public static DocNodeCustomIon Deserialize(XmlReader reader)
{
DocNodeCustomIon ion = new DocNodeCustomIon();
ion.ReadAttributes(reader);
return(ion);
}
public TransitionGroup(Peptide peptide, DocNodeCustomIon customIon, int precursorCharge, IsotopeLabelType labelType, bool unlimitedCharge, int?decoyMassShift)
{
_peptide = peptide;
CustomIon = customIon ?? Peptide.CustomIon; // If parent molecule is a custom ion, and none specified, use that
PrecursorCharge = precursorCharge;
LabelType = labelType;
DecoyMassShift = decoyMassShift;
Validate(unlimitedCharge ? 0 : precursorCharge);
}
public Peptide(DocNodeCustomIon customIon)
{
CustomIon = customIon;
Validate();
}
private static int? ValidateFormulaWithMz(SrmDocument document, ref string moleculeFormula, double mz, int? charge, out double monoMass, out double averageMass, out double? mzCalc)
{
// Is the ion's formula the old style where user expected us to add a hydrogen?
var tolerance = document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
int massShift;
var ion = new DocNodeCustomIon(moleculeFormula);
monoMass = ion.GetMass(MassType.Monoisotopic);
averageMass = ion.GetMass(MassType.Average);
double mass = (document.Settings.TransitionSettings.Prediction.FragmentMassType == MassType.Monoisotopic)
? monoMass
: averageMass;
// Does given charge, if any, agree with mass and mz?
mzCalc = charge.HasValue ? BioMassCalc.CalculateIonMz(mass, charge.Value) : (double?)null;
if (mzCalc.HasValue && tolerance >= (Math.Abs(mzCalc.Value - mz)))
{
return charge;
}
int nearestCharge;
charge = TransitionCalc.CalcCharge(mass, mz, tolerance, true, TransitionGroup.MIN_PRECURSOR_CHARGE,
TransitionGroup.MAX_PRECURSOR_CHARGE, new int[0],
TransitionCalc.MassShiftType.none, out massShift, out nearestCharge);
if (!charge.HasValue)
{
// That formula and this mz don't yield a reasonable charge state - try adding an H
var ion2 = new DocNodeCustomIon(BioMassCalc.AddH(ion.Formula));
monoMass = ion2.GetMass(MassType.Monoisotopic);
averageMass = ion2.GetMass(MassType.Average);
mass = (document.Settings.TransitionSettings.Prediction.FragmentMassType == MassType.Monoisotopic)
? monoMass
: averageMass;
charge = TransitionCalc.CalcCharge(mass, mz, tolerance, true, TransitionGroup.MIN_PRECURSOR_CHARGE,
TransitionGroup.MAX_PRECURSOR_CHARGE, new int[0], TransitionCalc.MassShiftType.none, out massShift, out nearestCharge);
if (charge.HasValue)
{
moleculeFormula = ion2.Formula;
}
else
{
monoMass = 0;
averageMass = 0;
}
}
return charge;
}
private double ValidateFormulaWithCharge(SrmDocument document, string moleculeFormula, int charge, out double monoMass, out double averageMass)
{
var massType = document.Settings.TransitionSettings.Prediction.PrecursorMassType;
var ion = new DocNodeCustomIon(moleculeFormula);
double mass = ion.GetMass(massType);
monoMass = ion.GetMass(MassType.Monoisotopic);
averageMass = ion.GetMass(MassType.Average);
return BioMassCalc.CalculateIonMz(mass, charge);
}
private PeptideDocNode GetMoleculePeptide(SrmDocument document, DataGridViewRow row, PeptideGroup group, bool requireProductInfo)
{
DocNodeCustomIon ion;
MoleculeInfo moleculeInfo;
try
{
moleculeInfo = ReadPrecursorOrProductColumns(document, row, true); // Re-read the precursor columns
if (moleculeInfo == null)
return null; // Some failure, but exception was already handled
ion = new DocNodeCustomIon(moleculeInfo.Formula, moleculeInfo.MonoMass, moleculeInfo.AverageMass,
Convert.ToString(row.Cells[INDEX_MOLECULE_NAME].Value)); // Short name
}
catch (ArgumentException e)
{
ShowTransitionError(new PasteError
{
Column = INDEX_MOLECULE_FORMULA,
