static MD()
{
matrices.Add("MD40", SubstitutionMatrix.Create("MD40", MatrixData.MD40, Routines.aminoAcidCodes));
matrices.Add("MD120", SubstitutionMatrix.Create("MD120", MatrixData.MD120, Routines.aminoAcidCodes));
matrices.Add("MD250", SubstitutionMatrix.Create("MD250", MatrixData.MD250, Routines.aminoAcidCodes));
matrices.Add("MD350", SubstitutionMatrix.Create("MD350", MatrixData.MD350, Routines.aminoAcidCodes));
}
//public static SubstitutionMatrix Create(string name, List<List<double>> matrixInfo, char[] residueCodes)
//// matrixInfo is a list of lists, with each sub-list containing a line from the substituion matrix
//// file, which is stored as the bottom-left triangle of the symmetrical matrix.
//{
// int maxResidues = residueCodes.Length;
// bool useNegativeMatrix = false;
// Dictionary<char, Dictionary<char, double>> matrix = new Dictionary<char, Dictionary<char, double>>(residueCodes.Length + 2);
// Dictionary<char, double> oldGapRow = new Dictionary<char, double>(residueCodes.Length + 2);
// Dictionary<char, double> newGapRow = new Dictionary<char, double>(residueCodes.Length + 2);
// for (int i = 0; i < maxResidues; i++)
// {
// int limit = matrixInfo[i].Count;
// Dictionary<char, double> row = new Dictionary<char, double>(residueCodes.Length + 2);
// for (int j = 0; j < limit; j++)
// {
// row.Add(residueCodes[j], matrixInfo[i][j] * 100);
// }
// for (int j = limit; j < maxResidues; j++)
// {
// row.Add(residueCodes[j], matrixInfo[j][i] * 100);
// }
// row.Add(Routines.oldGap, gapResidueValue);
// row.Add(Routines.newGap, gapResidueValue);
// matrix.Add(residueCodes[i], row);
// oldGapRow.Add(residueCodes[i], gapResidueValue);
// newGapRow.Add(residueCodes[i], gapResidueValue);
// }
// oldGapRow.Add(Routines.oldGap, gapGapValue);
// oldGapRow.Add(Routines.newGap, gapGapValue);
// newGapRow.Add(Routines.oldGap, gapGapValue);
// newGapRow.Add(Routines.newGap, gapGapValue);
// matrix.Add(Routines.oldGap, oldGapRow);
// matrix.Add(Routines.newGap, newGapRow);
// SubstitutionMatrix subMatrix = new SubstitutionMatrix(name, matrix, residueCodes);
// subMatrix.CalculateMatrixAverageScore();
// if (!useNegativeMatrix)
// {
// subMatrix.MakePositive();
// }
// return subMatrix;
//}
public static SubstitutionMatrix Create(string name, double[] matrixInfo, char[] residueCodes)
// matrixInfo is a single array containing the bottom-left triangle of the symmetrical matrix.
{
int maxResidues = residueCodes.Length;
bool useNegativeMatrix = false;
Dictionary <char, Dictionary <char, double> > matrix = new Dictionary <char, Dictionary <char, double> >(residueCodes.Length + 2);
Dictionary <char, double> oldGapRow = new Dictionary <char, double>(residueCodes.Length + 2);
Dictionary <char, double> newGapRow = new Dictionary <char, double>(residueCodes.Length + 2);
int rowStart = 0;
for (int i = 0; i < maxResidues; i++) // rows
{
Dictionary <char, double> row = new Dictionary <char, double>(residueCodes.Length + 2);
for (int j = 0; j <= i; j++) // Populate the row
{
row.Add(residueCodes[j], matrixInfo[rowStart + j] * 100);
}
matrix.Add(residueCodes[i], row);
for (int j = 0; j < i; j++) // Populate the column too
{
matrix[residueCodes[j]].Add(residueCodes[i], matrixInfo[rowStart + i]);
}
rowStart += i + 1;
oldGapRow.Add(residueCodes[i], gapResidueValue);
newGapRow.Add(residueCodes[i], gapResidueValue);
}
foreach (KeyValuePair <char, Dictionary <char, double> > row in matrix) // Add gap columns
{
row.Value.Add(Routines.oldGap, gapResidueValue);
row.Value.Add(Routines.newGap, gapResidueValue);
}
oldGapRow.Add(Routines.oldGap, gapGapValue);
oldGapRow.Add(Routines.newGap, gapGapValue);
newGapRow.Add(Routines.oldGap, gapGapValue);
newGapRow.Add(Routines.newGap, gapGapValue);
