/// <summary>
/// Run example.
/// </summary>
/// <seealso cref="http://en.wikipedia.org/wiki/Euclidean_vector#Scalar_multiplication">Multiply vector by scalar</seealso>
/// <seealso cref="http://en.wikipedia.org/wiki/Euclidean_vector#Dot_product">Multiply vector by vector (compute the dot product between two vectors)</seealso>
/// <seealso cref="http://en.wikipedia.org/wiki/Euclidean_vector#Addition_and_subtraction">Vector addition and subtraction</seealso>
/// <seealso cref="http://en.wikipedia.org/wiki/Outer_product">Outer Product of two vectors</seealso>
public void Run()
{
// Initialize IFormatProvider to print matrix/vector data
var formatProvider = (CultureInfo)CultureInfo.InvariantCulture.Clone();
formatProvider.TextInfo.ListSeparator = " ";
// Create vector "X"
var vectorX = new DenseVector(new[] { 1.0, 2.0, 3.0, 4.0, 5.0 });
Console.WriteLine(@"Vector X");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Create vector "Y"
var vectorY = new DenseVector(new[] { 5.0, 4.0, 3.0, 2.0, 1.0 });
Console.WriteLine(@"Vector Y");
Console.WriteLine(vectorY.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Multiply vector by scalar
// 1. Using Multiply method and getting result into different vector instance
var resultV = vectorX.Multiply(3.0);
Console.WriteLine(@"Multiply vector by scalar using method Multiply. (result = X.Multiply(3.0))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using operator "*"
resultV = 3.0 * vectorX;
Console.WriteLine(@"Multiply vector by scalar using operator *. (result = 3.0 * X)");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 3. Using Multiply method and updating vector itself
vectorX.Multiply(3.0, vectorX);
Console.WriteLine(@"Multiply vector by scalar using method Multiply. (X.Multiply(3.0, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Multiply vector by vector (compute the dot product between two vectors)
// 1. Using operator "*"
var dotProduct = vectorX * vectorY;
Console.WriteLine(@"Dot product between two vectors using operator *. (result = X * Y)");
Console.WriteLine(dotProduct);
Console.WriteLine();
// 2. Using DotProduct method and getting result into different vector instance
dotProduct = vectorX.DotProduct(vectorY);
Console.WriteLine(@"Dot product between two vectors using method DotProduct. (result = X.DotProduct(Y))");
Console.WriteLine(dotProduct.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Pointwise multiplies vector with another vector
// 1. Using PointwiseMultiply method and getting result into different vector instance
resultV = vectorX.PointwiseMultiply(vectorY);
Console.WriteLine(@"Pointwise multiplies vector with another vector using method PointwiseMultiply. (result = X.PointwiseMultiply(Y))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using PointwiseMultiply method and updating vector itself
vectorX.PointwiseMultiply(vectorY, vectorX);
Console.WriteLine(@"Pointwise multiplies vector with another vector using method PointwiseMultiply. (X.PointwiseMultiply(Y, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Pointwise divide vector with another vector
// 1. Using PointwiseDivide method and getting result into different vector instance
resultV = vectorX.PointwiseDivide(vectorY);
Console.WriteLine(@"Pointwise divide vector with another vector using method PointwiseDivide. (result = X.PointwiseDivide(Y))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using PointwiseDivide method and updating vector itself
vectorX.PointwiseDivide(vectorY, vectorX);
Console.WriteLine(@"Pointwise divide vector with another vector using method PointwiseDivide. (X.PointwiseDivide(Y, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Addition
// 1. Using operator "+"
resultV = vectorX + vectorY;
Console.WriteLine(@"Add vectors using operator +. (result = X + Y)");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using Add method and getting result into different vector instance
resultV = vectorX.Add(vectorY);
Console.WriteLine(@"Add vectors using method Add. (result = X.Add(Y))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 3. Using Add method and updating vector itself
vectorX.Add(vectorY, vectorX);
Console.WriteLine(@"Add vectors using method Add. (X.Add(Y, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Subtraction
// 1. Using operator "-"
resultV = vectorX - vectorY;
Console.WriteLine(@"Subtract vectors using operator -. (result = X - Y)");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using Subtract method and getting result into different vector instance
resultV = vectorX.Subtract(vectorY);
Console.WriteLine(@"Subtract vectors using method Subtract. (result = X.Subtract(Y))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 3. Using Subtract method and updating vector itself
vectorX.Subtract(vectorY, vectorX);
Console.WriteLine(@"Subtract vectors using method Subtract. (X.Subtract(Y, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Divide by scalar
// 1. Using Divide method and getting result into different vector instance
resultV = vectorX.Divide(3.0);
Console.WriteLine(@"Divide vector by scalar using method Divide. (result = A.Divide(3.0))");
Console.WriteLine(resultV.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using Divide method and updating vector itself
vectorX.Divide(3.0, vectorX);
Console.WriteLine(@"Divide vector by scalar using method Divide. (X.Divide(3.0, X))");
Console.WriteLine(vectorX.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// Outer Product of two vectors
// 1. Using instanse method OuterProduct
var resultM = vectorX.OuterProduct(vectorY);
Console.WriteLine(@"Outer Product of two vectors using method OuterProduct. (X.OuterProduct(Y))");
Console.WriteLine(resultM.ToString("#0.00\t", formatProvider));
Console.WriteLine();
// 2. Using static method of the Vector class
resultM = Vector.OuterProduct(vectorX, vectorY);
Console.WriteLine(@"Outer Product of two vectors using method OuterProduct. (Vector.OuterProduct(X,Y))");
Console.WriteLine(resultM.ToString("#0.00\t", formatProvider));
Console.WriteLine();
}
/// <summary>
/// The bhattacharyya distance.
/// </summary>
/// <param name="observedIsotopicPeakList">
/// The observed isotopic peak list.
/// </param>
/// <param name="expectedIsotopicPeakList">
/// The actual isotopic peak list.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
private static double BhattacharyyaDistance(List<double> observedIsotopicPeakList, List<Peak> expectedIsotopicPeakList)
{
// calculate angle between two isotopic vectors in the isotopic space
double[] actualIsotopicPeakListArray = expectedIsotopicPeakList.Select(x => (double)x.Height).ToArray();
Vector<double> A = new DenseVector(observedIsotopicPeakList.ToArray());
Vector<double> B = new DenseVector(actualIsotopicPeakListArray);
A = A.Normalize(2);
B = B.Normalize(2);
Vector<double> C = A.PointwiseMultiply(B);
// Pointwise sqrt. Implements here because Math.Net.2.5 doesn't supports Pointwise exp getting Math.Net 3.5 introducces
// package compatibility issues with Informed Proteomics / Multidimensional peak finding, etc.
// TODO: Use PointwiseExponent after getting Math.net 3.5
double[] cArray = C.ToArray();
int size = cArray.Count();
double sum = 0;
for (int i = 0; i < size; i++)
{
cArray[i] = Math.Sqrt(cArray[i]);
sum += cArray[i];
}
return sum;
}