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; }
public void TestBuild() { var aas = new Aminoacids(); aas['*'].ResetMass(79.9799, 79.9799); aas['C'].ResetMass(160.1652, 160.1652); var builder = new CIDPeptideB2SeriesBuilder<IonTypePeak>() { CurAminoacids = aas }; List<IonTypePeak> pkl = builder.Build("APYMEEQLQLLMCKYPEMT*LEDK"); //Output(pkl, IonType.B2); Assert.IsTrue(pkl.All(m => m.Charge == 2)); Assert.AreEqual(22, pkl.Count); AssertPeak(pkl[0], IonType.B2, 1, 36.5264); AssertPeak(pkl[1], IonType.B2, 2, 85.0528); AssertPeak(pkl[2], IonType.B2, 3, 166.5844); AssertPeak(pkl[3], IonType.B2, 4, 232.1047); AssertPeak(pkl[4], IonType.B2, 5, 296.6260); AssertPeak(pkl[5], IonType.B2, 6, 361.1473); AssertPeak(pkl[6], IonType.B2, 7, 425.1765); AssertPeak(pkl[7], IonType.B2, 8, 481.7186); AssertPeak(pkl[8], IonType.B2, 9, 545.7479); AssertPeak(pkl[9], IonType.B2, 10, 602.2899); AssertPeak(pkl[10], IonType.B2, 11, 658.8319); AssertPeak(pkl[11], IonType.B2, 12, 724.3522); AssertPeak(pkl[12], IonType.B2, 13, 804.4348); AssertPeak(pkl[13], IonType.B2, 14, 868.4823); AssertPeak(pkl[14], IonType.B2, 15, 950.0139); AssertPeak(pkl[15], IonType.B2, 16, 998.5403); AssertPeak(pkl[16], IonType.B2, 17, 1063.0616); AssertPeak(pkl[17], IonType.B2, 18, 1128.5818); AssertPeak(pkl[18], IonType.B2, 19, 1219.0956); AssertPeak(pkl[19], IonType.B2, 20, 1275.6377); AssertPeak(pkl[20], IonType.B2, 21, 1340.1590); AssertPeak(pkl[21], IonType.B2, 22, 1397.6724); }
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; }