public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
Task msgen = new GenericMSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
MSPeak testPeak = (MSPeak)run.PeakList[500];
PattersonChargeStateCalculator chargeCalc = new PattersonChargeStateCalculator();
short chargeState = chargeCalc.GetChargeState(run.XYData, run.PeakList, testPeak);
Console.WriteLine(testPeak.XValue + "; Charge = " + chargeState);
}
public void HardCase1()
{
// https://jira.pnnl.gov/jira/browse/OMCS-647
Run run = new XCaliburRun2(xcaliburTestfile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
//579.535
//TestUtilities.DisplayPeaks(run.PeakList);
var peak = run.PeakList.First(n => n.XValue > 579.53 && n.XValue < 579.54);
var chargeState = PattersonChargeStateCalculator.GetChargeState(run.XYData, run.PeakList, peak as MSPeak);
Assert.AreEqual(4, chargeState);
Console.WriteLine("charge State: " + chargeState);
var times = new List <long>();
// return;
for (var i = 0; i < 500; i++)
{
var sw = new Stopwatch();
sw.Start();
chargeState = PattersonChargeStateCalculator.GetChargeState(run.XYData, run.PeakList, peak as MSPeak);
sw.Stop();
times.Add(sw.ElapsedMilliseconds);
}
Console.WriteLine("average time in ms= " + times.Average());
}
public void EasyCase1()
{
// https://jira.pnnl.gov/jira/browse/OMCS-647
Run run = new XCaliburRun2(xcaliburTestfile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var peak = run.PeakList.First(n => n.XValue > 903.94 && n.XValue < 903.95);
var chargeState = PattersonChargeStateCalculator.GetChargeState(run.XYData, run.PeakList, peak as MSPeak);
Assert.AreEqual(2, chargeState);
}
/// <summary>
/// The main Thrash algorithm.
/// </summary>
/// <param name="originalXYData">Mass spec XY data</param>
/// <param name="mspeakList">Mass spec peak data</param>
/// <param name="backgroundIntensity"></param>
/// <param name="minPeptideIntensity"></param>
/// <param name="minMSFeatureToBackgroundRatio"></param>
/// <returns>List of isotopic profiles</returns>
public List <IsotopicProfile> PerformThrash(XYData originalXYData,
List <Peak> mspeakList,
double backgroundIntensity = 0,
double minPeptideIntensity = 0, double
minMSFeatureToBackgroundRatio = 3)
{
var isotopicProfiles = new List <IsotopicProfile>();
#region Paul Addition
var myIsotopicProfiles = new List <IsotopicProfile>();
var otherIsotopicProfiles = new List <IsotopicProfile>();
#endregion
if (Parameters.AreAllTheoreticalProfilesCachedBeforeStarting)
{
CreateAllTheoreticalProfilesForMassRange();
}
var minMSFeatureIntensity = backgroundIntensity * minMSFeatureToBackgroundRatio;
var xyData = new XYData();
xyData.Xvalues = originalXYData.Xvalues;
xyData.Yvalues = originalXYData.Yvalues;
var peaksThatWereProcessedInfo = new Dictionary <Peak, bool>();
var sortedPeaklist = new List <Peak>(mspeakList).OrderByDescending(p => p.Height).ToList();
var peaksAlreadyProcessed = new HashSet <Peak>();
var stringBuilder = new StringBuilder();
var listOfMonoMZs = new SortedDictionary <int, double>();
var currentUniqueMSFeatureIDNum = 0;
var peakCounter = -1;
foreach (var msPeak in sortedPeaklist)
{
//if (msPeak.XValue > 579.53 && msPeak.XValue < 579.54)
//{
// int x = 90;
//}
var indexOfCurrentPeak = mspeakList.IndexOf(msPeak);
if (peaksAlreadyProcessed.Contains(msPeak))
{
continue;
}
var peakIsBelowIntensityThreshold = (msPeak.Height < minMSFeatureIntensity);
if (peakIsBelowIntensityThreshold)
{
break;
}
peakCounter++;
if (peakCounter == 465)
{
// Console.WriteLine(peakCounter);
}
//get potential charge states
var ppmTolerance = (msPeak.Width / 2.35) / msPeak.XValue * 1e6; // peak's sigma value / mz * 1e6