Line = row.Index,
Message = e.Message
});
return null;
}
try
{
var pep = new Peptide(ion);
var tranGroup = GetMoleculeTransitionGroup(document, row, pep, requireProductInfo);
if (tranGroup == null)
return null;
return new PeptideDocNode(pep, document.Settings, null, null, moleculeInfo.ExplicitRetentionTime, new[] { tranGroup }, true);
}
catch (InvalidOperationException e)
{
ShowTransitionError(new PasteError
{
Column = INDEX_MOLECULE_FORMULA,
Line = row.Index,
Message = e.Message
});
return null;
}
}
public SrmDocument ConvertToSmallMolecules(SrmDocument document,
ConvertToSmallMoleculesMode mode = ConvertToSmallMoleculesMode.formulas,
bool invertCharges = false,
bool ignoreDecoys=false)
{
if (mode == ConvertToSmallMoleculesMode.none)
return document;
var newdoc = new SrmDocument(document.Settings);
var note = new Annotations(TestingConvertedFromProteomic, null, 1); // Mark this as a testing node so we don't sort it
newdoc = (SrmDocument)newdoc.ChangeIgnoreChangingChildren(true); // Retain copied results
foreach (var peptideGroupDocNode in document.MoleculeGroups)
{
if (!peptideGroupDocNode.IsProteomic)
{
newdoc = (SrmDocument)newdoc.Add(peptideGroupDocNode); // Already a small molecule
}
else
{
var newPeptideGroup = new PeptideGroup();
var newPeptideGroupDocNode = new PeptideGroupDocNode(newPeptideGroup,
peptideGroupDocNode.Annotations.Merge(note), peptideGroupDocNode.Name,
peptideGroupDocNode.Description, new PeptideDocNode[0],
peptideGroupDocNode.AutoManageChildren);
foreach (var mol in peptideGroupDocNode.Molecules)
{
var peptideSequence = mol.Peptide.Sequence;
// Create a PeptideDocNode with the presumably baseline charge and label
var precursorCharge = (mol.TransitionGroups.Any() ? mol.TransitionGroups.First().TransitionGroup.PrecursorCharge : 0) * (invertCharges ? -1 : 1);
var isotopeLabelType = mol.TransitionGroups.Any() ? mol.TransitionGroups.First().TransitionGroup.LabelType : IsotopeLabelType.light;
var moleculeCustomIon = ConvertToSmallMolecule(mode, document, mol, precursorCharge, isotopeLabelType);
var precursorCustomIon = moleculeCustomIon;
var newPeptide = new Peptide(moleculeCustomIon);
var newPeptideDocNode = new PeptideDocNode(newPeptide, newdoc.Settings, null, null,
null, null, mol.ExplicitRetentionTime, note, mol.Results, new TransitionGroupDocNode[0],
mol.AutoManageChildren);
foreach (var transitionGroupDocNode in mol.TransitionGroups)
{
if (transitionGroupDocNode.IsDecoy)
{
if (ignoreDecoys)
continue;
throw new Exception("There is no translation from decoy to small molecules"); // Not L10N
}
if (transitionGroupDocNode.TransitionGroup.PrecursorCharge != Math.Abs(precursorCharge) ||
!Equals(isotopeLabelType, transitionGroupDocNode.TransitionGroup.LabelType))
{
// Different charges or labels mean different ion formulas
precursorCharge = transitionGroupDocNode.TransitionGroup.PrecursorCharge * (invertCharges ? -1 : 1);
isotopeLabelType = transitionGroupDocNode.TransitionGroup.LabelType;
precursorCustomIon = ConvertToSmallMolecule(mode, document, mol, precursorCharge, isotopeLabelType);
}
var newTransitionGroup = new TransitionGroup(newPeptide, precursorCustomIon, precursorCharge, isotopeLabelType);
// Remove any library info, since for the moment at least small molecules don't support this and it won't roundtrip
var resultsNew = RemoveTransitionGroupChromInfoLibraryInfo(transitionGroupDocNode);
var newTransitionGroupDocNode = new TransitionGroupDocNode(newTransitionGroup,
transitionGroupDocNode.Annotations.Merge(note), document.Settings,
null, null, transitionGroupDocNode.ExplicitValues, resultsNew, null,
