Merge pull request #182 from smith-chem-wisc/StefanBranch

alrighty

Author: stefanks

InternalLogic/Calibration/CalibrationEngine.cs

@@ -67,7 +67,7 @@ protected override MyResults RunSpecific()
                 Status("Getting Training Points");
                 pointList = GetDataPoints(ref numMs1MassChargeCombinationsConsidered, ref numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, ref numMs2MassChargeCombinationsConsidered, ref numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
 
-                goodResult.Add(calibrationRound, numMs1MassChargeCombinationsConsidered, numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, pointList.Count, numMs2MassChargeCombinationsConsidered, numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
+                goodResult.Add(numMs1MassChargeCombinationsConsidered, numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, pointList.Count, numMs2MassChargeCombinationsConsidered, numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
 
                 if (calibrationRound >= 2 && pointList.Count <= trainingPointCounts[calibrationRound - 2])
                     break;
@@ -88,6 +88,8 @@ protected override MyResults RunSpecific()
 
                 CalibrationFunction combinedCalibration = Calibrate(pointList);
 
+                goodResult.Add(combinedCalibration);
+
                 if (combinedCalibration == null)
                     return new MyErroredResults(this, "Could not calibrate");
             }
@@ -131,12 +133,10 @@ private List<LabeledDataPoint> GetDataPoints(ref int numMs1MassChargeCombination
                 var SequenceWithChemicalFormulas = identification.thisPSM.SequenceWithChemicalFormulas;
                 int peptideCharge = identification.thisPSM.newPsm.scanPrecursorCharge;
 
-                int numFragmentsIdentified = -1;
-                var candidateTrainingPointsForPeptide = new List<LabeledDataPoint>();
-                Peptide coolPeptide = null;
-                coolPeptide = new Peptide(SequenceWithChemicalFormulas);
+                Peptide coolPeptide = new Peptide(SequenceWithChemicalFormulas);
 
-                candidateTrainingPointsForPeptide = SearchMS2Spectrum(myMsDataFile.GetOneBasedScan(ms2spectrumIndex), coolPeptide, peptideCharge, out numFragmentsIdentified, ref numMs2MassChargeCombinationsConsidered, ref numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
+                int numFragmentsIdentified;
+                var candidateTrainingPointsForPeptide = SearchMS2Spectrum(myMsDataFile.GetOneBasedScan(ms2spectrumIndex), coolPeptide, peptideCharge, out numFragmentsIdentified, ref numMs2MassChargeCombinationsConsidered, ref numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
 
                 // If MS2 has low evidence for peptide, skip and go to next one
                 if (numFragmentsIdentified < numFragmentsNeededForEveryIdentification)

InternalLogic/Calibration/CalibrationFunctions/ConstantCalibrationFunction.cs

@@ -1,13 +1,33 @@
 using MathNet.Numerics.Statistics;
 using System.Collections.Generic;
 using System.Linq;
+using System.Text;
 
 namespace InternalLogicCalibration
 {
     public class ConstantCalibrationFunction : CalibrationFunction
     {
+
+        #region Public Fields
+
         public double a;
 
+        #endregion Public Fields
+
+        #region Public Methods
+
+        public override string ToString()
+        {
+            StringBuilder sb = new StringBuilder();
+            sb.Append("Constant");
+            sb.Append(" a = " + a);
+            return sb.ToString();
+        }
+
+        #endregion Public Methods
+
+        #region Internal Methods
+
         internal override double Predict(double[] t)
         {
             return a;
@@ -17,5 +37,8 @@ internal void Train(IEnumerable<LabeledDataPoint> trainingList)
         {
             a = trainingList.Select(b => b.output).Median();
         }
+
+        #endregion Internal Methods
+
     }
 }

InternalLogic/Calibration/CalibrationFunctions/IdentityCalibrationFunction.cs

@@ -1,14 +1,29 @@
-namespace InternalLogicCalibration
+using System.Text;
+
+namespace InternalLogicCalibration
 {
     public class IdentityCalibrationFunction : CalibrationFunction
     {
+
         #region Public Methods
 
+        public override string ToString()
+        {
+            StringBuilder sb = new StringBuilder();
+            sb.Append("Identity");
+            return sb.ToString();
+        }
+
+        #endregion Public Methods
+
+        #region Internal Methods
+
         internal override double Predict(double[] t)
         {
             return 0;
         }
 