HashSet <int> potentialChargeStates;
// HashSet<int> potentialChargeStatesbyPaul;
if (UseAutocorrelationChargeDetermination && false)
{
var chargeState = PattersonChargeStateCalculator.GetChargeState(xyData, mspeakList, msPeak as MSPeak);
potentialChargeStates = new HashSet <int>();
potentialChargeStates.Add(chargeState);
}
else
{ //Paul subtraction
IqLogger.Log.Debug("MZ value: " + msPeak.XValue + "\n");
potentialChargeStates = GetPotentialChargeStates(indexOfCurrentPeak, mspeakList, ppmTolerance);
#region Paul Addition
// ChromCorrelatingChargeDecider chargeDecider= new ChromCorrelatingChargeDecider(_run);
// potentialChargeStatesbyPaul=chargeDecider.GetPotentialChargeState(indexOfCurrentPeak, mspeakList, ppmTolerance);
//potentialChargeStates = potentialChargeStatesbyPaul;
#endregion
}
var reportString201 = "potentialChargeStates: ";
foreach (var charge in potentialChargeStates)
{
reportString201 += charge + "\t";
}
IqLogger.Log.Debug(reportString201 + "\n");
var potentialMSFeaturesForGivenChargeState = new List <IsotopicProfile>();
foreach (var potentialChargeState in potentialChargeStates)
{
var bestFitVal = 1.0; // 1.0 is worst fit value. Start with 1.0 and see if we can find better fit value
IsotopicProfile theorIso;
//TODO: there could be a problem here
var msFeature = GetMSFeature(mspeakList, xyData, potentialChargeState, msPeak, ref bestFitVal, out theorIso);
if (msFeature != null)
{
msFeature.Score = bestFitVal;
msFeature.IntensityMostAbundant = msFeature.getMostIntensePeak().Height;
var indexMostAbundantPeakTheor = theorIso.GetIndexOfMostIntensePeak();
//Paul edit. "&& indexMostAbundantPeakTheor>=0"
if (msFeature.Peaklist.Count > indexMostAbundantPeakTheor && indexMostAbundantPeakTheor >= 0)
{
msFeature.IntensityMostAbundantTheor = msFeature.Peaklist[indexMostAbundantPeakTheor].Height;
}
else
{
msFeature.IntensityMostAbundantTheor = msFeature.IntensityMostAbundant;
}
var msFeatureAlreadyPresentInAnotherChargeState = listOfMonoMZs.ContainsValue(msFeature.MonoPeakMZ);
if (!msFeatureAlreadyPresentInAnotherChargeState)
{
potentialMSFeaturesForGivenChargeState.Add(msFeature);
}
else
{
//Console.WriteLine( "Nope... not using this charge state... MSFeature already found with same MonoMZ. \tcurrent peak= \t" +msPeak.XValue.ToString("0.0000") + "\tmsfeature= " + msFeature);
}
}
}
IsotopicProfile msfeature = null;//Paul Addition "=null"
if (potentialMSFeaturesForGivenChargeState.Count == 0)
{
stringBuilder.Append(msPeak.XValue.ToString("0.00000") + "\tNo profile found.\n");
msfeature = null;
}
else if (potentialMSFeaturesForGivenChargeState.Count == 1)
{
msfeature = potentialMSFeaturesForGivenChargeState[0];
stringBuilder.Append(msPeak.XValue.ToString("0.00000") + "\t" +
msfeature.MonoPeakMZ.ToString("0.0000") + "\t" +
msfeature.ChargeState + "\t" + msfeature.Score + "\t" + ppmTolerance + "\n");
}
else
{
stringBuilder.Append("Multiple candidates found...." + "\n");
foreach (var isotopicProfile in potentialMSFeaturesForGivenChargeState)
{
stringBuilder.Append(msPeak.XValue.ToString("0.00000") + "\t" +
isotopicProfile.MonoPeakMZ.ToString("0.0000") + "\t" +
isotopicProfile.ChargeState + "\t" + isotopicProfile.Score + "\t" + ppmTolerance + "\n");
}
stringBuilder.Append(Environment.NewLine);
if (Parameters.CheckAllPatternsAgainstChargeState1)
{
msfeature = potentialMSFeaturesForGivenChargeState.FirstOrDefault(n => n.ChargeState == 1);
}
else
{
#region Paul addition
//TODO: [Paul] This is the major means of deciding between charge states and where we need to do better.
