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;
}