transitionGroupDocNode.AutoManageChildren);
var mzShift = invertCharges ? 2.0 * BioMassCalc.MassProton : 0; // We removed hydrogen rather than added
Assume.IsTrue((Math.Abs(newTransitionGroupDocNode.PrecursorMz + mzShift - transitionGroupDocNode.PrecursorMz) - Math.Abs(transitionGroupDocNode.TransitionGroup.PrecursorCharge * BioMassCalc.MassElectron)) <= 1E-5);
foreach (var transition in transitionGroupDocNode.Transitions)
{
double mass = 0;
var transitionCharge = transition.Transition.Charge * (invertCharges ? -1 : 1);
var ionType = IonType.custom;
CustomIon transitionCustomIon;
double mzShiftTransition = 0;
if (transition.Transition.IonType == IonType.precursor)
{
ionType = IonType.precursor;
transitionCustomIon = new DocNodeCustomIon(precursorCustomIon.Formula,
string.IsNullOrEmpty(precursorCustomIon.Formula) ? precursorCustomIon.MonoisotopicMass : (double?) null,
string.IsNullOrEmpty(precursorCustomIon.Formula) ? precursorCustomIon.AverageMass : (double?) null,
SmallMoleculeNameFromPeptide(peptideSequence, transitionCharge));
mzShiftTransition = invertCharges ? 2.0 * BioMassCalc.MassProton : 0; // We removed hydrogen rather than added
}
else if (transition.Transition.IonType == IonType.custom)
{
transitionCustomIon = transition.Transition.CustomIon;
mass = transitionCustomIon.MonoisotopicMass;
}
else
{
// TODO - try to get fragment formula?
mass = BioMassCalc.CalculateIonMassFromMz(transition.Mz, transition.Transition.Charge);
transitionCustomIon = new DocNodeCustomIon(mass, mass,// We can't really get at mono vs average mass from m/z, but for test purposes this is fine
transition.Transition.FragmentIonName);
}
if (mode == ConvertToSmallMoleculesMode.masses_and_names)
{
// Discard the formula if we're testing the use of mass-with-names (for matching in ratio calcs) target specification
transitionCustomIon = new DocNodeCustomIon(transitionCustomIon.MonoisotopicMass, transitionCustomIon.AverageMass,
transition.Transition.FragmentIonName);
}
else if (mode == ConvertToSmallMoleculesMode.masses_only)
{
// Discard the formula and name if we're testing the use of mass-only target specification
transitionCustomIon = new DocNodeCustomIon(transitionCustomIon.MonoisotopicMass, transitionCustomIon.AverageMass);
}
var newTransition = new Transition(newTransitionGroup, ionType,
null, transition.Transition.MassIndex, transition.Transition.Charge * (invertCharges ? -1 : 1), null,
transitionCustomIon);
if (ionType == IonType.precursor)
{
mass = document.Settings.GetFragmentMass(transitionGroupDocNode.TransitionGroup.LabelType, null, newTransition, newTransitionGroupDocNode.IsotopeDist);
}
var newTransitionDocNode = new TransitionDocNode(newTransition, transition.Annotations.Merge(note),
null, mass, transition.IsotopeDistInfo, null,
transition.Results);
Assume.IsTrue((Math.Abs(newTransitionDocNode.Mz + mzShiftTransition - transition.Mz) - Math.Abs(transitionGroupDocNode.TransitionGroup.PrecursorCharge * BioMassCalc.MassElectron)) <= 1E-5, String.Format("unexpected mz difference {0}-{1}={2}", newTransitionDocNode.Mz , transition.Mz, newTransitionDocNode.Mz - transition.Mz)); // Not L10N
newTransitionGroupDocNode =
(TransitionGroupDocNode)newTransitionGroupDocNode.Add(newTransitionDocNode);
}
if (newPeptideDocNode != null)
newPeptideDocNode = (PeptideDocNode)newPeptideDocNode.Add(newTransitionGroupDocNode);
}
newPeptideGroupDocNode =
(PeptideGroupDocNode)newPeptideGroupDocNode.Add(newPeptideDocNode);
}
newdoc = (SrmDocument)newdoc.Add(newPeptideGroupDocNode);
}
}
// No retention time prediction for small molecules (yet?)
