public Peak(double mz, double intensity, IonSpectrum spectrum)
{
this.mz = mz;
this.intensity = intensity;
this.spectrum = spectrum;
this.consecutiveNeutralLossIndex = 0;
}
public static bool AreEqual(IonSpectrum a, IonSpectrum b)
{
if (a.lineIndex_begin == b.lineIndex_begin && a.lineIndex_end == b.lineIndex_end && a.title == b.title &&
a.pepmass == b.pepmass && a.pepmass_intensity == b.pepmass_intensity && a.charge == b.charge && a.z == b.z &&
a.retentionTime == b.retentionTime && a.scans == b.scans && a.isPositiveIonMode == b.isPositiveIonMode)
{
if (a.peaks.Count == b.peaks.Count)
{
return true;
}
}
return false;
}
public SpectrumViewer(IonSpectrum spectrum, List<Peak> peaks)
{
InitializeComponent();
this.Activate();
this.Focus();
this.Topmost = true;
this.Title = "Spectrum Viewer - " + spectrum.title;
// Set up LineSeries Chart - see example at http://wpf.codeplex.com/discussions/232267
this.spectrum = spectrum;
DataContext = this;
_data = new ObservableCollection<KeyValuePair<double, double>>();
foreach (Peak p in spectrum.peaks)
data.Add(new KeyValuePair<double, double>(p.mz, p.intensity));
_highlightedPeaks = new ObservableCollection<KeyValuePair<double, double>>();
foreach (Peak p in peaks)
_highlightedPeaks.Add(new KeyValuePair<double, double>(p.mz, p.intensity));
}
public IonSpectrum getIonSpectrum2()
{
IonSpectrum expectedSpectrum2 = new IonSpectrum();
expectedSpectrum2.title = "File565 Spectrum2 scans: 4";
expectedSpectrum2.pepmass = "506.38400";
expectedSpectrum2.pepmass_intensity = "3076.27000";
expectedSpectrum2.charge = "2+";
expectedSpectrum2.retentionTime = 2;
expectedSpectrum2.scans = 4;
expectedSpectrum2.AddPeak(157.043, 5.19905);
expectedSpectrum2.AddPeak(175.127, 5.34553);
expectedSpectrum2.AddPeak(202.957, 4.52134);
expectedSpectrum2.AddPeak(208.036, 2.51525);
expectedSpectrum2.AddPeak(216.957, 2.84039);
expectedSpectrum2.AddPeak(221.419, 3.91015);
expectedSpectrum2.AddPeak(223.048, 4.78027);
expectedSpectrum2.AddPeak(228.053, 3.37681);
expectedSpectrum2.AddPeak(228.835, 1.09891);
expectedSpectrum2.AddPeak(230.047, 4.48171);
expectedSpectrum2.AddPeak(246.991, 7.47876);
expectedSpectrum2.AddPeak(260.046, 4.58196);
expectedSpectrum2.AddPeak(265.090, 5.2341);
expectedSpectrum2.AddPeak(265.811, 12.9218);
expectedSpectrum2.AddPeak(268.218, 3.58545);
expectedSpectrum2.AddPeak(269.078, 5.97038);
return expectedSpectrum2;
}
public IonSpectrum getIonSpectrum1()
{
IonSpectrum expectedSpectrum1 = new IonSpectrum();
expectedSpectrum1.title = "File565 Spectrum1 scans: 3";
expectedSpectrum1.pepmass = "508.90073";
expectedSpectrum1.pepmass_intensity = "1994.07000";
expectedSpectrum1.charge = "2+";
expectedSpectrum1.retentionTime = 2;
expectedSpectrum1.scans = 3;
expectedSpectrum1.AddPeak(170.084, 1.30444);
expectedSpectrum1.AddPeak(195.201, 3.68346);
expectedSpectrum1.AddPeak(202.326, 7.06028);
expectedSpectrum1.AddPeak(211.204, 3.53445);
expectedSpectrum1.AddPeak(213.118, 2.86394);
expectedSpectrum1.AddPeak(221.046, 8.60954);
expectedSpectrum1.AddPeak(239.047, 2.50649);
return expectedSpectrum1;
}
//
