public static AminoAcid GetAminoAcid(char c)
{
if (!AminoAcids.IsStandardAminoAcid(c))
{
return(null);
}
return(AminoAcidList[c]);
}
static public bool CheckPeptideList(List <string> peptides, int length, out List <string> warnings, out List <string> errors)
{
warnings = new List <string>();
errors = new List <string>();
bool ret = true;
try
{
foreach (string p in peptides)
{
if (Regex.Matches(p, @"[a-zA-Z]").Count < p.Length)
{
errors.Add("Invalid characters in " + p);
}
else
{
if (p.Length < length)
{
warnings.Add("Length inconsistency in " + p);
}
foreach (char c in p.Substring(0, Math.Min(p.Length, length)))
{
if (!AminoAcids.IsStandardAminoAcid(c))
{
warnings.Add("Non-standard amino acid in " + p);
break;
}
}
}
}
return(ret);
}
catch (Exception exc)
{
errors.Add("Unhandled exception: " + exc.Message);
return(false);
}
}
static private List <string> GenerateCombinations(string input)
{
int start = input.IndexOf('[');
if (start < 0)
{
return new List <string>()
{
input
}
}
;
int end = input.IndexOf(']', start + 1);
if (end < 0)
{
throw new Exception();
}
List <string> comb = new List <string>();
string chars = input.Substring(start + 1, end - start - 1);
string firstpart = start > 0 ? input.Substring(0, start) : "";
string lastpart = end < input.Length - 1 ? input.Substring(end + 1) : "";
if (chars.Substring(0, 1) == "-" || chars == "X") //use all aminoacids except the ones listed - X: use all
{
string charstouse = "";
foreach (AminoAcid aa in AminoAcids.GetAminoAcidList())
{
if (!chars.Contains(aa.Abbrev1))
{
charstouse += aa.Abbrev1;
}
}
chars = charstouse;
}
List <string> withinbrackets = new List <string>();
while (chars != "")
{
char c = chars.First();
if (c == '{')
{
end = chars.IndexOf('}', 1);
if (end < 0)
{
throw new Exception();
}
withinbrackets.Add(chars.Substring(1, end - 1));
chars = chars.Substring(end + 1);
continue;
}
withinbrackets.Add(c.ToString());
chars = chars.Substring(1);
}
foreach (string s in withinbrackets)
{
string subpart = firstpart + s + lastpart;
comb.AddRange(GenerateCombinations(subpart));
}
return(comb);
}
}
private Bitmap GetLetterImage(Char c, int width, int height, Color color)
{
if (width <= 0 || height <= 0)
{
return(null);
}
var scaledBitmap = new Bitmap(width, height);
Bitmap bmp = Settings.GetAminoAcidImage(c, color != Common.ColorNegative);
if (bmp != null)
{
try
{
var sourceRectangle = SelectFilledPixels(bmp);
RectangleF destinationRectangle = new RectangleF(0, 0, width, height);
using (var destination = Graphics.FromImage(scaledBitmap))
{
destination.SmoothingMode = System.Drawing.Drawing2D.SmoothingMode.HighQuality;
destination.DrawImage(bmp, destinationRectangle, sourceRectangle, GraphicsUnit.Pixel);
}
return(scaledBitmap);
}
catch (Exception exc) { }
}
var initialFontSize = (int)(Math.Max(width, height) / 1.5);
var fullSizeBitmap = new Bitmap(initialFontSize * 2, initialFontSize * 2);
using (var source = Graphics.FromImage(fullSizeBitmap))
using (var destination = Graphics.FromImage(scaledBitmap))
using (var font = new Font("Arial", initialFontSize, FontStyle.Bold))
using (var brush = new SolidBrush(color))
{
source.FillRectangle(Brushes.White, 0, 0, fullSizeBitmap.Width, fullSizeBitmap.Height);
AminoAcid aa = AminoAcids.GetAminoAcid(c); //aa?.MolecularWeight.ToString() ??
