/// <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.");
}