public static double ScorePeak(double totalArea, double peakCount, bool isIdentified)
{
double logUnforcedArea = LegacyLogUnforcedAreaCalc.Score(totalArea, 0);
return(LegacyScoringModel.Score(logUnforcedArea, peakCount, 0, isIdentified ? 1 : 0));
}
/// <summary>
/// Trains a legacy model, checks that it saves correctly in the list and the document,
/// modifies it without changing its name and checks that the list and document models update correctly
/// </summary>
protected void TestModelChangesAndSave()
{
LegacyScoringModel peakScoringModelBase = null;
// Test legacy model
var reintegrateDlg = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
var editDlg = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlg.AddPeakScoringModel);
RunUI(() =>
{
Assert.AreEqual(editDlg.PeakScoringModelName, "");
editDlg.PeakScoringModelName = "legacy1"; // Not L10N
editDlg.SelectedModelItem = LegacyScoringModel.DEFAULT_NAME;
Assert.AreEqual(editDlg.PeakScoringModelName, "legacy1");
editDlg.TrainModelClick();
VerifyBias(editDlg, SCORES_AND_WEIGHTS[4]);
VerifyCellValues(editDlg, SCORES_AND_WEIGHTS[5]);
editDlg.UsesSecondBest = true;
editDlg.UsesDecoys = false;
editDlg.TrainModelClick();
VerifyBias(editDlg, SCORES_AND_WEIGHTS[6]);
VerifyCellValues(editDlg, SCORES_AND_WEIGHTS[7]);
editDlg.UsesSecondBest = false;
peakScoringModelBase = editDlg.PeakScoringModel as LegacyScoringModel;
});
// Unchecking decoys and second best leads to error on training
RunDlg <MessageDlg>(editDlg.TrainModelClick, messageDlg =>
{
Assert.AreEqual(string.Format(Resources.EditPeakScoringModelDlg_btnTrainModel_Click_Cannot_train_model_without_either_decoys_or_second_best_peaks_included_),
messageDlg.Message);
messageDlg.OkDialog();
});
OkDialog(editDlg, editDlg.OkDialog);
RunUI(() => reintegrateDlg.ComboPeakScoringModelSelected = "legacy1");
OkDialog(reintegrateDlg, reintegrateDlg.OkDialog);
RunUI(() =>
{
// Test modification of legacy scoring model
SkylineWindow.SaveDocument();
var peakScoringModel = SkylineWindow.DocumentUI.Settings.PeptideSettings.Integration.PeakScoringModel as LegacyScoringModel;
var listModels = Settings.Default.PeakScoringModelList;
Assert.AreEqual(listModels.Count, 4);
var peakScoringModelList = listModels[3] as LegacyScoringModel;
// Check that model in EditList, document model, and model from the dialog are all the same
AssertEqualNotNull(new List <LegacyScoringModel> {
peakScoringModel, peakScoringModelList, peakScoringModelBase
});
// Check document model is the last model we trained
// ReSharper disable PossibleNullReferenceException
Assert.AreEqual(peakScoringModel.Name, "legacy1");
// ReSharper restore PossibleNullReferenceException
});
LegacyScoringModel peakScoringModelBaseNew = null;
RunEditPeakScoringDlg("legacy1", editDlgTemp =>
{
editDlgTemp.UsesDecoys = true;
editDlgTemp.TrainModelClick();
peakScoringModelBaseNew = editDlgTemp.PeakScoringModel as LegacyScoringModel;
editDlgTemp.OkDialog();
});
RunUI(() =>
{
SkylineWindow.SaveDocument();
var peakScoringModelNew = SkylineWindow.DocumentUI.Settings.PeptideSettings.Integration.PeakScoringModel as LegacyScoringModel;
var listModels = Settings.Default.PeakScoringModelList;
var peakScoringModelListNew = listModels[3] as LegacyScoringModel;
// Check that model in EditList, document model, and model from the dialog are all the same
AssertEqualNotNull(new List <LegacyScoringModel> {
peakScoringModelNew, peakScoringModelListNew, peakScoringModelBaseNew
});
// Check document model has changed
// ReSharper disable PossibleNullReferenceException
Assert.IsTrue(peakScoringModelNew.UsesDecoys);
// ReSharper restore PossibleNullReferenceException
});
// Test changing legacy to mProphet model without changing name
MProphetPeakScoringModel peakScoringModelMProphetBase = null;
RunEditPeakScoringDlg("legacy1", editDlgTemp =>
{
// Switch to mProphet model
editDlgTemp.SelectedModelItem = "mProphet";
editDlgTemp.TrainModelClick();
peakScoringModelMProphetBase = editDlgTemp.PeakScoringModel as MProphetPeakScoringModel;
editDlgTemp.OkDialog();
}
);
RunUI(() =>
{
SkylineWindow.SaveDocument();
var peakScoringModelMProphet = SkylineWindow.DocumentUI.Settings.PeptideSettings.Integration.PeakScoringModel as MProphetPeakScoringModel;
var listModels = Settings.Default.PeakScoringModelList;
var peakScoringModelMProphetList = listModels[3] as MProphetPeakScoringModel;
// Check that model in EditList, document model, and model from the dialog are all the same
AssertEqualNotNull(new List <MProphetPeakScoringModel> {
peakScoringModelMProphet,
peakScoringModelMProphetList,
peakScoringModelMProphetBase
});
// Check document model has changed
Assert.AreNotEqual(peakScoringModelBaseNew, peakScoringModelMProphet);
// ReSharper disable PossibleNullReferenceException
Assert.IsTrue(peakScoringModelMProphet.UsesDecoys);
// ReSharper restore PossibleNullReferenceException
Assert.AreEqual(peakScoringModelMProphet.PeakFeatureCalculators.Count, 23);
});
}
