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 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 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; } }