-        #endregion Public Methods
+        #endregion Internal Methods
+
     }
 }

InternalLogic/Calibration/CalibrationFunctions/LinearCalibrationFunctionMathNet.cs

@@ -2,21 +2,46 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Text;
 
 namespace InternalLogicCalibration
 {
     internal class LinearCalibrationFunctionMathNet : CalibrationFunction
     {
-        private Func<double[], double> f;
+
+        #region Private Fields
+
         private readonly int numFeatures;
         private readonly TransformFunction transformFunction;
+        private Func<double[], double> f;
+
+        #endregion Private Fields
+
+        #region Public Constructors
 
         public LinearCalibrationFunctionMathNet(TransformFunction transformFunction)
         {
             this.transformFunction = transformFunction;
             numFeatures = transformFunction.numOutputs;
         }
 
+        #endregion Public Constructors
+
+        #region Public Methods
+
+        public override string ToString()
+        {
+            StringBuilder sb = new StringBuilder();
+            sb.Append("Linear");
+            sb.Append(" numFeatures: " + numFeatures);
+            sb.Append(" transform num outputs: " + transformFunction.numOutputs);
+            return sb.ToString();
+        }
+
+        #endregion Public Methods
+
+        #region Internal Methods
+
         internal override double Predict(double[] t)
         {
             return f(transformFunction.Transform(t));
@@ -42,5 +67,8 @@ internal void Train(IEnumerable<LabeledDataPoint> trainingList)
             }
             f = Fit.LinearMultiDimFunc(ok, ok2, ye);
         }
+
+        #endregion Internal Methods
+
     }
 }

InternalLogic/Calibration/CalibrationFunctions/QuadraticCalibrationFunctionMathNet.cs

@@ -2,16 +2,18 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Text;
 
 namespace InternalLogicCalibration
 {
     internal class QuadraticCalibrationFunctionMathNet : CalibrationFunction
     {
+
         #region Private Fields
 
-        private Func<double[], double> f;
         private readonly int numFeatures;
         private readonly int numFeaturesExpanded;
+        private Func<double[], double> f;
         private TransformFunction transform;
 
         #endregion Private Fields
@@ -29,6 +31,20 @@ public QuadraticCalibrationFunctionMathNet(TransformFunction transform)
 
         #region Public Methods
 
+        public override string ToString()
+        {
+            StringBuilder sb = new StringBuilder();
+            sb.Append("Quadratic");
+            sb.Append(" numFeatures: " + numFeatures);
+            sb.Append(" numFeaturesExpanded: " + numFeaturesExpanded);
+            sb.Append(" transform: " + transform.numOutputs);
+            return sb.ToString();
+        }
+
+        #endregion Public Methods
+
+        #region Internal Methods
+
         internal override double Predict(double[] t)
         {
             return f(ExpandFeatures(transform.Transform(t)));
@@ -55,7 +71,7 @@ internal void Train(IEnumerable<LabeledDataPoint> trainingList)
             f = Fit.LinearMultiDimFunc(ok, ok2, ye);
         }
 
-        #endregion Public Methods
+        #endregion Internal Methods
 
         #region Private Methods
 
@@ -77,5 +93,6 @@ private double[] ExpandFeatures(double[] input)
         }
 
         #endregion Private Methods
+
     }
 }

InternalLogic/Calibration/CalibrationFunctions/SeparateCalibrationFunction.cs

@@ -2,20 +2,34 @@
 {
     internal class SeparateCalibrationFunction : CalibrationFunction
     {
-        private readonly CalibrationFunction calibrationFunction1;
-        private readonly CalibrationFunction calibrationFunction2;
+
+        #region Public Constructors
 
         public SeparateCalibrationFunction(CalibrationFunction calibrationFunction1, CalibrationFunction calibrationFunction2)
         {
-            this.calibrationFunction1 = calibrationFunction1;
-            this.calibrationFunction2 = calibrationFunction2;
+            this.CalibrationFunction1 = calibrationFunction1;
+            this.CalibrationFunction2 = calibrationFunction2;
         }
 