//We need some test cases to capture this problem.
var stopwatch = new Stopwatch();
if (doPaulMethod)
{
var peaksNotLoaded = _run.ResultCollection.MSPeakResultList == null ||
_run.ResultCollection.MSPeakResultList.Count == 0;
if (peaksNotLoaded)// || !importedFULLPeaks)
{
stopwatch.Start();
LoadPeaks(_run);
//importedFULLPeaks = true;
stopwatch.Stop();
IqLogger.Log.Debug("stopwatch: " + stopwatch.Elapsed);
}
var brain = new ChromCorrelatingChargeDecider(_run);
msfeature = brain.DetermineCorrectIsotopicProfile(potentialMSFeaturesForGivenChargeState.Where(n => n.Score < .50).ToList());
//if (msfeature==null)
//{
// msfeature = brain.DetermineCorrectIsotopicProfile(potentialMSFeaturesForGivenChargeState);
//}
//hitcounter2++;
}
else//do it the regular way.
{
#endregion
msfeature = (from n in potentialMSFeaturesForGivenChargeState
where n.Score < 0.15
orderby n.ChargeState descending
select n).FirstOrDefault();
if (msfeature == null)
{
msfeature = (from n in potentialMSFeaturesForGivenChargeState
orderby n.Score
select n).First();
}
#region Paul Addition
}
//line outputs.
if (null != msfeature)
{
var reportString309 = "\nM/Z = " + msfeature.MonoPeakMZ +
"\nCHOSEN CHARGE: " + msfeature.ChargeState + "\n\n";
IqLogger.Log.Debug(reportString309);
//tabular output
//string reportString309 = "\tM/Z = \t" + msfeature.MonoPeakMZ +
// "\tCHOSEN CHARGE: \t" + msfeature.ChargeState+ "\n";
//IqLogger.Log.Debug(reportString309);
}
#endregion
}
}
if (msfeature != null)
{
listOfMonoMZs.Add(currentUniqueMSFeatureIDNum, msfeature.MonoPeakMZ);
currentUniqueMSFeatureIDNum++;
isotopicProfiles.Add(msfeature);
//hitcounter++;//Paul Addition
foreach (var peak in msfeature.Peaklist)
{
//For debugging
//if (peak.XValue > 534.76515 && peak.XValue < 534.78515) //(peak.XValue>579.62 && peak.XValue<579.65) || (peak.XValue>579.75 && peak.XValue<579.8))
//{
// int x = 39843;
//}
peaksAlreadyProcessed.Add(peak);
}
}
}//end of foreach peak loop
//Console.WriteLine(stringBuilder.ToString());
var uniqueIsotopicProfiles = removeDuplicatesFromFoundMSFeatures(isotopicProfiles);
#region Paul Addition
//IqLogger.Log.Debug("Hit counter: " + hitcounter);
//IqLogger.Log.Debug("Hit counter2: " + hitcounter2);
//var uniqueOtherIsotopicProfiles = removeDuplicatesFromFoundMSFeatures(isotopicProfiles);
//IqLogger.Log.Debug("old non unique count: " + otherIsotopicProfiles.Count + "\n" +
// "new non unique count: " + myIsotopicProfiles.Count + "\n");
//var uniqueMyIsotopicProfiles = removeDuplicatesFromFoundMSFeatures(myIsotopicProfiles);
//IqLogger.Log.Debug("\nOld unique profile count: " + uniqueOtherIsotopicProfiles.Count + "\n" +
// "New unique profile count: " + uniqueMyIsotopicProfiles.Count);
//IqLogger.Log.Debug("\nunique profile count: " + uniqueIsotopicProfiles.Count + "\n");
#endregion
//NOTE: we don't need to do the reordering, but I do this so I can compare to the old THRASH
uniqueIsotopicProfiles = uniqueIsotopicProfiles.OrderByDescending(p => p.IntensityMostAbundantTheor).ToList();
return(uniqueIsotopicProfiles);
}