startx;

            int starty;

            int endx;

            int endy;



            startx = wordMatch.sequence1Start;

            starty = wordMatch.sequence2Start;



            endx = wordMatch.sequence1Start + wordMatch.length - 1;

            endy = wordMatch.sequence2Start + wordMatch.length - 1;



            // Is it in the top right live zone?

            if (startx > deadx2 && starty > deady2)

            {

                return false;

            }



            // Is it in the bottom right live zone?

            if (endx < deadx1 && endy < deady1)

            {

                return false;

            }



            // Is it in the top left dead zone? 

            if (starty >= deady1 && endx <= deadx2)

            {

                return true;

            }



            // Is it in the bottom right dead zone?

            if (endy <= deady2 && startx >= deadx1)

            {

                return true;

            }



            if (endy < deady2)

            {

                if (startx - starty < deadx1 - deady1)

                {

                    // Crosses deady1

                    wordMatch.length = deady1 - starty;

                }

                else if (startx - starty > deadx1 - deady1)

                {

                    // Crosses deadx1

                    wordMatch.length = deadx1 - startx;

                }

            }

            else if (starty > deady1)

            {

                if (startx - starty < deadx1 - deady1)

                {

                    // Crosses deadx2

                    wordMatch.length = endx - deadx2;

                    wordMatch.sequence1Start = deadx2 + 1;

                    wordMatch.sequence2Start += deadx2 - startx + 1;

                }

                else if (startx - starty > deadx1 - deady1)

                {

                    // Crosses deady2

                    wordMatch.length = endy - deady2;

                    wordMatch.sequence1Start += deady2 - starty + 1;

                    wordMatch.sequence2Start = deady2 + 1;

                }

            }



            if (wordMatch.length < wordLength)

            {

                return true;

            }



            return false;

        }



        /// <summary>

        /// Finds the sequence in the list of IKmer and returns the list of position

        /// of the Kmers.

        /// </summary>

        /// <param name="sequence">Sequence which has to be matched in the list of IKmer.</param>

        /// <param name="kmerList">List of IKmer.</param>

        /// <returns>Returns the list of position of IKmer.</returns>

        private static IList<long> FindCorrespondingMatch(string sequence, KmersOfSequence kmerList)

        {

            IList<long> positions = null;



            foreach (KmersOfSequence.KmerPositions kmer in kmerList.Kmers)

            {

                string kmerString = new string(kmerList.KmerToSequence(kmer).Select(a => (char)a).ToArray());

                

                if (sequence.Equals(kmerString))

                {

                    positions = kmer.Positions;

                    break;

                }

            }



            return positions;

        }



        /// <summary>

        /// Overrides hash function for a particular type.

        /// </summary>

        /// <returns>hash code</returns>

        public override int GetHashCode()

        {

            return base.GetHashCode();

        }



        /// <summary>

        /// Overrides the equal method

        /// </summary>

        /// <param name="obj">Object to be checked</param>

        /// <returns>Is equals</returns>

        public override bool Equals(object obj)

        {

            if (obj == null || GetType() != obj.GetType())

            {

                return false;

            }



            return base.Equals(obj);

        }



        /// <summary>

        /// Override equal operator

        /// </summary>

        /// <param name="leftHandSideObject">LHS object</param>

        /// <param name="rightHandSideObject">RHS object</param>

        /// <returns>Is LHS == RHS</returns>

        public static bool operator ==(WordMatch leftHandSideObject, WordMatch rightHandSideObject)

        {

            if (System.Object.ReferenceEquals(leftHandSideObject, rightHandSideObject))

            {

                return true;

            }

            else

            {

                return false;

            }

        }



        /// <summary>

        /// Override not equal operator

        /// </summary>

        /// <param name="leftHandSideObject">LHS object</param>

        /// <param name="rightHandSideObject">RHS object</param>

        /// <returns>Is LHS == RHS</returns>

        public static bool operator !=(WordMatch leftHandSideObject, WordMatch rightHandSideObject)

        {

            return !(leftHandSideObject == rightHandSideObject);

        }



        /// <summary>

        /// Override less than operator

        /// </summary>

        /// <param name="leftHandSideObject">LHS object</param>

        /// <param name="rightHandSideObject">RHS object</param>

        /// <returns>Is LHS == RHS</returns>

        public static bool operator <(WordMatch leftHandSideObject, WordMatch rightHandSideObject)

        {

            if (object.ReferenceEquals(leftHandSideObject, null) || object.ReferenceEquals(rightHandSideObject, null))

            {

                return false;

            }



            return (leftHandSideObject.CompareTo(rightHandSideObject) < 0);

        }



        /// <summary>

        /// Override greater than operator

        /// </summary>

        /// <param name="leftHandSideObject">LHS object</param>

        /// <param name="rightHandSideObject">RHS object</param>

        /// <returns>Is LHS == RHS</returns>

        public static bool operator >(WordMatch leftHandSideObject, WordMatch rightHandSideObject)

        {

            if (object.ReferenceEquals(leftHandSideObject, null) || object.ReferenceEquals(rightHandSideObject, null))

            {

                return false;

            }



            return (leftHandSideObject.CompareTo(rightHandSideObject) > 0);

        }

    }

}