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;
}
private void AddIonSeries(GraphPane peakPane, GraphPane ppmPane, PeakList <MatchedPeak> mgf, double mzTolerance, double minIntensity, IPeptideFragmentationBuilder <MatchedPeak> builder, string sequence, Color tagColor)
{
MatchedPeakUtils.Match(mgf, builder.Build(sequence), mzTolerance, minIntensity);
var ionType = builder.SeriesType.ToString();
var matchedIons = (from m in mgf
where m.Matched && m.PeakType == builder.SeriesType
select m).ToList();
var ppl = new PointPairList();
foreach (var m in matchedIons)
{
ppl.Add(new PointPair(m.Mz, m.Intensity, m.Information));
}
peakPane.AddIndividualLine("", ppl, Color.Black, tagColor);
if (ppmPane != null)
{
var diff = new PointPairList();
foreach (var m in matchedIons)
{
if (isPPM)
{
diff.Add(new PointPair(m.Mz, PrecursorUtils.mz2ppm(m.Mz, m.Mz - m.MatchedMZ)));
}
else
{
diff.Add(new PointPair(m.Mz, m.Mz - m.MatchedMZ));
}
}
ppmPane.AddPoints(diff, tagColor);
}
}
