/// <summary>
/// The Thermo decon result filename is assumed to be the same as the spectra file name
/// </summary>
private static AnnotatedSpecies GetThermoDeconSpecies(string line, StreamReader reader, string fileName)
{
string[] items = line.Split(ItemDelimiter);
int numCharges = int.Parse(items[3]); // TODO: get this from header, not hardcoded
List <int> chargeList = new List <int>();
double mass = double.Parse(items[MonoisotopicMassColumn]);
string speciesName = items[SpeciesNameColumn] + " (" + mass.ToString("F1") + ")";
double apexRt = double.Parse(items[RetentionTimeColumn]);
string rtRange = items[FeatureRtStartColumn];
double rtStart = double.Parse(rtRange.Split('-')[0].Trim());
double rtEnd = double.Parse(rtRange.Split('-')[1].Trim());
for (int i = 0; i < numCharges + 1; i++)
{
var nextLine = reader.ReadLine();
var chargeLineSplit = nextLine.Split(ItemDelimiter);
if (chargeLineSplit[1].Trim().Equals("Charge State", StringComparison.OrdinalIgnoreCase))
{
continue;
}
chargeList.Add(int.Parse(chargeLineSplit[1]));
}
var deconFeature = new DeconvolutionFeature(mass, apexRt, rtStart, rtEnd, chargeList, fileName);
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
private void SpeciesListView_SelectedItemChanged(object sender, RoutedPropertyChangedEventArgs <object> e)
{
AnnotatedSpecies species = ((TreeView)sender).SelectedItem as AnnotatedSpecies;
MsDataScan scan = null;
var file = SpectraFiles.FirstOrDefault(p => System.IO.Path.GetFileNameWithoutExtension(p.Key)
== species.DeconvolutionFeature.SpectraFileNameWithoutExtension);
if (file.Value == null)
{
MessageBox.Show("The spectra file '" + species.DeconvolutionFeature.SpectraFileNameWithoutExtension + "' has not been loaded");
}
CurrentlySelectedSpectraFile = file;
for (int i = 1; i < 10000000; i++)
{
var theScan = file.Value.GetOneBasedScanFromDynamicConnection(i);
if (theScan.RetentionTime >= species.DeconvolutionFeature.ApexRt && theScan.MsnOrder == 1)
{
scan = theScan;
break;
}
}
PlotSpecies(species, scan);
}
private static AnnotatedSpecies GetTdPortalSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string baseSequence = items[SpeciesNameColumn];
string modSequence = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
// TD portal does not report precursor charge
var id = new Identification(baseSequence, modSequence, mass, -1);
var species = new AnnotatedSpecies(id);
return(species);
}
private static AnnotatedSpecies GetMetaMorpheusSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string baseSequence = items[SpeciesNameColumn];
string modSequence = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int charge = int.Parse(items[ChargeColumn]);
var id = new Identification(baseSequence, modSequence, mass, charge);
var species = new AnnotatedSpecies(id);
return(species);
}
private static AnnotatedSpecies GetFlashDeconvSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string identifier = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int minChargeState = int.Parse(items[MinChargeColumn]);
int maxChargeState = int.Parse(items[MaxChargeColumn]);
var chargeList = Enumerable.Range(minChargeState, maxChargeState - minChargeState + 1).ToList();
double apexRt = double.Parse(items[RetentionTimeColumn]) / 60;
double rtStart = double.Parse(items[FeatureRtStartColumn]) / 60;
double rtEnd = double.Parse(items[FeatureRtEndColumn]) / 60;
string fileName = items[SpectraFileNameColumn];
var deconFeature = new DeconvolutionFeature(mass, apexRt, rtStart, rtEnd, chargeList, fileName);
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
private static AnnotatedSpecies GetProteoformExplorerSpecies(string line, StreamReader reader)
{
line = line.Replace("\"", string.Empty);
string[] items = line.Split(ItemDelimiter);
string identifier = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int charge = int.Parse(items[ChargeColumn]);
double apexRt = double.Parse(items[RetentionTimeColumn]);
string fileName = items[SpectraFileNameColumn];
int scan = int.Parse(items[ScanNumberColumn]);
var peaks = items[PeaksListColumn].Split(',').Select(p => double.Parse(p)).ToList();
var annotEnvelope = new AnnotatedEnvelope(scan, apexRt, charge, peaks);
var deconFeature = new DeconvolutionFeature(mass, apexRt, apexRt, apexRt, new List <int> {
charge
}, fileName, new List <AnnotatedEnvelope> {
annotEnvelope
});
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
