Пример #1
0
        /// <summary>
        /// This is the algorithm to find the Shortest Middle Snake (SMS).
        /// </summary>
        /// <param name="dataA">sequence A</param>
        /// <param name="lowerA">lower bound of the actual range in DataA</param>
        /// <param name="upperA">upper bound of the actual range in DataA (exclusive)</param>
        /// <param name="dataB">sequence B</param>
        /// <param name="lowerB">lower bound of the actual range in DataB</param>
        /// <param name="upperB">upper bound of the actual range in DataB (exclusive)</param>
        /// <param name="downVector">a vector for the (0,0) to (x,y) search. Passed as a parameter for speed reasons.</param>
        /// <param name="upVector">a vector for the (u,v) to (N,M) search. Passed as a parameter for speed reasons.</param>
        /// <returns>a MiddleSnakeData record containing x,y and u,v</returns>
        private ShortestMiddleSnakeReturnData ShortestMiddleSnake(
            DiffData dataA,
            int lowerA,
            int upperA,
            DiffData dataB,
            int lowerB,
            int upperB,
            int[] downVector,
            int[] upVector)
        {
            var ret = new ShortestMiddleSnakeReturnData();
            int max = dataA.Length + dataB.Length + 1;

            int downK = lowerA - lowerB; // the k-line to start the forward search
            int upK   = upperA - upperB; // the k-line to start the reverse search

            int  delta    = (upperA - lowerA) - (upperB - lowerB);
            bool oddDelta = (delta & 1) != 0;

            // The vectors in the publication accepts negative indexes. the vectors implemented here are 0-based
            // and are access using a specific offset: UpOffset UpVector and DownOffset for DownVektor
            int downOffset = max - downK;
            int upOffset   = max - upK;

            int maxD = ((upperA - lowerA + upperB - lowerB) / 2) + 1;

            // Debug.Write(2, "SMS", String.Format("Search the box: A[{0}-{1}] to B[{2}-{3}]", LowerA, UpperA, LowerB, UpperB));

            // init vectors
            downVector[downOffset + downK + 1] = lowerA;
            upVector[upOffset + upK - 1]       = upperA;

            for (int d = 0; d <= maxD; d++)
            {
                // Extend the forward path.
                for (int k = downK - d; k <= downK + d; k += 2)
                {
                    // Debug.Write(0, "SMS", "extend forward path " + k.ToString());

                    // find the only or better starting point
                    int x;
                    if (k == downK - d)
                    {
                        x = downVector[downOffset + k + 1]; // down
                    }
                    else
                    {
                        x = downVector[downOffset + k - 1] + 1; // a step to the right
                        if ((k < downK + d) && (downVector[downOffset + k + 1] >= x))
                        {
                            x = downVector[downOffset + k + 1]; // down
                        }
                    }

                    int y = x - k;

                    // find the end of the furthest reaching forward D-path in diagonal k.
                    while ((x < upperA) && (y < upperB) && (dataA.Data[x] == dataB.Data[y]))
                    {
                        x++;
                        y++;
                    }

                    downVector[downOffset + k] = x;

                    // overlap ?
                    if (oddDelta && (upK - d < k) && (k < upK + d))
                    {
                        if (upVector[upOffset + k] <= downVector[downOffset + k])
                        {
                            ret.X = downVector[downOffset + k];
                            ret.Y = downVector[downOffset + k] - k;
                            return(ret);
                        }
                    }
                }

                // Extend the reverse path.
                for (int k = upK - d; k <= upK + d; k += 2)
                {
                    // Debug.Write(0, "SMS", "extend reverse path " + k.ToString());

                    // find the only or better starting point
                    int x, y;
                    if (k == upK + d)
                    {
                        x = upVector[upOffset + k - 1]; // up
                    }
                    else
                    {
                        x = upVector[upOffset + k + 1] - 1; // left
                        if ((k > upK - d) && (upVector[upOffset + k - 1] < x))
                        {
                            x = upVector[upOffset + k - 1]; // up
                        }
                    }

                    y = x - k;

                    while ((x > lowerA) && (y > lowerB) && (dataA.Data[x - 1] == dataB.Data[y - 1]))
                    {
                        x--;
                        y--; // diagonal
                    }

                    upVector[upOffset + k] = x;

