public async static void AnalysisDBTest()
{
var snapshot1 = new ArrivalTimeSnapShot();
snapshot1.DriftTubeVoltageInVolt = 1000;
snapshot1.MeasuredArrivalTimeInMs = 22;
snapshot1.PressureInTorr = 4;
snapshot1.TemperatureInKelvin = 10;
var iso1 = new IdentifiedIsomerInfo(2 ,222, 0.9, 10.5, 115, 123, new List<ArrivalTimeSnapShot>(){snapshot1}, 100, AnalysisStatus.Positive, new PeakScores(1.0, 0.8, 0.7), new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), 0.1, 0);
var idens = new List<IdentifiedIsomerInfo>() {iso1};
PeakScores scores = new PeakScores(0, 0.5, 1);
CrossSectionWorkflowResult result1 = new CrossSectionWorkflowResult("ABC_Dataset_01", new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.2), scores, 0.5, OutputFileDir, "123");
CrossSectionWorkflowResult result2 = new CrossSectionWorkflowResult("ABC_Dataset_02", new MolecularTarget("C2H4O16P2", IonizationMethod.Protonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result3 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C2H4O16P2", IonizationMethod.Deprotonated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result4 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C2H4O16P2", IonizationMethod.Sodiumated, "testamin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result5 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C10H40", IonizationMethod.Protonated, "googlin"), AnalysisStatus.Positive, new AssociationHypothesisInfo(0.1, 0.4), idens, scores, 0.8, OutputFileDir, "123");
CrossSectionWorkflowResult result6 = new CrossSectionWorkflowResult("ABC_Dataset_03", new MolecularTarget("C10H40", IonizationMethod.Protonated, "googlin"), AnalysisStatus.Negative, null, idens, scores, 0.8, OutputFileDir, "123");
string fileName = @"output\test.sqlite";
AnalysisLibrary lib = new AnalysisLibrary(fileName);
await lib.CreateTables();
await lib.InsertResult(result1);
await lib.InsertResult(result2);
await lib.InsertResult(result3);
await lib.InsertResult(result4);
await lib.InsertResult(result5);
await lib.InsertResult(result6);
}
/// <summary>
/// The sum feature scores.
/// </summary>
/// <param name="a">
/// The a.
/// </param>
/// <param name="b">
/// The b.
/// </param>
/// <returns>
/// The <see cref="double"/>.
/// </returns>
public static PeakScores AddFeatureScores(PeakScores a, PeakScores b)
{
double intensityScore = a.IntensityScore + b.IntensityScore;
double isotopicScore = a.IsotopicScore + b.IsotopicScore;
double peakShapeScore = a.PeakShapeScore + b.PeakShapeScore;
return new PeakScores(intensityScore, isotopicScore, peakShapeScore);
}
/// <summary>
/// Initializes a new instance of the <see cref="ObservedPeak"/> class with peak and its calculated statistics.
/// </summary>
/// <param name="group">
/// The group.
/// </param>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="statistics">
/// The Statistics.
/// </param>
public ObservedPeak(VoltageGroup group, StandardImsPeak peak, PeakScores statistics)
{
this.VoltageGroup = group;
this.Peak = peak;
this.Statistics = statistics;
this.ObservationType = ObservationType.Peak;
this.mobilityPoint = null;
}
public static void SerializerDeserializerTest()
{
IList<CrossSectionWorkflowResult> results = new List<CrossSectionWorkflowResult>();
// create fake result 1
IdentifiedIsomerInfo holyGrail1 = new IdentifiedIsomerInfo(10, 250, 6, 10, 22, 4, null, 5, AnalysisStatus.Positive, new PeakScores(1,2,3), new MolecularTarget("C2H34", IonizationMethod.APCI, "Carbon"), 1, 2);
PeakScores averageFeatureScores1 = new PeakScores(3, 4, 5);
IImsTarget target1 = new MolecularTarget("C2H5OH", IonizationMethod.Deprotonated, "Ginger ale");
IImsTarget target2 = new MolecularTarget("C2H5OH", IonizationMethod.Sodiumated, "Volka");
CrossSectionWorkflowResult result1 = new CrossSectionWorkflowResult(
"France",
target1,
AnalysisStatus.Positive,
null,averageFeatureScores1,
4,
"",
"");
results.Add(result1);
// Serialize fake result struct
IFormatter formatter = new BinaryFormatter();
using (Stream stream = new FileStream("serialized_result.bin", FileMode.Create, FileAccess.Write, FileShare.None))
{
formatter.Serialize(stream, results);
}
IList<CrossSectionWorkflowResult> newResults;
// deserialize fake result struct
using (Stream stream = new FileStream("serialized_result.bin", FileMode.Open, FileAccess.Read, FileShare.Read))
{
newResults = (IList<CrossSectionWorkflowResult>)formatter.Deserialize(stream);
}
CrossSectionWorkflowResult result2 = newResults.First();
// Compare it
var result = newResults.First();
Assert.AreEqual(result.AnalysisStatus, result1.AnalysisStatus);
Assert.AreEqual(result.DatasetName, result2.DatasetName);
Assert.AreEqual(result.AverageObservedPeakStatistics.IntensityScore, result2.AverageObservedPeakStatistics.IntensityScore);
}
/// <summary>
/// The average feature scores.