public static List <AnnotatedSpecies> ReadSpeciesFromFile(string filePath, out List <string> errors)
{
var fileType = InputSourceType.Unknown;
errors = new List <string>();
var listOfSpecies = new List <AnnotatedSpecies>();
// open the file to read
StreamReader reader;
try
{
reader = new StreamReader(filePath);
}
catch (Exception e)
{
errors.Add("Error reading file " + filePath + "\n" + e.Message);
return(listOfSpecies);
}
// read the file
int lineNum = 0;
while (reader.Peek() > 0)
{
string line = reader.ReadLine();
lineNum++;
// determine file type from the header
if (lineNum == 1)
{
fileType = GetFileTypeFromHeader(line);
if (fileType == InputSourceType.Unknown)
{
errors.Add("Could not interpret header labels from file: " + filePath);
return(listOfSpecies);
}
continue;
}
// read the line + create the species object
AnnotatedSpecies species = null;
switch (fileType)
{
case InputSourceType.MetaMorpheus:
species = GetMetaMorpheusSpecies(line);
break;
case InputSourceType.FlashDeconv:
species = GetFlashDeconvSpecies(line);
break;
case InputSourceType.TDPortal:
species = GetTdPortalSpecies(line);
break;
case InputSourceType.ThermoDecon:
species = GetThermoDeconSpecies(line, reader, filePath);
break;
case InputSourceType.ProteoformExplorer:
species = GetProteoformExplorerSpecies(line, reader);
break;
}
// add the item to the list
if (species != null)
{
listOfSpecies.Add(species);
}
}
return(listOfSpecies);
}
private void PlotSpeciesIsotopeXics(AnnotatedSpecies species, MsDataScan scan, int?charge = null)
{
double rtWindowHalfWidth = 2.5;
MsDataScan startScan = null;
for (int i = scan.OneBasedScanNumber; i >= 1; i--)
{
var theScan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(i);
if (theScan.RetentionTime < scan.RetentionTime - rtWindowHalfWidth)
{
break;
}
startScan = theScan;
}
List <MsDataScan> scans = new List <MsDataScan>();
for (int i = startScan.OneBasedScanNumber; i < 1000000; i++)
{
var theScan = CurrentlySelectedSpectraFile.Value.GetOneBasedScanFromDynamicConnection(i);
if (theScan.RetentionTime > scan.RetentionTime + rtWindowHalfWidth)
{
break;
}
if (theScan.MsnOrder == 1)
{
scans.Add(theScan);
}
}
int z = species.DeconvolutionFeature.Charges[species.DeconvolutionFeature.Charges.Count / 2];
for (int i = 0; i < 10; i++)
{
List <Datum> xicData = new List <Datum>();
double isotopeMass = species.DeconvolutionFeature.MonoisotopicMass + i * Constants.C13MinusC12;
Tolerance t = new PpmTolerance(5);
foreach (var item in scans)
{
int index = item.MassSpectrum.GetClosestPeakIndex(isotopeMass.ToMz(z));
if (t.Within(item.MassSpectrum.XArray[index], isotopeMass.ToMz(z)))
{
xicData.Add(new Datum(item.RetentionTime, item.MassSpectrum.YArray[index]));
}
else
{
xicData.Add(new Datum(item.RetentionTime, 0));
}
}
if (i == 0)
{
XicPlot = new LinePlot(topPlotView, xicData);
}
else
{
XicPlot.AddLinePlot(xicData);
}
}
}
private void PlotSpecies(AnnotatedSpecies species, MsDataScan scan)
{
PlotSpeciesIsotopeXics(species, scan);
PlotSpeciesInSpectrum(species, scan);
}
private void PlotSpeciesInSpectrum(AnnotatedSpecies species, MsDataScan scan, int?charge = null)
{
// add non-annotated peaks
List <Datum> spectrumData = new List <Datum>();
for (int i = 0; i < scan.MassSpectrum.XArray.Length; i++)
{
spectrumData.Add(new Datum(scan.MassSpectrum.XArray[i], scan.MassSpectrum.YArray[i]));
}
SpectrumPlot = new SpectrumPlot(bottomPlotView, spectrumData);
// add annotated peaks
List <Datum> annotatedData = new List <Datum>();
List <int> chargesToPlot = new List <int>();
if (species.DeconvolutionFeature != null)
{
double mass = species.DeconvolutionFeature.MonoisotopicMass;
if (charge == null)
{
chargesToPlot.AddRange(species.DeconvolutionFeature.Charges);
}
else
{
chargesToPlot.Add(charge.Value);
}
foreach (var z in chargesToPlot)
{
Tolerance t = new PpmTolerance(5);
bool peakHasBeenObserved = false;
for (int i = 0; i < 20; i++)
{
double isotopeMass = (mass + i * Constants.C13MinusC12).ToMz(z);
int index = scan.MassSpectrum.GetClosestPeakIndex(isotopeMass);
double expMz = scan.MassSpectrum.XArray[index];
if (t.Within(expMz.ToMass(z), isotopeMass.ToMass(z)))
{
annotatedData.Add(new Datum(scan.MassSpectrum.XArray[index], scan.MassSpectrum.YArray[index]));
peakHasBeenObserved = true;
}
//else if (peakHasBeenObserved)
//{
// break;
//}
}
}
}
else if (species.Identification != null)
{
//TODO
}
SpectrumPlot.AddSpectrumPlot(annotatedData, OxyPlot.OxyColors.Blue, 2.0);
ZoomAxes(annotatedData, SpectrumPlot);
}