                    // overlap ?
                    if (!oddDelta && (downK - d <= k) && (k <= downK + d))
                    {
                        if (upVector[upOffset + k] <= downVector[downOffset + k])
                        {
                            ret.X = downVector[downOffset + k];
                            ret.Y = downVector[downOffset + k] - k;
                            return(ret);
                        }
                    }
                }
            }

            throw new Exception("the algorithm should never come here.");
        }
        /// <summary>
        /// This is the algorithm to find the Shortest Middle Snake (SMS).
        /// </summary>
        /// <param name="dataA">sequence A</param>
        /// <param name="lowerA">lower bound of the actual range in DataA</param>
        /// <param name="upperA">upper bound of the actual range in DataA (exclusive)</param>
        /// <param name="dataB">sequence B</param>
        /// <param name="lowerB">lower bound of the actual range in DataB</param>
        /// <param name="upperB">upper bound of the actual range in DataB (exclusive)</param>
        /// <param name="downVector">a vector for the (0,0) to (x,y) search. Passed as a parameter for speed reasons.</param>
        /// <param name="upVector">a vector for the (u,v) to (N,M) search. Passed as a parameter for speed reasons.</param>
        /// <returns>a MiddleSnakeData record containing x,y and u,v</returns>
        private ShortestMiddleSnakeReturnData ShortestMiddleSnake(
            DiffData dataA,
            int lowerA,
            int upperA,
            DiffData dataB,
            int lowerB,
            int upperB,
            int[] downVector,
            int[] upVector)
        {
            var ret = new ShortestMiddleSnakeReturnData();
            int max = dataA.Length + dataB.Length + 1;

            int downK = lowerA - lowerB; // the k-line to start the forward search
            int upK = upperA - upperB; // the k-line to start the reverse search

            int delta = (upperA - lowerA) - (upperB - lowerB);
            bool oddDelta = (delta & 1) != 0;

            // The vectors in the publication accepts negative indexes. the vectors implemented here are 0-based
            // and are access using a specific offset: UpOffset UpVector and DownOffset for DownVektor
            int downOffset = max - downK;
            int upOffset = max - upK;

            int maxD = ((upperA - lowerA + upperB - lowerB) / 2) + 1;

            // Debug.Write(2, "SMS", String.Format("Search the box: A[{0}-{1}] to B[{2}-{3}]", LowerA, UpperA, LowerB, UpperB));

            // init vectors
            downVector[downOffset + downK + 1] = lowerA;
            upVector[upOffset + upK - 1] = upperA;

            for (int d = 0; d <= maxD; d++)
            {
                // Extend the forward path.
                for (int k = downK - d; k <= downK + d; k += 2)
                {
                    // Debug.Write(0, "SMS", "extend forward path " + k.ToString());

                    // find the only or better starting point
                    int x;
                    if (k == downK - d)
                    {
                        x = downVector[downOffset + k + 1]; // down
                    }
                    else
                    {
                        x = downVector[downOffset + k - 1] + 1; // a step to the right
                        if ((k < downK + d) && (downVector[downOffset + k + 1] >= x))
                        {
                            x = downVector[downOffset + k + 1]; // down
                        }
                    }

                    int y = x - k;

                    // find the end of the furthest reaching forward D-path in diagonal k.
                    while ((x < upperA) && (y < upperB) && (dataA.Data[x] == dataB.Data[y]))
                    {
                        x++;
                        y++;
                    }

                    downVector[downOffset + k] = x;

                    // overlap ?
                    if (oddDelta && (upK - d < k) && (k < upK + d))
                    {
                        if (upVector[upOffset + k] <= downVector[downOffset + k])
                        {
                            ret.X = downVector[downOffset + k];
                            ret.Y = downVector[downOffset + k] - k;
                            return ret;
                        }
                    }
                }

                // Extend the reverse path.
                for (int k = upK - d; k <= upK + d; k += 2)
                {
                    // Debug.Write(0, "SMS", "extend reverse path " + k.ToString());

                    // find the only or better starting point
                    int x, y;
                    if (k == upK + d)
                    {
                        x = upVector[upOffset + k - 1]; // up
                    }
                    else
                    {
                        x = upVector[upOffset + k + 1] - 1; // left
                        if ((k > upK - d) && (upVector[upOffset + k - 1] < x))
                        {
                            x = upVector[upOffset + k - 1]; // up
                        }
                    }

                    y = x - k;

                    while ((x > lowerA) && (y > lowerB) && (dataA.Data[x - 1] == dataB.Data[y - 1]))
                    {
                        x--;
                        y--; // diagonal
                    }

                    upVector[upOffset + k] = x;

                    // overlap ?
                    if (!oddDelta && (downK - d <= k) && (k <= downK + d))
                    {
                        if (upVector[upOffset + k] <= downVector[downOffset + k])
                        {
                            ret.X = downVector[downOffset + k];
                            ret.Y = downVector[downOffset + k] - k;
                            return ret;
                        }
                    }
                }
            }

            throw new Exception("the algorithm should never come here.");
        }