+        #endregion Public Constructors
+
+        #region Public Properties
+
+        public CalibrationFunction CalibrationFunction1 { get; private set; }
+        public CalibrationFunction CalibrationFunction2 { get; private set; }
+
+        #endregion Public Properties
+
+        #region Internal Methods
+
         internal override double Predict(double[] t)
         {
             if (t[0] < 0)
-                return calibrationFunction1.Predict(t);
-            return calibrationFunction2.Predict(t);
+                return CalibrationFunction1.Predict(t);
+            return CalibrationFunction2.Predict(t);
         }
+
+        #endregion Internal Methods
+
     }
 }

InternalLogic/Calibration/CalibrationResults.cs

@@ -11,12 +11,12 @@ public class CalibrationResults : MyResults
 
         #region Private Fields
 
-        private List<int> calibrationRoundList;
         private List<int> numMs1MassChargeCombinationsConsideredList;
         private List<int> numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList;
         private List<int> numMs2MassChargeCombinationsConsideredList;
         private List<int> numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList;
         private List<int> countList;
+        private List<SeparateCalibrationFunction> calibrationFunctions;
 
         #endregion Private Fields
 
@@ -25,7 +25,7 @@ public class CalibrationResults : MyResults
         public CalibrationResults(IMsDataFile<IMzSpectrum<MzPeak>> myMSDataFile, CalibrationEngine s) : base(s)
         {
             this.MyMSDataFile = myMSDataFile;
-            calibrationRoundList = new List<int>();
+            calibrationFunctions = new List<SeparateCalibrationFunction>();
             numMs1MassChargeCombinationsConsideredList = new List<int>();
             numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList = new List<int>();
             numMs2MassChargeCombinationsConsideredList = new List<int>();
@@ -48,15 +48,20 @@ protected override string StringForOutput
             get
             {
                 var sb = new StringBuilder();
-                for (int i = 0; i < calibrationRoundList.Count; i++)
+                for (int i = 0; i < countList.Count; i++)
                 {
-                    sb.AppendLine("\t\tRound " + calibrationRoundList[i]);
+                    sb.AppendLine("\t\tRound " + (i + 1));
                     sb.AppendLine("\t\t\tTraining points: " + countList[i]);
+                    sb.AppendLine("\t\t\tMs1MassChargeSeen: " + numMs1MassChargeCombinationsConsideredList[i]);
+                    sb.AppendLine("\t\t\tMs1MassChargeSeenAndIgnoredBecause too many: " + numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList[i]);
                     sb.AppendLine("\t\t\tMs2MassChargeSeen: " + numMs2MassChargeCombinationsConsideredList[i]);
                     sb.AppendLine("\t\t\tMs2MassChargeSeenAndIgnoredBecause too many: " + numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList[i]);
 
-                    sb.AppendLine("\t\t\tMs1MassChargeSeen: " + numMs1MassChargeCombinationsConsideredList[i]);
-                    sb.AppendLine("\t\t\tMs1MassChargeSeenAndIgnoredBecause too many: " + numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList[i]);
+                    if (i < calibrationFunctions.Count)
+                    {
+                        sb.AppendLine("\t\t\tMs1Calibration function: " + calibrationFunctions[i].CalibrationFunction1.ToString());
+                        sb.AppendLine("\t\t\tMs2Calibration function: " + calibrationFunctions[i].CalibrationFunction2.ToString());
+                    }
                 }
                 return sb.ToString();
             }
@@ -66,16 +71,20 @@ protected override string StringForOutput
 
         #region Internal Methods
 
-        internal void Add(int calibrationRound, int numMs1MassChargeCombinationsConsidered, int numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, int count, int numMs2MassChargeCombinationsConsidered, int numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks)
+        internal void Add(int numMs1MassChargeCombinationsConsidered, int numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, int count, int numMs2MassChargeCombinationsConsidered, int numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks)
         {
-            calibrationRoundList.Add(calibrationRound);
             numMs1MassChargeCombinationsConsideredList.Add(numMs1MassChargeCombinationsConsidered);
             numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList.Add(numMs1MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
             numMs2MassChargeCombinationsConsideredList.Add(numMs2MassChargeCombinationsConsidered);
             numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaksList.Add(numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks);
             countList.Add(count);
         }
 
+        internal void Add(CalibrationFunction combinedCalibration)
+        {
+            calibrationFunctions.Add((SeparateCalibrationFunction)combinedCalibration);
+        }
+
         #endregion Internal Methods
 
     }