public void TestBuild() { var aas = new Aminoacids(); aas['*'].ResetMass(79.9799, 79.9799); aas['C'].ResetMass(160.1652, 160.1652); var builder = new CIDPeptideBSeriesBuilder<IonTypePeak>() { CurAminoacids = aas }; List<IonTypePeak> pkl = builder.Build("R.CGETVES*GDEKDLAK.A"); //Output(pkl, IonType.B); Assert.AreEqual(14, pkl.Count); AssertPeak(pkl[0], IonType.B, 1, 161.1730); AssertPeak(pkl[1], IonType.B, 2, 218.1945); AssertPeak(pkl[2], IonType.B, 3, 347.2371); AssertPeak(pkl[3], IonType.B, 4, 448.2848); AssertPeak(pkl[4], IonType.B, 5, 547.3532); AssertPeak(pkl[5], IonType.B, 6, 676.3958); AssertPeak(pkl[6], IonType.B, 7, 843.4077); AssertPeak(pkl[7], IonType.B, 8, 900.4292); AssertPeak(pkl[8], IonType.B, 9, 1015.4561); AssertPeak(pkl[9], IonType.B, 10, 1144.4987); AssertPeak(pkl[10], IonType.B, 11, 1272.5937); AssertPeak(pkl[11], IonType.B, 12, 1387.6206); AssertPeak(pkl[12], IonType.B, 13, 1500.7047); AssertPeak(pkl[13], IonType.B, 14, 1571.7418); }
public MatchImageBuilder(string mgfFile, string targetDir) { var mgfReader = new Mascot.MascotGenericFormatReader <MatchedPeak>(); var spectra = mgfReader.ReadFromFile(mgfFile); spectra.ForEach(m => m.Experimental = m.Experimental.Substring(0, m.Experimental.Length - 4)); mgfMap = spectra.ToDictionary(m => string.Format("{0}_{1}", m.Experimental, m.ScanTimes[0].Scan)); var mods = new Dictionary <char, double>(); mods['&'] = 7.017166; mods['#'] = 3.010071; mods['@'] = 6.013809; mods['*'] = 15.994919; mods['C'] = 57.021464 + aas['C'].MonoMass; // 160.16523; mods['K'] = 8.014206 + aas['K'].MonoMass; mods['R'] = 10.008270 + aas['R'].MonoMass; aas.SetModification(mods); yBuilder = new CIDPeptideYSeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; bBuilder = new CIDPeptideBSeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; y2Builder = new CIDPeptideY2SeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; b2Builder = new CIDPeptideB2SeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; zgcPeaks = new ZedGraphControl(); zgcPeaks.Width = 1600; zgcPeaks.Height = 1200; zgcPeaks.MasterPane.Border.IsVisible = false; zgcPeaks.InitMasterPanel(Graphics.FromImage(zgcPeaks.GetImage()), 2, ""); zgcPeaks.IsSynchronizeXAxes = true; if (!Directory.Exists(targetDir)) { Directory.CreateDirectory(targetDir); } this.targetDir = targetDir; }
private void btnOpen_Click(object sender, EventArgs e) { //var mgf = @"E:\backup\data\SAP\20111116_ZDSu_v_SAP_26_JPT_HCD.raw.mgf"; if (mgfFile.GetFileDialog().ShowDialog(this) == System.Windows.Forms.DialogResult.OK) { var mgf = mgfFile.GetFileDialog().FileName; var mgfReader = new Mascot.MascotGenericFormatReader <MatchedPeak>(); var spectra = mgfReader.ReadFromFile(mgf); spectra.ForEach(m => m.Experimental = m.Experimental.Substring(0, m.Experimental.Length - 4)); mgfMap = spectra.ToDictionary(m => string.Format("{0}_{1}", m.Experimental, m.ScanTimes[0].Scan)); } else { return; } //var peptideFile = @"E:\backup\data\SAP\final.peptides.type1.paired.one2one.mut"; if (pepFile.GetFileDialog().ShowDialog(this) == System.Windows.Forms.DialogResult.OK) { var peptideFile = pepFile.GetFileDialog().FileName; peptides = new MascotPeptideTextFormat().ReadFromFile(peptideFile); } else { return; } var annKeys = new string[] { "OriginalSequence", "PepMutation", "_PepCount", "_OriginalCount" }; foreach (var key in peptides[0].Annotations.Keys) { if (annKeys.Any(m => key.Contains(m))) { gvPeptides.Columns.Add(new DataGridViewTextBoxColumn() { HeaderText = key, Tag = 1 }); } } var mods = new Dictionary <char, double>(); mods['&'] = 7.017166; mods['#'] = 3.010071; mods['@'] = 6.013809; mods['*'] = 15.994919; mods['C'] = 57.021464 + aas['C'].MonoMass; // 160.16523; mods['K'] = 8.01 + aas['K'].MonoMass; mods['R'] = 10.01 + aas['R'].MonoMass; aas.SetModification(mods); yBuilder = new CIDPeptideYSeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; bBuilder = new CIDPeptideBSeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; y2Builder = new CIDPeptideY2SeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; b2Builder = new CIDPeptideB2SeriesBuilder <MatchedPeak>() { CurAminoacids = aas }; zgcPeaks.InitMasterPanel(this.CreateGraphics(), 2, ""); zgcPeaks.IsSynchronizeXAxes = true; gvPeptides.DataSource = peptides; }