newdoc = newdoc.ChangeSettings(newdoc.Settings.ChangePeptideSettings(newdoc.Settings.PeptideSettings.ChangePrediction(
newdoc.Settings.PeptideSettings.Prediction.ChangeRetentionTime(null))));
return newdoc;
}
public static DocNodeCustomIon ConvertToSmallMolecule(ConvertToSmallMoleculesMode mode,
SrmDocument document, PeptideDocNode nodePep, int precursorCharge = 0, IsotopeLabelType isotopeLabelType = null)
{
// We're just using this masscalc to get the ion formula, so mono vs average doesn't matter
isotopeLabelType = isotopeLabelType ?? IsotopeLabelType.light;
var peptideSequence = nodePep.Peptide.Sequence;
var masscalc = document.Settings.TryGetPrecursorCalc(isotopeLabelType, nodePep.ExplicitMods) ?? new SequenceMassCalc(MassType.Monoisotopic);
// Determine the molecular formula of the charged/labeled peptide
var moleculeFormula = masscalc.GetIonFormula(peptideSequence, precursorCharge);
var moleculeCustomIon = new DocNodeCustomIon(moleculeFormula,
SmallMoleculeNameFromPeptide(peptideSequence, precursorCharge));
if (mode == ConvertToSmallMoleculesMode.masses_only)
{
// No formulas or names, just masses - see how we handle that
moleculeCustomIon = new DocNodeCustomIon(moleculeCustomIon.MonoisotopicMass,
moleculeCustomIon.AverageMass);
}
else if (mode == ConvertToSmallMoleculesMode.masses_and_names)
{
// Just masses and names - see how we handle that
moleculeCustomIon = new DocNodeCustomIon(moleculeCustomIon.MonoisotopicMass,
moleculeCustomIon.AverageMass, moleculeCustomIon.Name);
}
return moleculeCustomIon;
}
public TransitionGroup(Peptide peptide, DocNodeCustomIon customIon, int precursorCharge, IsotopeLabelType labelType)
: this(peptide, customIon, precursorCharge, labelType, false, null)
{
}
protected override void DoTest()
{
const int molCount = 1;
var doc = SkylineWindow.Document;
for (var loop=0; loop < 3; loop++)
{
// Should be able to synchronize of both sibs have formula, or neither, but not one of each
string testname;
switch (loop)
{
case 0:
testname = "ions_testing_mixed.sky";
break;
case 1:
testname = "ions_testing.sky";
break;
default:
testname = "ions_testing_masses.sky";
break;
}
string testPath = TestFilesDir.GetTestPath(testname);
RunUI(() => SkylineWindow.OpenFile(testPath));
doc = WaitForDocumentChange(doc);
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add precursor transition to it
var pickList = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(0, true);
pickList.AutoManageChildren = false;
pickList.IsSynchSiblings = true; // Cause a precursor transition to be added to heavy group
});
OkDialog(pickList, pickList.OnOk);
WaitForClosedForm(pickList);
doc = WaitForDocumentChange(doc);
if (loop == 0)
{
// No synch is possible - one ion is formula based, the other mass only
Assert.AreEqual(1, doc.MoleculeTransitions.Count());
}
else
{
// There should now be a precursor transition for the second, heavy labeled transition group, and it
// should match the mz of the transition group
Assert.AreNotEqual(doc.MoleculeTransitionGroups.ToArray()[0].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
Assert.AreEqual(doc.MoleculeTransitionGroups.ToArray()[1].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
}
}
//
// Now with isotope distributions
//
var documentPath = TestFilesDir.GetTestPath("ions_testing_isotopes.sky");
RunUI(() => SkylineWindow.OpenFile(documentPath));
WaitForDocumentLoaded();
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add isotope labeled precursor transitions to it
var pickList0 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList0.ApplyFilter(false);
pickList0.SetItemChecked(0, true);
pickList0.SetItemChecked(1, true);
pickList0.SetItemChecked(2, true);
pickList0.AutoManageChildren = false;
Assert.IsTrue(pickList0.CanSynchSiblings);
pickList0.IsSynchSiblings = true; // Cause precursor transitions to be added to heavy group
});
OkDialog(pickList0, pickList0.OnOk);
WaitForClosedForm(pickList0);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz,
SkylineWindow.Document.MoleculeTransitions.ToArray()[4].Mz);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz + 1.00349556477,
SkylineWindow.Document.MoleculeTransitions.ToArray()[5].Mz, 1e-6);
// Verify that adding a custom transition prevents the synch siblings checkbox from appearing
