public pHistBumpViewModel()
{
// Initialize this view model with default values
searchParams = new SearchParams();
mgf = null;
}
public SearchParams getDefaultSearchParams()
{
SearchParams searchParams = new SearchParams();
searchParams.isDeNovoSearch = false;
searchParams.neutralLossMass = "98";
searchParams.errorTolerance = "0.2500";
searchParams.intensityCutoff = "75";
searchParams.RTWindow = "120";
searchParams.maxNumberOfLosses = "1";
return searchParams;
}
public List<PeakResultView> findAllNeutralLossPeaks(SearchParams searchParams)
{
if (ionSpectra == null)
return null;
List<PeakResultView> neutralLossPeaks = new List<PeakResultView>();
foreach (IonSpectrum spectrum in ionSpectra)
{
// Filter out peaks that are below the intesity threshold. For our purposes, these are considered to be "noise" peaks
double maxIntensity = spectrum.getMaxIntensity();
List<Peak> peaksAboveIntensityThreshold = spectrum.peaks.FindAll(p => (p.intensity/maxIntensity)*100 >= searchParams.intensityCutoff_num);
// Search for neutral losses of the current parent ion
double pepmass = 0;
if (!Double.TryParse(spectrum.pepmass, out pepmass))
{
Console.WriteLine("Warning: Skipping spectrum, " + spectrum.title + ", because its pepmass is unreadable.");
continue;
}
List<Peak> peakList = spectrum.findNeutralLossPeaks(pepmass, searchParams);
// If we find any neutral loss peaks, add them to the list
if (peakList != null && peakList.Count > 0)
{
List<PeakResultView> peakResultView = new List<PeakResultView>();
double RT_begin = Math.Max((spectrum.retentionTime - (searchParams.RTWindow_num / 2)) / 60, 0);
double RT_end = (spectrum.retentionTime + (searchParams.RTWindow_num / 2)) / 60;
foreach (Peak p in peakList)
{
peakResultView.Add(new PeakResultView(p, maxIntensity, RT_begin, RT_end));
}
neutralLossPeaks.InsertRange(0, peakResultView);
}
}
neutralLossPeaks = neutralLossPeaks.OrderBy(p => p.spectrumTitle).ThenBy(p => p.pepmass).ToList();
return neutralLossPeaks;
}
public List<Peak> findNeutralLossPeaks(double parentMZ, SearchParams searchParams)
{
if (z == 0 || !isPositiveIonMode)
{
Console.WriteLine("Error: Cannot perform neutral loss search if precursor ion charge is invalid");
return null;
}
List<Peak> NLPeaks = new List<Peak>();
List<double> NLMassesFound = new List<double>();
double currentMaxIntensity = getMaxIntensity();
// Specify which NL Ions are primary NL ions we would like to search for (we don't want to search as if all the peaks input are primary NL peaks - that likely increases FP rate)
// TODO: implement UI interface to toggle a NL ion as a "primary" or "secondary" NL ion
List<double> primaryNLIons = new List<double>();
primaryNLIons.Add(searchParams.neutralLossMass_num[0]); // TODO: change - this is hardcoding that only the first ion is the primary NL peak
for (int NLMassIndex = 0; NLMassIndex < searchParams.neutralLossMass_num.Count; NLMassIndex++) // Cycle through each "parent"/primary neutral loss search ion
{
bool currentNLMassFound = false;
double currentNLMass = searchParams.neutralLossMass_num[NLMassIndex];
if (!primaryNLIons.Contains(currentNLMass))
continue; // Skip non-primary NL ions
for (int i = 0; i < searchParams.maxNumberOfLosses_num; i++) // Find the maximum number of neutral losses for the current primary NL ion
{
double searchMass = parentMZ - (Convert.ToDouble(i + 1) * currentNLMass) / z;
double searchMass_min = searchMass - (searchParams.errorTolerance_num);
double searchMass_max = searchMass + (searchParams.errorTolerance_num);
List<Peak> matchingPeaks = peaks.FindAll(anyPeak => anyPeak.mz <= searchMass_max && anyPeak.mz >= searchMass_min &&
(anyPeak.intensity / currentMaxIntensity) * 100 >= searchParams.intensityCutoff_num);
if (matchingPeaks != null)
{
if (matchingPeaks.Count > 0 && currentNLMassFound == false)
{
currentNLMassFound = true;
if (!NLMassesFound.Contains(currentNLMass))
NLMassesFound.Add(currentNLMass);
// Since we found a primary NL peak, find secondary ions with the secondary peak intensity cutoff
for (int NLMassIndex2 = 0; NLMassIndex2 < searchParams.neutralLossMass_num.Count; NLMassIndex2++)
{
if (NLMassIndex2 == NLMassIndex)
continue; // Skip the neutral loss mass that is currently the primary neutral loss
bool currentNLMassFound2 = false;
double currentNLMass2 = searchParams.neutralLossMass_num[NLMassIndex2];
double searchMass2 = parentMZ - (Convert.ToDouble(i + 1) * currentNLMass2) / z;
double searchMass_min2 = searchMass2 - (searchParams.errorTolerance_num);
double searchMass_max2 = searchMass2 + (searchParams.errorTolerance_num);
List<Peak> matchingPeaks2 = peaks.FindAll(anyPeak => anyPeak.mz <= searchMass_max2 && anyPeak.mz >= searchMass_min2 &&
(anyPeak.intensity / currentMaxIntensity) * 100 >= searchParams.intensityCutoff2_num);
// Account for the secondary peak being found
if (matchingPeaks2.Count > 0 && currentNLMassFound2 == false)
{
currentNLMassFound2 = true;
if (!NLMassesFound.Contains(currentNLMass2))
NLMassesFound.Add(currentNLMass2);
}
// Add the secondary peaks to the matching peak list
foreach (Peak p_secondary in matchingPeaks2)
{
if (!matchingPeaks.Exists(somePeak => Peak.AreEqual(somePeak, p_secondary)))
matchingPeaks.Add(p_secondary);
}
}
}
// Assign each peak in matchingPeaks a consecutive neutral loss index, then add the peak to the
// NLPeaks master list if it doesn't already exist within it
foreach (Peak p in matchingPeaks)
{
p.consecutiveNeutralLossIndex = i + 1;
if ( !NLPeaks.Exists(somePeak => Peak.AreEqual(somePeak, p)) )
NLPeaks.Add(p);
}
}
}
}
if (searchParams.allNLsRequiredPerSpectrum)
{
if (NLMassesFound.Count == searchParams.neutralLossMass_num.Count)
return NLPeaks;
else
return new List<Peak>();
}
else
return NLPeaks;
}