private void TestSettingIonsUI() { var ions = new MeasuredIon[0]; var ionList = new MeasuredIonList(); ionList.AddRange(ions); Settings.Default.MeasuredIonList = ionList; RunUI(() => SkylineWindow.ModifyDocument("Change measured ions", document => document.ChangeSettings( document.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(ions))))); var tranSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); var editMeasuredIonList = ShowDialog <EditListDlg <SettingsListBase <MeasuredIon>, MeasuredIon> >( tranSettings.EditSpecialTransitionsList); var editMeasuredIon1 = ShowDialog <EditMeasuredIonDlg>(editMeasuredIonList.AddItem); RunUI(() => { editMeasuredIon1.SwitchToCustom(); editMeasuredIon1.TextName = "Water"; editMeasuredIon1.Formula = "H2O"; }); var errorDlg = ShowDialog <MessageDlg>(() => editMeasuredIon1.Charge = -1); // Negative charge states are valid for small molecule only, not for reporter ions AssertEx.AreComparableStrings(String.Format(Resources.MessageBoxHelper_ValidateDecimalTextBox__0__must_be_greater_than_or_equal_to__1__, String.Empty, 1), errorDlg.Message); RunUI(() => errorDlg.OkDialog()); // Dismiss the warning RunUI(() => { editMeasuredIon1.Charge = 1; }); OkDialog(editMeasuredIon1, editMeasuredIon1.OkDialog); var editMeasuredIon2 = ShowDialog <EditMeasuredIonDlg>(editMeasuredIonList.AddItem); RunUI(() => { editMeasuredIon2.SwitchToCustom(); editMeasuredIon2.TextName = "Carbon"; editMeasuredIon2.Charge = 1; editMeasuredIon2.Formula = "CO2"; }); OkDialog(editMeasuredIon2, editMeasuredIon2.OkDialog); OkDialog(editMeasuredIonList, editMeasuredIonList.OkDialog); RunUI(() => { tranSettings.SetListAlwaysAdd(0, true); // optional water tranSettings.SetListAlwaysAdd(0, true); // default water tranSettings.SetListAlwaysAdd(1, true); // optional carbon }); OkDialog(tranSettings, tranSettings.OkDialog); RunUI(() => SkylineWindow.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"), 2, true, string.Empty)); var newDoc = SkylineWindow.Document; var water = new MeasuredIon("Water", "H2O", null, null, 1); var carbon = new MeasuredIon("Carbon", "CO2", null, null, 1, true); var nodeTranFirst = newDoc.MoleculeTransitions.ElementAt(0); Assert.IsTrue(nodeTranFirst.Transition.IsCustom()); Assert.AreEqual(water.CustomIon, nodeTranFirst.Transition.CustomIon); // Sort-of unit test forray away from actually using the UI var nodeGroup = newDoc.PeptideTransitionGroups.ElementAt(0); var filteredWaterNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, true) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, water.CustomIon)); Assert.AreEqual(1, filteredWaterNodes.Count()); var filteredCarbonNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, true) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon)); var unfilteredCarbonNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, false) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon)); Assert.AreEqual(0, filteredCarbonNodes.Count()); Assert.AreEqual(1, unfilteredCarbonNodes.Count()); // Back to the UI: make sure removing the custom ion from settings // removes it from the document, which was once an issue that lead // to a document that could not be roundtripped RunUI(() => SkylineWindow.SelectedPath = newDoc.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0)); // Add carbon ion RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg => { dlg.ApplyFilter(false); dlg.ToggleItem(2); // precursor, water, carbon dlg.OnOk(); }); var docWithCarbon = WaitForDocumentChange(newDoc); var nodeTranCarbon = docWithCarbon.MoleculeTransitions.ElementAt(1); Assert.IsTrue(nodeTranCarbon.Transition.IsCustom()); Assert.AreEqual(carbon.CustomIon, nodeTranCarbon.Transition.CustomIon); RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, tranSettings2 => { tranSettings2.SetListAlwaysAdd(0, false); // remove water tranSettings2.OkDialog(); }); var docWithoutWater = WaitForDocumentChange(docWithCarbon); Assert.AreEqual(0, docWithoutWater.PeptideTransitions.Count(t => Equals(water.CustomIon, t.Transition.CustomIon))); Assert.AreEqual(1, docWithoutWater.PeptideTransitions.Count(t => Equals(carbon.CustomIon, t.Transition.CustomIon))); AssertEx.RoundTrip(docWithoutWater); RunDlg <PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg => { dlg.AutoManageChildren = true; dlg.OnOk(); }); var docWithoutCustom = WaitForDocumentChange(docWithoutWater); Assert.AreEqual(0, docWithoutCustom.PeptideTransitions.Count(t => t.Transition.IsCustom())); AssertEx.RoundTrip(docWithoutCustom); }
private void TestSettingIonsUI() { var ions = new MeasuredIon[0]; var ionList = new MeasuredIonList(); ionList.AddRange(ions); Settings.Default.MeasuredIonList = ionList; RunUI(() => SkylineWindow.ModifyDocument("Change measured ions", document => document.ChangeSettings( document.