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
var moleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
var C12H12 = "C12H12";
var testNametextA = "y1";
RunUI(() =>
{
moleculeDlg.FormulaBox.Formula = C12H12;
moleculeDlg.NameText = testNametextA;
moleculeDlg.Charge = 1;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var newDoc = SkylineWindow.Document;
var compareIon = new DocNodeCustomIon(C12H12, testNametextA);
const int transY1Index = 3;
Assert.AreEqual(compareIon, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.CustomIon);
Assert.AreEqual(1, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.Charge);
var pickList1 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.AutoManageChildren = true;
Assert.IsFalse(pickList1.CanSynchSiblings);
});
OkDialog(pickList1, pickList1.OnOk);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
// Long as we're here, check mz filtering
var transitionSettings = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings.MinMz = 160; // Should drop that custom ion
});
OkDialog(transitionSettings, transitionSettings.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
RunUI(() => { SkylineWindow.Undo(); });
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.Nodes[1];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList2 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsFalse(pickList2.CanSynchSiblings); // The light set has a non-precursor transition
});
OkDialog(pickList2, pickList2.OnOk);
var transitionSettings2 = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings2.MinMz = 300; // Should drop that custom ion
});
OkDialog(transitionSettings2, transitionSettings2.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
var pickList3 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsTrue(pickList3.CanSynchSiblings);
});
OkDialog(pickList3, pickList3.OnOk);
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible && !helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
return;
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
Charge = charge; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
if (string.IsNullOrEmpty(_formulaBox.Formula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
return;
if (!_formulaBox.ValidateMonoText(helper))
return;
}
var formula = _formulaBox.Formula;
var monoMass = _formulaBox.MonoMass ?? 0;
var averageMass = _formulaBox.AverageMass ?? 0;
if (monoMass < CustomIon.MIN_MASS || averageMass < CustomIon.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomIon.MIN_MASS));
return;
}
if (monoMass > CustomIon.MAX_MASS || averageMass > CustomIon.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(Resources.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__, CustomIon.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(monoMass, charge)) ||
!_transitionSettings.IsMeasurablePrecursor(BioMassCalc.CalculateIonMz(averageMass, charge))))
{
_formulaBox.ShowTextBoxErrorFormula(helper, Resources.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
if (!string.IsNullOrEmpty(_formulaBox.Formula))
{
try
{
ResultCustomIon = new DocNodeCustomIon(formula, textName.Text);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
ResultCustomIon = new DocNodeCustomIon(monoMass, averageMass, textName.Text);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
_driverLabelType.GetHeavyModifications(), // This is the only thing the user may have altered
_peptideSettings.Modifications.InternalStandardTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
// Only update if anything changed
if (!Equals(settings, _peptideSettings))
{
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorCharge, Charge) && !ReferenceEquals(t, _initialId);
}))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_charge_and_label_type_already_exists_, textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return transition != null && ((transition.Charge == Charge) && Equals(transition.CustomIon, ResultCustomIon)) && !ReferenceEquals(t, _initialId);
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
public static DocNodeCustomIon Deserialize(XmlReader reader)
{
DocNodeCustomIon ion = new DocNodeCustomIon();
ion.ReadAttributes(reader);
return ion;
}
// Note: this potentially returns a node with a different ID, which has to be Inserted rather than Replaced