//You can use the following additional attributes as you write your tests:
//
public static bool AreSpectraEqual(IonSpectrum spectrum1, IonSpectrum spectrum2)
{
if (spectrum1 == null || spectrum2 == null)
{
if (spectrum1 == spectrum2)
return true;
else
return false;
}
if (spectrum1.title != spectrum2.title)
return false;
if (spectrum1.pepmass != spectrum2.pepmass)
return false;
if (spectrum1.charge != spectrum2.charge)
return false;
if (spectrum1.retentionTime != spectrum2.retentionTime)
return false;
if (spectrum1.scans != spectrum2.scans)
return false;
if (spectrum1.peaks.Count != spectrum2.peaks.Count)
return false;
for (int i = 0; i < spectrum1.peaks.Count; i++)
{
if (spectrum1.peaks[i].mz != spectrum2.peaks[i].mz)
return false;
if (spectrum1.peaks[i].intensity != spectrum2.peaks[i].intensity)
return false;
}
return true;
}
public IonSpectrum getTestIonSpectrum()
{
IonSpectrum spectrum = new IonSpectrum();
spectrum.charge = "2+";
// Add a phosphate neutral loss series
spectrum.AddPeak(228.2, 100);
spectrum.AddPeak(179.2, 90);
spectrum.AddPeak(130.3, 76);
// Add a near-miss phosphate peaks
spectrum.AddPeak(179.39, 84);
spectrum.AddPeak(132.0, 80);
// Add some random noise
spectrum.AddPeak(140.17, 48);
spectrum.AddPeak(130.1, 10);
spectrum.AddPeak(77, 33);
spectrum.AddPeak(61.9, 2);
spectrum.AddPeak(35, 11);
spectrum.AddPeak(33, 19);
spectrum.AddPeak(31, 7);
spectrum.AddPeak(22, 24);
return spectrum;
}
public IonSpectrum parseSpectrum(int ionStartLineIndex, System.IO.StreamReader sr)
{
IonSpectrum spectrum = null;
bool isInsideIonSpectrum = false;
int i = ionStartLineIndex;
if (i < 0)
return null;
string line = "";
isInsideIonSpectrum = true; // We're assuming the passed "sr" variable is currently AT the "BEGIN IONS" line
spectrum = new IonSpectrum();
spectrum.lineIndex_begin = i;
while((line = sr.ReadLine()) != null)
{
i++;
if (isInsideIonSpectrum)
{
if (line.Contains("TITLE="))
spectrum.title = line.Substring(6);
else if (line.Contains("PEPMASS="))
{
string[] pepmassInfo = line.Substring(8).Split(' ');
if (pepmassInfo.Length == 2)
{
spectrum.pepmass = pepmassInfo[0];
spectrum.pepmass_intensity = pepmassInfo[1];
}
else if (pepmassInfo.Length == 1)
spectrum.pepmass = pepmassInfo[0];
}
else if (line.Contains("CHARGE="))
spectrum.charge = line.Substring(7);
else if (line.Contains("RTINSECONDS="))
spectrum.retentionTime = Double.Parse(line.Substring(12));
else if (line.Contains("SCANS="))
spectrum.scans = Int32.Parse(line.Substring(6));
else if (line.Trim().Equals("END IONS"))
{
isInsideIonSpectrum = false;
spectrum.lineIndex_end = i;
break;
}
else
{
string[] tokens = line.Trim().Split(' ');
if (tokens.Length != 2)
Console.WriteLine("Failed to parse the line, " + line + ". Skipping line.");
else
{
try
{
double mz = Double.Parse(tokens[0]);
double intensity = Double.Parse(tokens[1]);
spectrum.AddPeak(mz, intensity);
}
catch
{
Console.WriteLine("Failed to parse the line, " + line + ". Skipping line.");
}
}
}
}
}
if (isInsideIonSpectrum)
{
Console.WriteLine("Warning: An ion's MS2 spectrum was not closed by the line, END IONS.");
spectrum.lineIndex_end = -1;
}
return spectrum;
}