/// </summary>
/// <param name="scoreHolders">
/// The score holders.
/// </param>
/// <returns>
/// The <see cref="PeakScores"/>.
/// </returns>
public static PeakScores AverageFeatureStatistics(IEnumerable<PeakScores> scoreHolders)
{
int count = 0;
PeakScores statistics = new PeakScores(0, 0, 0);
foreach (var scoreHolder in scoreHolders)
{
count++;
statistics = AddFeatureScores(statistics, scoreHolder);
}
if (count == 0)
{
return statistics;
}
else
{
double intensityScore = statistics.IntensityScore / count;
double isotopicScore = statistics.IsotopicScore / count;
double peakShapeScore = statistics.PeakShapeScore / count;
return new PeakScores(intensityScore, isotopicScore, peakShapeScore);
}
}
/// Initializes a new instance of the <see cref="CrossSectionWorkflowResult"/> class.
/// Constructor for no isomer result.
public CrossSectionWorkflowResult(
string datasetPath,
IImsTarget target,
AnalysisStatus analysisStatus,
AssociationHypothesisInfo associationHypothesisInfo,
PeakScores averageObservedPeakStatistics,
double averageVoltageGroupStability,
string analysisDirectory, string dateTime)
: this(datasetPath,
target,
analysisStatus,
associationHypothesisInfo,
new List<IdentifiedIsomerInfo>(),
averageObservedPeakStatistics,
averageVoltageGroupStability,
analysisDirectory,
dateTime)
{
}
/// <summary>
/// Initializes a new instance of the <see cref="CrossSectionWorkflowResult"/> class.
/// Multiple isomer result constructor
/// </summary>
/// <param name="datasetName">
/// The dataset name.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="analysisStatus">
/// The analysis status.
/// </param>
/// <param name="associationHypothesisInfo">
/// The analysis scores holder.
/// </param>
/// <param name="isomerResults">
/// The isomer results.
/// </param>
/// <param name="averageObservedPeakStatistics"></param>
/// <param name="averageVoltageGroupStability"></param>
/// <param name="datasetPath"></param>
/// <param name="analysisDirectory"></param>
/// <param name="dateTime"></param>
public CrossSectionWorkflowResult(
string datasetPath,
IImsTarget target,
AnalysisStatus analysisStatus,
AssociationHypothesisInfo associationHypothesisInfo,
IList<IdentifiedIsomerInfo> isomerResults,
PeakScores averageObservedPeakStatistics,
double averageVoltageGroupStability,
string analysisDirectory,
string dateTime)
{
this.Target = target;
this.AnalysisStatus = analysisStatus;
this.AssociationHypothesisInfo = associationHypothesisInfo;
this.isomerResults = isomerResults;
this.AverageObservedPeakStatistics = averageObservedPeakStatistics;
this.AverageVoltageGroupStability = averageVoltageGroupStability;
this.AnalysisDirectory = analysisDirectory;
this.DateTime = dateTime;
this.DatasetPath = datasetPath;
this.DatasetName = Path.GetFileNameWithoutExtension(datasetPath);
this.DateTime = dateTime;
}
/// <summary>
/// The compare feature input.
/// </summary>
/// <param name="a">
/// The a.
/// </param>
/// <param name="b">
/// The b.
/// </param>
/// <param name="likelihoodFunc">
/// The likelihood Func.
/// </param>
/// <returns>
/// The <see cref="int"/>.
/// </returns>
private static int CompareFeatureScore(PeakScores a, PeakScores b, LikelihoodFunc likelihoodFunc)
{
return likelihoodFunc(a).CompareTo(likelihoodFunc(b));
}
/// <summary>
/// The report feature evaluation.
/// </summary>
/// <param name="peak">
/// The peak.
