public static double UnnormalisedSmithWatermanSimilarity(string source, string target)
{
double GapCost = DefaultGapCost;
if (source == null || target == null)
{
return(DefaultMismatchScore);
}
int length = source.Length;
int num2 = target.Length;
if (length == 0)
{
return(num2);
}
if (num2 == 0)
{
return(length);
}
double[][] numArray = new double[length][];
for (int i = 0; i < length; i++)
{
numArray[i] = new double[num2];
}
double num4 = 0.0;
for (int j = 0; j < length; j++)
{
double thirdNumber = Get01Cost(source, j, target, 0);
if (j == 0)
{
numArray[0][0] = MathFunctions.MaxOf3(0.0, -GapCost, thirdNumber);
}
else
{
numArray[j][0] = MathFunctions.MaxOf3(0.0, numArray[j - 1][0] - GapCost, thirdNumber);
}
if (numArray[j][0] > num4)
{
num4 = numArray[j][0];
}
}
for (int k = 0; k < num2; k++)
{
double num8 = Get01Cost(source, 0, target, k);
if (k == 0)
{
numArray[0][0] = MathFunctions.MaxOf3(0.0, -GapCost, num8);
}
else
{
numArray[0][k] = MathFunctions.MaxOf3(0.0, numArray[0][k - 1] - GapCost, num8);
}
if (numArray[0][k] > num4)
{
num4 = numArray[0][k];
}
}
for (int m = 1; m < length; m++)
{
for (int n = 1; n < num2; n++)
{
double num11 = Get01Cost(source, m, target, n);
numArray[m][n] = MathFunctions.MaxOf4(0.0, numArray[m - 1][n] - GapCost, numArray[m][n - 1] - GapCost, numArray[m - 1][n - 1] + num11);
if (numArray[m][n] > num4)
{
num4 = numArray[m][n];
}
}
}
return(num4);
} // end unnormallized
public static double UnnormalisedSmithWatermanSimilarity(this string firstWord, string secondWord)
{
if (firstWord == null || secondWord == null)
{
return(0.0);
}
int length = firstWord.Length;
int num2 = secondWord.Length;
if (length == 0)
{
return(num2);
}
if (num2 == 0)
{
return(length);
}
double[][] numArray = new double[length][];
for (int i = 0; i < length; i++)
{
numArray[i] = new double[num2];
}
double num4 = 0.0;
for (int j = 0; j < length; j++)
{
double num6 = DCostFunction.GetCost(firstWord, j, secondWord, 0);
if (j == 0)
{
numArray[0][0] = Math.Max(0.0, num6);
}
else
{
double num7 = 0.0;
int num8 = j - _windowSize;
if (num8 < 1)
{
num8 = 1;
}
for (int n = num8; n < j; n++)
{
num7 = Math.Max(num7, numArray[j - n][0] - GGapFunction.GetCost(firstWord, j - n, j));
}
numArray[j][0] = MathFunctions.MaxOf3(0.0, num7, num6);
}
if (numArray[j][0] > num4)
{
num4 = numArray[j][0];
}
}
for (int k = 0; k < num2; k++)
{
double num11 = DCostFunction.GetCost(firstWord, 0, secondWord, k);
if (k == 0)
{
numArray[0][0] = Math.Max(0.0, num11);
}
else
{
double num12 = 0.0;
int num13 = k - _windowSize;
if (num13 < 1)
{
num13 = 1;
}
for (int num14 = num13; num14 < k; num14++)
{
num12 = Math.Max(num12, numArray[0][k - num14] - GGapFunction.GetCost(secondWord, k - num14, k));
}
numArray[0][k] = MathFunctions.MaxOf3(0.0, num12, num11);
}
if (numArray[0][k] > num4)
{
num4 = numArray[0][k];
}
}
for (int m = 1; m < length; m++)
{
for (int num16 = 1; num16 < num2; num16++)
{
double num17 = DCostFunction.GetCost(firstWord, m, secondWord, num16);
double num18 = 0.0;
double num19 = 0.0;
int num20 = m - _windowSize;
if (num20 < 1)
{
num20 = 1;
}
for (int num21 = num20; num21 < m; num21++)
{
num18 = Math.Max(num18, numArray[m - num21][num16] - GGapFunction.GetCost(firstWord, m - num21, m));
}
num20 = num16 - _windowSize;
if (num20 < 1)
{
num20 = 1;
}
for (int num22 = num20; num22 < num16; num22++)
{
num19 = Math.Max(num19, numArray[m][num16 - num22] - GGapFunction.GetCost(secondWord, num16 - num22, num16));
}
numArray[m][num16] = MathFunctions.MaxOf4(0.0, num18, num19, numArray[m - 1][num16 - 1] + num17);
if (numArray[m][num16] > num4)
{
num4 = numArray[m][num16];
}
}
}
return(num4);
}