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(ions))))); var tranSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); var editMeasuredIonList = ShowDialog <EditListDlg <SettingsListBase <MeasuredIon>, MeasuredIon> >( tranSettings.EditSpecialTransitionsList); var editMeasuredIon1 = ShowDialog <EditMeasuredIonDlg>(editMeasuredIonList.AddItem); RunUI(() => { editMeasuredIon1.SwitchToCustom(); editMeasuredIon1.TextName = "Water"; editMeasuredIon1.Formula = "H2O"; }); var errorDlg = ShowDialog <MessageDlg>(() => editMeasuredIon1.Charge = -1); // Negative charge states are valid for small molecule only, not for reporter ions AssertEx.AreComparableStrings(String.Format(Resources.MessageBoxHelper_ValidateDecimalTextBox__0__must_be_greater_than_or_equal_to__1__, String.Empty, 1), errorDlg.Message); RunUI(() => errorDlg.OkDialog()); // Dismiss the warning RunUI(() => { editMeasuredIon1.Charge = 1; }); OkDialog(editMeasuredIon1, editMeasuredIon1.OkDialog); var editMeasuredIon2 = ShowDialog <EditMeasuredIonDlg>(editMeasuredIonList.AddItem); RunUI(() => { editMeasuredIon2.SwitchToCustom(); editMeasuredIon2.TextName = "Carbon"; editMeasuredIon2.Charge = 1; editMeasuredIon2.Formula = "CO2"; }); OkDialog(editMeasuredIon2, editMeasuredIon2.OkDialog); OkDialog(editMeasuredIonList, editMeasuredIonList.OkDialog); RunUI(() => { tranSettings.SetListAlwaysAdd(0, true); tranSettings.SetListAlwaysAdd(0, true); tranSettings.SetListAlwaysAdd(1, true); }); OkDialog(tranSettings, tranSettings.OkDialog); IdentityPath path; var newDoc = SkylineWindow.Document.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"), true, IdentityPath.ROOT, out path); TransitionGroupDocNode nodeGroup = newDoc.PeptideTransitionGroups.ElementAt(0); var water = new MeasuredIon("Water", "H2O", null, null, 1); var carbon = new MeasuredIon("Carbon", "CO2", null, null, 1, true); var filteredWaterNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, true) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, water.CustomIon)); Assert.AreEqual(1, filteredWaterNodes.Count()); var filteredCarbonNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, true) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon)); var unfilteredCarbonNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, newDoc.Settings, newDoc.Peptides.ElementAt(0).ExplicitMods, false) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, carbon.CustomIon)); Assert.AreEqual(0, filteredCarbonNodes.Count()); Assert.AreEqual(1, unfilteredCarbonNodes.Count()); }
public void ReporterIonTest() { // Test the code that updates old-style formulas Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2")); Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2")); var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy! IdentityPath path; SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"), true, IdentityPath.ROOT, out path); // One of the prolines should have caused an extra transition Assert.AreEqual(4, docPeptide.PeptideTransitionCount); Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8)); const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1 const string hydrogenPeroxide = "Hydrogen Perxoide"; var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, 1), new MeasuredIon(hydrogenPeroxide, formula, null, null, 2), new MeasuredIon(hydrogenPeroxide, formula, null, null, 3), MeasuredIonList.NTERM_PROLINE }; SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(reporterIons))); AssertEx.IsDocumentTransitionCount(docReporterIon, 7); //Check With Monoisotopic double mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula); for (int i = 0; i < 3; i++) { TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i); Transition tran = tranNode.Transition; Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon); Assert.AreEqual(tran.Charge, i + 1); Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100); Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100); } //Check with Average TransitionPrediction predSettings = docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average); TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings); SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings); SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings); mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula); for (int i = 0; i < 3; i++) { TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i); Transition tran = tranNode.Transition; Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon); Assert.AreEqual(tran.Charge, i + 1); Assert.AreEqual(BioMassCalc.AVERAGE.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100); Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100); } //Make sure the rest of the transitions aren't reporter ions for (int i = 3; i < 7; i++) { Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition; Assert.AreNotEqual(tran.CustomIon, reporterIons); } var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null, 1, true); SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(new[] { optionalIon }))); Assert.AreEqual(3, optionalDoc.PeptideTransitionCount); optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter => filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(false) }))); AssertEx.IsDocumentTransitionCount(optionalDoc, 4); Assert.AreEqual(optionalIon.ChangeIsOptional(false).CustomIon, optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon); optionalDoc = optionalDoc.ChangeSettings( optionalDoc.Settings.ChangeTransitionFilter( filter => filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(true) }))); TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0); var filteredNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings, optionalDoc.Molecules.ElementAt(0).ExplicitMods, true) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon)); var unfilteredNodes = TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings, optionalDoc.Molecules.ElementAt(0).ExplicitMods, false) .Cast <TransitionDocNode>() .Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon)); Assert.AreEqual(0, filteredNodes.Count()); Assert.AreEqual(1, unfilteredNodes.Count()); }