/// </param>
/// <param name="scores">
/// The scores.
/// </param>
/// <param name="verbose">
/// The verbose.
/// </param>
/// <param name="target">
/// The target.
/// </param>
/// <param name="badScanRange">
/// The bad scan range.
/// </param>
/// <param name="lowAbsoluteIntensity">
/// The low intensity.
/// </param>
/// <param name="lowRelativeIntensity"></param>
/// <param name="badPeakShape">
/// The bad peak shape.
/// </param>
/// <param name="lowIsotopicAffinity">
/// The low isotopic affinity.
/// </param>
/// <returns>
/// If the feature pass all the filters <see cref="bool"/>.
/// </returns>
private static string ReportFeatureEvaluation(StandardImsPeak peak, PeakScores scores, bool verbose, IImsTarget target, bool badScanRange, bool lowAbsoluteIntensity, bool lowRelativeIntensity, bool badPeakShape, bool lowIsotopicAffinity)
{
Trace.WriteLine(string.Format(" Candidate feature found at [centerMz = {0:F4}, drift time = {1:F2} ms(#{2})] ", peak.PeakApex.MzCenterInDalton, peak.PeakApex.DriftTimeCenterInMs, peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(string.Format(" IntensityScore: {0:F4}", scores.IntensityScore));
if (!lowAbsoluteIntensity)
{
Trace.WriteLine(string.Format(" peakShapeScore: {0:F4}", scores.PeakShapeScore));
if (target.HasCompositionInfo)
{
Trace.WriteLine(string.Format(" isotopicScore: {0:F4}", scores.IsotopicScore));
}
}
string rejectionReason = badScanRange ? "[Bad scan range] " :
lowAbsoluteIntensity ? "[Low Absolute Intensity] " :
badPeakShape ? "[Bad Peak Shape] " :
lowIsotopicAffinity ? "[Different Isotopic Profile] " :
lowRelativeIntensity ? "[Low Relative Intensity] " : string.Empty;
bool rejected = badScanRange || lowAbsoluteIntensity || lowIsotopicAffinity || badPeakShape || lowRelativeIntensity;
if (verbose)
{
if (rejected)
{
Trace.WriteLine(" " + rejectionReason);
}
else
{
Trace.WriteLine(" [PASS]");
}
Trace.WriteLine(string.Empty);
}
return rejectionReason;
}
/// <summary>
/// Initializes a new instance of the <see cref="IdentifiedIsomerInfo"/> class.
/// </summary>
/// <param name="numberOfFeaturePointsUsed">
/// The number of feature points used.
/// </param>
/// <param name="mzInDalton"></param>
/// <param name="rSquared">
/// The r squred.
/// </param>
/// <param name="mobility">
/// The mobility.
/// </param>
/// <param name="crossSectionalArea">
/// The cross sectional area.
/// </param>
/// <param name="averageVoltageGroupStabilityScore">
/// The average voltage group stability score.
/// </param>
/// <param name="arrivalTimeSnapShots">
/// The arrival time snap shots.
/// </param>
/// <param name="viperCompatibleMass">
/// The viper Compatible Mass.
/// </param>
/// <param name="analysisStatus"></param>
/// <param name="peakScores"></param>
/// <param name="target"></param>
public IdentifiedIsomerInfo(
int numberOfFeaturePointsUsed,
double mzInDalton,
double rSquared,
double mobility,
double crossSectionalArea,
double averageVoltageGroupStabilityScore,
IEnumerable<ArrivalTimeSnapShot> arrivalTimeSnapShots,
double viperCompatibleMass,
AnalysisStatus analysisStatus,
PeakScores peakScores,
IImsTarget target,
double t0,
double bestMzInPpm)
{
this.NumberOfFeaturePointsUsed = numberOfFeaturePointsUsed;
this.RSquared = rSquared;
this.Mobility = mobility;
this.CrossSectionalArea = crossSectionalArea;
this.AverageVoltageGroupStabilityScore = averageVoltageGroupStabilityScore;
this.ArrivalTimeSnapShots = arrivalTimeSnapShots;
this.ViperCompatibleMass = viperCompatibleMass;
this.AnalysisStatus = analysisStatus;
this.PeakScores = peakScores;
this.T0 = t0;
this.MzInDalton = mzInDalton;
this.MzInPpm = Metrics.DaltonToPpm(mzInDalton - target.MassWithAdduct, target.MassWithAdduct);
this.RelativeMzInPpm = Math.Abs(MzInPpm - bestMzInPpm);
}
