public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
{
return;
}
if (_existing.Contains(m => !ReferenceEquals(_measuredIon, m) && Equals(name, m.Name)))
{
helper.ShowTextBoxError(textName, Resources.EditMeasuredIonDlg_OkDialog_The_special_ion__0__already_exists, name);
return;
}
if (radioFragment.Checked)
{
string cleavage;
if (!ValidateAATextBox(helper, textFragment, false, out cleavage))
{
return;
}
string restrict;
if (!ValidateAATextBox(helper, textRestrict, true, out restrict))
{
return;
}
SequenceTerminus direction = (comboDirection.SelectedIndex == 0 ?
SequenceTerminus.C : SequenceTerminus.N);
int minAas;
if (!helper.ValidateNumberTextBox(textMinAas, MeasuredIon.MIN_MIN_FRAGMENT_LENGTH,
MeasuredIon.MAX_MIN_FRAGMENT_LENGTH, out minAas))
{
return;
}
_measuredIon = new MeasuredIon(name, cleavage, restrict, direction, minAas);
}
else
{
var customIon = ValidateCustomIon(name);
if (customIon == null)
{
return;
}
_measuredIon = customIon;
}
DialogResult = DialogResult.OK;
}
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 static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
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, Adduct.SINGLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.DOUBLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.TRIPLY_PROTONATED), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
var 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].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), 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].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), 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, Adduct.SINGLY_PROTONATED, 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).SettingsCustomIon,
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 =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
var unfilteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
Assert.AreEqual(0, filteredNodes.Count());
Assert.AreEqual(1, unfilteredNodes.Count());
}
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);
const string fasta = ">peptide1\nPEPMCIDEPR";
RunUI(() => SkylineWindow.ImportFasta(new StringReader(fasta), 2, true, string.Empty,
new SkylineWindow.ImportFastaInfo(false, fasta)));
var newDoc = SkylineWindow.Document;
var water = new MeasuredIon("Water", "H2O", null, null, Adduct.M_PLUS); // Charge-only adduct, ionizing elements assumed to be part of formula
var carbon = new MeasuredIon("Carbon", "CO2", null, null, Adduct.M_PLUS, true);
var nodeTranFirst = newDoc.MoleculeTransitions.ElementAt(0);
Assert.IsTrue(nodeTranFirst.Transition.IsCustom());
Assert.AreEqual(water.SettingsCustomIon, nodeTranFirst.Transition.CustomIon);
// Sort-of unit test forray away from actually using the UI
var nodeGroup = newDoc.PeptideTransitionGroups.ElementAt(0);
var filteredWaterNodes = nodeGroup.GetPrecursorChoices(newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, water.SettingsCustomIon));
Assert.AreEqual(1, filteredWaterNodes.Count());
var filteredCarbonNodes =
nodeGroup.GetPrecursorChoices(newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, carbon.SettingsCustomIon));
var unfilteredCarbonNodes =
nodeGroup.GetPrecursorChoices(newDoc.Settings,
newDoc.Peptides.ElementAt(0).ExplicitMods, false)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, carbon.SettingsCustomIon));
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.SettingsCustomIon, 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.SettingsCustomIon, t.Transition.CustomIon)));
Assert.AreEqual(1, docWithoutWater.PeptideTransitions.Count(t => Equals(carbon.SettingsCustomIon, 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);
}