//source.DrawString(c=='X'?"X":aa?.pI.ToString(), font, brush, 0, 0);
source.DrawString(c.ToString(), font, brush, 0, 0);
var sourceRectangle = SelectFilledPixels(fullSizeBitmap);
RectangleF destinationRectangle;
if (c == 'I')
{
double newwidth = 5 * sourceRectangle.Width * height / sourceRectangle.Height;
if (newwidth > width / 3)
{
newwidth = width / 3;
}
destinationRectangle = new RectangleF((int)(width - newwidth) / 2, 0, (int)newwidth, height);
}
else
{
destinationRectangle = new RectangleF(0, 0, width, height);
}
destination.SmoothingMode = System.Drawing.Drawing2D.SmoothingMode.HighQuality;
destination.DrawImage(fullSizeBitmap, destinationRectangle, sourceRectangle, GraphicsUnit.Pixel);
}
return(scaledBitmap);
}
private void GenerateMatrices(string[,] values, out string error)
{
error = "";
try
{
if (values == null)
{
return;
}
RowCount = values.GetLength(0) - 1;
ColCount = values.GetLength(1) - 1;
QuantificationMatrix = new double[RowCount, ColCount];
NormalizedMatrix = new double[RowCount, ColCount];
WildTypePeptide = new string('X', PermutationXAxis ? RowCount : ColCount);
#region Generate permutation, position, and NormBy arrays
if (PermutationXAxis)
{
NormBy = new double[RowCount];
for (int iRow = 1; iRow <= RowCount; iRow++)
{
NormBy[iRow - 1] = 0;
}
Permutation = new char[ColCount];
PositionCaptions = new string[RowCount];
for (int iCol = 1; iCol <= ColCount; iCol++)
{
string s = values[0, iCol].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
error = "Not a valid permutation string";
return;
}
Permutation[iCol - 1] = s[0];
}
//PositionYAxisTopToBottom is not used in setting the position captions. What user sees should not change. Use it only during the motif generation
for (int iRow = 1; iRow <= RowCount; iRow++)
{
string s = values[iRow, 0].Trim();
PositionCaptions[iRow - 1] = s;
}
}
else //if(PermutationYAxis)
{
NormBy = new double[ColCount];
for (int iCol = 1; iCol <= ColCount; iCol++)
{
NormBy[iCol - 1] = 0;
}
Permutation = new char[RowCount];
PositionCaptions = new string[ColCount];
for (int iRow = 1; iRow <= RowCount; iRow++)
{
string s = values[iRow, 0].Trim();
if (AminoAcids.GetAminoAcid(s[0]) == null)
{
error = "Not a valid permutation string";
return;
}
Permutation[iRow - 1] = s[0];
}
for (int iCol = 1; iCol <= ColCount; iCol++)
{
string s = values[0, iCol].Trim();
PositionCaptions[iCol - 1] = s;
}
}
#endregion
//Generate Matrices and Normalization values
for (int iRow = 0; iRow < RowCount; iRow++)
{
for (int iCol = 0; iCol < ColCount; iCol++)
{
double d = 0;
if (double.TryParse(values[iRow + 1, iCol + 1], out d))
{
QuantificationMatrix[iRow, iCol] = d;
}
else if (string.IsNullOrEmpty(values[iRow + 1, iCol + 1]))
{
d = 0;
}
else
{
error = "Wrongly formatted data.";
return;
}
if (PermutationXAxis)
{
NormBy[iRow] = Math.Max(d, NormBy[iRow]);
}
else
{
NormBy[iCol] = Math.Max(d, NormBy[iCol]);
}
}
}
for (int iRow = 0; iRow < RowCount; iRow++)
{
for (int iCol = 0; iCol < ColCount; iCol++)
{
double normby = PermutationXAxis ? NormBy[iRow] : NormBy[iCol];
if (normby != 0)
{
NormalizedMatrix[iRow, iCol] = QuantificationMatrix[iRow, iCol] / normby;
}
}
}
NormalizationValue = NormBy.Max();
GenerateNormalizedPeptideWeights();
}
catch (Exception exc)
{
error = "Unhandled exception: " + exc.Message;
}
}
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;
}
}