matrix.Add(Routines.oldGap, oldGapRow);
matrix.Add(Routines.newGap, newGapRow);
SubstitutionMatrix subMatrix = new SubstitutionMatrix(name, matrix, residueCodes);
subMatrix.CalculateMatrixAverageScore();
if (!useNegativeMatrix)
{
subMatrix.MakePositive();
}
return(subMatrix);
}
static PAM()
{
matrices.Add("PAM20", SubstitutionMatrix.Create("PAM20", MatrixData.PAM20, Routines.aminoAcidCodes));
matrices.Add("PAM60", SubstitutionMatrix.Create("PAM60", MatrixData.PAM60, Routines.aminoAcidCodes));
matrices.Add("PAM120", SubstitutionMatrix.Create("PAM120", MatrixData.PAM120, Routines.aminoAcidCodes));
matrices.Add("PAM160", SubstitutionMatrix.Create("PAM160", MatrixData.PAM160, Routines.aminoAcidCodes));
matrices.Add("PAM250", SubstitutionMatrix.Create("PAM250", MatrixData.PAM250, Routines.aminoAcidCodes));
matrices.Add("PAM350", SubstitutionMatrix.Create("PAM350", MatrixData.PAM350, Routines.aminoAcidCodes));
}
static Gonnet()
{
matrices.Add("Gonnet40", SubstitutionMatrix.Create("Gonnet40", MatrixData.Gonnet40, Routines.aminoAcidCodes));
matrices.Add("Gonnet80", SubstitutionMatrix.Create("Gonnet80", MatrixData.Gonnet80, Routines.aminoAcidCodes));
matrices.Add("Gonnet120", SubstitutionMatrix.Create("Gonnet120", MatrixData.Gonnet120, Routines.aminoAcidCodes));
matrices.Add("Gonnet160", SubstitutionMatrix.Create("Gonnet160", MatrixData.Gonnet160, Routines.aminoAcidCodes));
matrices.Add("Gonnet250", SubstitutionMatrix.Create("Gonnet250", MatrixData.Gonnet250, Routines.aminoAcidCodes));
matrices.Add("Gonnet300", SubstitutionMatrix.Create("Gonnet300", MatrixData.Gonnet300, Routines.aminoAcidCodes));
matrices.Add("Gonnet350", SubstitutionMatrix.Create("Gonnet350", MatrixData.Gonnet350, Routines.aminoAcidCodes));
}
static BLOSUM()
{
matrices.Add("BLOSUM30", SubstitutionMatrix.Create("BLOSUM30", MatrixData.BLOSUM30, Routines.aminoAcidCodes));
matrices.Add("BLOSUM35", SubstitutionMatrix.Create("BLOSUM35", MatrixData.BLOSUM35, Routines.aminoAcidCodes));
matrices.Add("BLOSUM40", SubstitutionMatrix.Create("BLOSUM40", MatrixData.BLOSUM40, Routines.aminoAcidCodes));
matrices.Add("BLOSUM45", SubstitutionMatrix.Create("BLOSUM45", MatrixData.BLOSUM45, Routines.aminoAcidCodes));
matrices.Add("BLOSUM50", SubstitutionMatrix.Create("BLOSUM50", MatrixData.BLOSUM50, Routines.aminoAcidCodes));
matrices.Add("BLOSUM55", SubstitutionMatrix.Create("BLOSUM55", MatrixData.BLOSUM55, Routines.aminoAcidCodes));
matrices.Add("BLOSUM62", SubstitutionMatrix.Create("BLOSUM62", MatrixData.BLOSUM62, Routines.aminoAcidCodes));
matrices.Add("BLOSUM62x2", SubstitutionMatrix.Create("BLOSUM62x2", MatrixData.BLOSUM62x2, Routines.aminoAcidCodes));
matrices.Add("BLOSUM65", SubstitutionMatrix.Create("BLOSUM65", MatrixData.BLOSUM65, Routines.aminoAcidCodes));
matrices.Add("BLOSUM70", SubstitutionMatrix.Create("BLOSUM70", MatrixData.BLOSUM70, Routines.aminoAcidCodes));
matrices.Add("BLOSUM75", SubstitutionMatrix.Create("BLOSUM75", MatrixData.BLOSUM75, Routines.aminoAcidCodes));
matrices.Add("BLOSUM80", SubstitutionMatrix.Create("BLOSUM80", MatrixData.BLOSUM80, Routines.aminoAcidCodes));
matrices.Add("BLOSUM90", SubstitutionMatrix.Create("BLOSUM90", MatrixData.BLOSUM90, Routines.aminoAcidCodes));
}
static IUB() // Also referred to as SW_GAP in Clustal code
{
matrix = SubstitutionMatrix.Create("IUB", MatrixData.IUB, Routines.nucleotideCodes);
}
static AminoAcidIdentity()
{
matrix = SubstitutionMatrix.Create("Identity", MatrixData.AminoAcidIdentity, Routines.aminoAcidCodes);
}
static NucleotideIdentity() // Also referred to as ClustalVDNA in Clustal code, or ClustalW (1.6)
{
matrix = SubstitutionMatrix.Create("Identity", MatrixData.NucleotideIdentity, Routines.nucleotideCodes);
}