Soften calibration tolerance (#2423)

* update mzlib nuget package to 551

* revise path to selection of calibration tolerances

* fasd

* works

* u

* zCX

* revert most changes run on dataAcquisition and one calibration

* fas

* delete unused code in DataPointAcquisitionResults

* calibration task unit test coverage existing toml

* no calibration psms unit test

* correctly update experimental design file after failed calibration

MetaMorpheus/EngineLayer/Calibration/CalibrationEngine.cs

@@ -63,12 +63,6 @@ protected override MetaMorpheusEngineResults RunSpecific()
             //generate new scans
             MsDataScan[] calibratedScans = new MsDataScan[originalScans.Count];
 
-            //hard copy original scans
-            for (int i = 0; i < originalScans.Count; i++)
-            {
-                calibratedScans[i] = originalScans[i];
-            }
-
             //apply a smoothing function, so that outlier scans aren't wildly shifted
             double[] ms1SmoothedErrors = SmoothErrors(ms1RelativeErrors);
             double[] ms2SmoothedErrors = new double[ms2RelativeErrors.Length];

MetaMorpheus/EngineLayer/Calibration/DataPointAcquisitionEngine.cs

@@ -236,6 +236,9 @@ private static List<LabeledDataPoint> SearchMS2Spectrum(Ms2ScanWithSpecificMass
                 double theoreticalMass = matchedIon.NeutralTheoreticalProduct.NeutralMass;
                 //get envelopes that match
                 var envelopesThatMatch = isotopicEnvelopes.Where(x => ms2Tolerance.Within(x.MonoisotopicMass, theoreticalMass)).OrderBy(x => Math.Abs(x.MonoisotopicMass - theoreticalMass)).ToList();
+
+                if(envelopesThatMatch.Count == 0)
+                    continue;
                 //only allow one envelope per charge state
                 bool[] chargeStateFound = new bool[envelopesThatMatch.Max(x => x.Charge) + 1];
 

MetaMorpheus/EngineLayer/Calibration/DataPointAquisitionResults.cs

@@ -7,6 +7,9 @@
 
 namespace EngineLayer.Calibration
 {
+    /// <summary>
+    /// Returns PSMs that can be used for calibration based on tolerance limits passed from the calibration task
+    /// </summary>
     public class DataPointAquisitionResults : MetaMorpheusEngineResults
     {
         public DataPointAquisitionResults(
@@ -27,19 +30,9 @@ public DataPointAquisitionResults(
 
             var ms1Range = Ms1List.Select(b => b.ExperimentalMz - b.TheoreticalMz).ToArray();
             var ms2Range = Ms2List.Select(b => b.ExperimentalMz - b.TheoreticalMz).ToArray();
-            Ms1InfoTh = new Tuple<double, double>(ArrayStatistics.Mean(ms1Range), ArrayStatistics.StandardDeviation(ms1Range));
-            Ms2InfoTh = new Tuple<double, double>(ArrayStatistics.Mean(ms2Range), ArrayStatistics.StandardDeviation(ms2Range));
-
 
             var ms1PpmRange = Ms1List.Select(b => (b.ExperimentalMz - b.TheoreticalMz) / b.TheoreticalMz).ToArray();
             var ms2PpmRange = Ms2List.Select(b => (b.ExperimentalMz - b.TheoreticalMz) / b.TheoreticalMz).ToArray();
-            Ms1InfoPpm = new Tuple<double, double>(ArrayStatistics.Mean(ms1PpmRange), ArrayStatistics.StandardDeviation(ms1PpmRange));
-            Ms2InfoPpm = new Tuple<double, double>(ArrayStatistics.Mean(ms2PpmRange), ArrayStatistics.StandardDeviation(ms2PpmRange));
-
-            NumMs1MassChargeCombinationsConsidered = numMs1MassChargeCombinationsConsidered;
-            NumMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks;
-            NumMs2MassChargeCombinationsConsidered = numMs2MassChargeCombinationsConsidered;
-            NumMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks;
 
             var precursorErrors = psms.Select(p => (p.ScanPrecursorMass - p.BioPolymerWithSetModsMonoisotopicMass.Value) / p.BioPolymerWithSetModsMonoisotopicMass.Value * 1e6).ToList();
             PsmPrecursorIqrPpmError = precursorErrors.InterquartileRange();
@@ -50,16 +43,6 @@ public DataPointAquisitionResults(
             PsmProductMedianPpmError = productErrors.Median();
         }
 
-        public Tuple<double, double> Ms1InfoTh { get; }
-        public Tuple<double, double> Ms2InfoTh { get; }
-        public Tuple<double, double> Ms1InfoPpm { get; }
-        public Tuple<double, double> Ms2InfoPpm { get; }
-
-        public int NumMs1MassChargeCombinationsConsidered { get; }
-        public int NumMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks { get; }
-        public int NumMs2MassChargeCombinationsConsidered { get; }
-        public int NumMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks { get; }
-
         public List<LabeledDataPoint> Ms1List { get; }
         public List<LabeledDataPoint> Ms2List { get; }
 
@@ -69,8 +52,6 @@ public DataPointAquisitionResults(
         public readonly double PsmProductIqrPpmError;
         public readonly List<SpectralMatch> Psms;
 
-        public int Count { get { return Ms1List.Count + Ms2List.Count; } }
-
         public override string ToString()
         {
             var sb = new StringBuilder();

MetaMorpheus/GUI/MainWindow.xaml.cs

@@ -27,7 +27,7 @@ namespace MetaMorpheusGUI
     /// </summary>
     public partial class MainWindow : Window
     {
-        private readonly ObservableCollection<RawDataForDataGrid> SpectraFiles = new ObservableCollection<RawDataForDataGrid>();
+       private readonly ObservableCollection<RawDataForDataGrid> SpectraFiles = new ObservableCollection<RawDataForDataGrid>();
         private ObservableCollection<ProteinDbForDataGrid> ProteinDatabases = new ObservableCollection<ProteinDbForDataGrid>();
         private readonly ObservableCollection<PreRunTask> PreRunTasks = new ObservableCollection<PreRunTask>();
         private readonly ObservableCollection<RawDataForDataGrid> SelectedSpectraFiles = new ObservableCollection<RawDataForDataGrid>();