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);
}
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);
}
public static bool FilterOnRelativeIntensity(IdentifiedIsomerInfo feature, double highestIntensities)
{
return true;
}
public static bool FilterOnPpmError(IdentifiedIsomerInfo feature, double ppmTolerance)
{
return (Math.Abs(feature.MzInPpm) < ppmTolerance);
}
/// <summary>
/// The export identified isomer info.
/// </summary>
/// <param name="viperCompatibleMass">
/// The viper compatible mass.
/// </param>
/// <param name="minFitPoints">
/// The min fit points.
/// </param>
/// <param name="minR2">
/// The min r 2.
/// </param>
/// <param name="target"></param>
/// <returns>
/// The <see cref="IdentifiedIsomerInfo"/>.
/// </returns>
public IdentifiedIsomerInfo ExportIdentifiedIsomerInfo(double viperCompatibleMass, int minFitPoints, double minR2, IImsTarget target, double bestMzInPpm)
{
double averageVoltageGroupStabilityScore = VoltageGroupScoring.ComputeAverageVoltageGroupStabilityScore(this.definedVoltageGroups);
IList<ArrivalTimeSnapShot> snapshots = new List<ArrivalTimeSnapShot>();
foreach (var observation in this.observedPeaks)
{
snapshots.Add(this.ExtractArrivalTimeSnapShot(observation));
}
IdentifiedIsomerInfo info = new IdentifiedIsomerInfo(
this.observedPeaks.Count,
this.AverageMzInDalton,
this.mobilityInfo.RSquared,
this.mobilityInfo.Mobility,
this.mobilityInfo.CollisionCrossSectionArea,
averageVoltageGroupStabilityScore,
snapshots,
viperCompatibleMass,
this.ConcludeStatus(minFitPoints, minR2),
this.TrackStatistics,
target,
this.mobilityInfo.T0,
bestMzInPpm
);
return info;
}
private async Task<long> InsertIdentifications(SQLiteCommand cmd, IdentifiedIsomerInfo result, long analysisID)
{
cmd.CommandText = "INSERT INTO identifications (detection_analysis , measured_mz_in_dalton, ppm_error, viper_compatible_mz, r2 , analysis_status, intensity_score , peak_shape_score , isotopic_score , collision_cross_section, mobility, t0, relative_ppm) VALUES (@detection_analysis , @measured_mz_in_dalton, @ppm_error, @viper_compatible_mz, @r2, @analysis_status, @intensity_score, @peak_shape_score, @isotopic_score, @collision_cross_section, @mobility, @t0, @relative_ppm)";
cmd.Parameters.AddWithValue("@detection_analysis", analysisID);
cmd.Parameters.AddWithValue("@measured_mz_in_dalton", result.MzInDalton);
cmd.Parameters.AddWithValue("@ppm_error", result.MzInPpm);
cmd.Parameters.AddWithValue("@viper_compatible_mz", result.ViperCompatibleMass);
cmd.Parameters.AddWithValue("@r2", result.RSquared);
cmd.Parameters.AddWithValue("@analysis_status", result.AnalysisStatus.ToString());
cmd.Parameters.AddWithValue("@intensity_score", result.PeakScores.IntensityScore);
cmd.Parameters.AddWithValue("@peak_shape_score", result.PeakScores.PeakShapeScore);
cmd.Parameters.AddWithValue("@isotopic_score", result.PeakScores.IsotopicScore);
cmd.Parameters.AddWithValue("@collision_cross_section", result.CrossSectionalArea);
cmd.Parameters.AddWithValue("@mobility", result.Mobility);
cmd.Parameters.AddWithValue("@t0", result.T0);
cmd.Parameters.AddWithValue("@relative_ppm", result.RelativeMzInPpm);
await Task.Run(() => cmd.ExecuteNonQuery());
return await this.LastID(cmd);
}
/// <summary>
/// The fuse isomer result.
/// </summary>
/// <param name="A">
/// The a.
/// </param>
/// <param name="B">
/// The b.
/// </param>
/// <param name="weightA">
/// The weight a.
/// </param>
/// <param name="weightB">
/// The weight b.
/// </param>
/// <returns>
/// The <see cref="IdentifiedIsomerInfo"/>.
/// </returns>
private static IdentifiedIsomerInfo FuseIsomerResult(IdentifiedIsomerInfo A, IdentifiedIsomerInfo B, double weightA, double weightB)
{
double sum = weightA + weightB;
weightB /= sum;
weightA /= sum;
IEnumerable<ArrivalTimeSnapShot> arivalTimeSnapShots = A.ArrivalTimeSnapShots.Concat(B.ArrivalTimeSnapShots);
int numberOfFeaturePointsUsed = A.NumberOfFeaturePointsUsed + B.NumberOfFeaturePointsUsed;
IdentifiedIsomerInfo newIsomer = new IdentifiedIsomerInfo(
numberOfFeaturePointsUsed,
(A.MzInDalton + B.MzInDalton) / 2,
A.RSquared * weightA + B.RSquared * weightB,
A.Mobility * weightA + B.Mobility * weightB,
A.CrossSectionalArea * weightA + B.CrossSectionalArea * weightB,
A.AverageVoltageGroupStabilityScore * weightA + B.AverageVoltageGroupStabilityScore * weightB,
arivalTimeSnapShots,
A.ViperCompatibleMass + B.ViperCompatibleMass,
A.AnalysisStatus,
null,
null, A.T0 * weightA + B.T0 * weightB,
A.RelativeMzInPpm * weightA + B.RelativeMzInPpm * weightB);
return newIsomer;
}
/// <summary>
/// The check conflict.
/// </summary>
/// <param name="A">
/// The a.
/// </param>
/// <param name="B">
/// The b.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
private static bool CheckConflict(IdentifiedIsomerInfo A, IdentifiedIsomerInfo B)
{
if (Math.Abs(A.CrossSectionalArea - B.CrossSectionalArea) > CollisionCrossSectionTolerance)
{
return true;
}
return false;
}