private void AddNormalizedPeptideWeight(double weight, int pos, char replaceBy)
{
if (string.IsNullOrEmpty(WildTypePeptide))
{
return;
}
string s = "", e = "";
if (pos > 0)
{
s = WildTypePeptide.Substring(0, pos);
}
if (pos < WildTypePeptide.Length - 1)
{
e = WildTypePeptide.Substring(pos + 1);
}
string peptide = s + replaceBy + e;
if (/*peptide == WildTypePeptide && */ NormalizedPeptideWeights.ContainsKey(peptide))
{
return;
}
NormalizedPeptideWeights.Add(peptide, weight);
}
private void GenerateMatrices(string[,] values, out List <string> warnings, out string error)
{
error = "";
warnings = new List <string>();
if (values == null)
{
return;
}
try
{
RowCount = values.GetLength(0) - 1;
ColCount = values.GetLength(1) - 1;
PeptideMatrix = new string[RowCount, ColCount];
QuantificationMatrix = new double[RowCount, ColCount];
NormalizedMatrix = new double[RowCount, ColCount];
bool nswwarning = false;
bool nspwarning = false;
//Generate Permutation and Wildtype arrays
if (PermutationXAxis)
{
NormBy = new double[RowCount];
for (int iRow = 1; iRow <= RowCount; iRow++)
{
string s = values[iRow, 0].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
if (s.Length == 1)
{
if (!nswwarning)
{
warnings.Add("Non-standard amino acid in wildtype peptide.");
}
nswwarning = true;
}
else
{
error = "Not a valid wildtype peptide";
return;
}
}
if (WildTypeYAxisTopToBottom)
{
WildTypePeptide += s[0];
}
else
{
WildTypePeptide = s[0] + WildTypePeptide; //read from bottom to top
}
}
Permutation = new char[ColCount];
for (int iCol = 1; iCol <= ColCount; iCol++)
{
string s = values[0, iCol].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
if (s.Length == 1)
{
if (!nspwarning)
{
warnings.Add("Non-standard amino acid in permutation string.");
}
nspwarning = true;
}
else
{
error = "Not a valid permutation string";
return;
}
}
Permutation[iCol - 1] = s[0];
}
}
else //if(PermutationYAxis)
{
NormBy = new double[ColCount];
for (int iCol = 1; iCol <= ColCount; iCol++)
{
string s = values[0, iCol].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
if (s.Length == 1)
{
if (!nswwarning)
{
warnings.Add("Non-standard amino acid in wildtype peptide.");
}
nswwarning = true;
}
else
{
error = "Not a valid wildtype peptide";
return;
}
}
WildTypePeptide += s[0];
}
Permutation = new char[RowCount];
for (int iRow = 1; iRow <= RowCount; iRow++)
{
string s = values[iRow, 0].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
if (s.Length == 1)
{
if (!nspwarning)
{
warnings.Add("Non-standard amino acid in permutation string.");
}
nspwarning = true;
}
else
{
error = "Not a valid permutation string";
return;
}
}
Permutation[iRow - 1] = s[0];
}
}
//Generate Matrices and Normalization values
int wtl = WildTypePeptide.Length;
int counter = 0;
double totalNorm = 0;
for (int iRow = 0; iRow < RowCount; iRow++)
{
for (int iCol = 0; iCol < ColCount; iCol++)
{
if (double.TryParse(values[iRow + 1, iCol + 1], out double d))
{
QuantificationMatrix[iRow, iCol] = d;
}
else if (string.IsNullOrEmpty(values[iRow + 1, iCol + 1]))
{
d = 0;
}
else
{
error = "Wrongly formatted data.";
return;
}
if (PermutationXAxis) //wildTypeYAxis
{
if (WildTypeYAxisTopToBottom)
{
PeptideMatrix[iRow, iCol] = (iRow >= 1 ? WildTypePeptide.Substring(0, iRow) : "") + Permutation[iCol] + (iRow < WildTypePeptide.Length - 1 ? WildTypePeptide.Substring(iRow + 1) : "");
}
else //from bottom to top
{
PeptideMatrix[iRow, iCol] = (iRow < wtl - 1 ? WildTypePeptide.Substring(0, wtl - iRow - 1) : "") + Permutation[iCol] + (iRow > 0 ? WildTypePeptide.Substring(wtl - iRow) : "");
}
}
else
{
PeptideMatrix[iRow, iCol] = (iCol >= 1 ? WildTypePeptide.Substring(0, iCol) : "") + Permutation[iRow] + (iCol < WildTypePeptide.Length - 1 ? WildTypePeptide.Substring(iCol + 1) : "");
}
if (PeptideMatrix[iRow, iCol] == WildTypePeptide)
{
if (d > 0)
{
counter++;
totalNorm += d;
}
if (PermutationXAxis)
{
NormBy[iRow] = d;
}
else
{
NormBy[iCol] = d;
}
}
}
}
if (counter > 0 && counter < NormBy.GetLength(0)) //fill the blanks with average
{
for (int i = 0; i < NormBy.GetLength(0); i++)
{
if (NormBy[i] < 0.0001)
{
NormBy[i] = totalNorm / counter;
}
}
}
NormalizationValue = totalNorm / counter;
GenerateNormalizedPeptideWeights();
}
catch (Exception exc)
{
error = "Unhandled exception: " + exc.Message;
}
}