public PeptideDocNode ChangeCustomIonValues(SrmSettings settings, DocNodeCustomIon customIon, ExplicitRetentionTimeInfo explicitRetentionTime)
{
var newPeptide = new Peptide(customIon);
Helpers.AssignIfEquals(ref newPeptide, Peptide);
if (Equals(Peptide, newPeptide))
{
return Equals(ExplicitRetentionTime, explicitRetentionTime) ? this : ChangeExplicitRetentionTime(explicitRetentionTime);
}
else
{
// ID Changes impact all children, because IDs have back pointers to their parents
var children = new List<TransitionGroupDocNode>();
foreach (var nodeGroup in TransitionGroups)
{
children.Add(nodeGroup.UpdateSmallMoleculeTransitionGroup(newPeptide, null, settings));
}
return new PeptideDocNode(newPeptide, settings, ExplicitMods, SourceKey, explicitRetentionTime, children.ToArray(), AutoManageChildren);
}
}
private void TestAddingSmallMoleculePrecursor()
{
// Position ourselves on the first molecule
var newDoc = SkylineWindow.Document;
SelectNode(SrmDocument.Level.Molecules, 0);
var moleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
const int charge = 1;
var heavyFormula = COOO13H.Replace("O13", "O12O'");
RunUI(() =>
{
moleculeDlg.NameText = heavyFormula;
moleculeDlg.FormulaBox.Formula = heavyFormula;
moleculeDlg.IsotopeLabelType = IsotopeLabelType.light; // This should provoke a failure - can't have two of the same label and charge
});
RunDlg<MessageDlg>(moleculeDlg.OkDialog, dlg =>
{
// Trying to exit the dialog should cause a warning about charge
Assert.AreEqual(
Resources.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_charge_and_label_type_already_exists_, dlg.Message);
dlg.OkDialog(); // Dismiss the warning
});
RunUI(() =>
{
moleculeDlg.IsotopeLabelType = IsotopeLabelType.heavy;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var compareIonHeavy = new DocNodeCustomIon(heavyFormula, heavyFormula);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(heavyFormula, newDoc.MoleculeTransitionGroups.ElementAt(1).CustomIon.Name);
Assert.AreEqual(compareIonHeavy, newDoc.MoleculeTransitionGroups.ElementAt(1).CustomIon);
Assert.AreEqual(charge, newDoc.MoleculeTransitionGroups.ElementAt(1).TransitionGroup.PrecursorCharge);
var predictedMz = BioMassCalc.MONOISOTOPIC.CalculateIonMz(heavyFormula, charge);
var actualMz = newDoc.MoleculeTransitionGroups.ElementAt(1).PrecursorMz;
Assert.AreEqual(predictedMz, actualMz, Math.Pow(10, -SequenceMassCalc.MassPrecision));
// Now verify that we are OK with different charge same label
SelectNode(SrmDocument.Level.Molecules, 0);
var moleculeDlg2 = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
RunUI(() =>
{
moleculeDlg2.FormulaBox.Formula = COOO13H + "H";
moleculeDlg2.Charge = charge + 1;
moleculeDlg2.IsotopeLabelType = IsotopeLabelType.light; // This should not provoke a failure
});
OkDialog(moleculeDlg2, moleculeDlg2.OkDialog);
// Verify that the transition group sort order is enforced in the document
// Select the last precursor, bump its charge state to drop its mz - should result in doc node reordering
CheckTransitionGroupSortOrder(newDoc);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.LastNode;
});
var editMoleculeDlgB = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.ModifySmallMoleculeTransitionGroup);
RunUI(() =>
{
editMoleculeDlgB.Charge = 5;
});
OkDialog(editMoleculeDlgB, editMoleculeDlgB.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
CheckTransitionGroupSortOrder(newDoc);
RunUI(SkylineWindow.Undo);
newDoc = WaitForDocumentChange(newDoc);
CheckTransitionGroupSortOrder(newDoc);
}
private static void TestAddingTransition()
{
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
var moleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
RunUI(() =>
{
moleculeDlg.FormulaBox.Formula = C12H12;
moleculeDlg.NameText = testNametextA;
moleculeDlg.Charge = 1;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var newDoc = SkylineWindow.Document;
var compareIon = new DocNodeCustomIon(C12H12, testNametextA);
Assert.AreEqual(compareIon,newDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
Assert.AreEqual(1,newDoc.MoleculeTransitions.ElementAt(0).Transition.Charge);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode);
});
}
private static void TestAddingSmallMolecule()
{
RunUI(() => SkylineWindow.SelectedPath = new IdentityPath(SkylineWindow.Document.MoleculeGroups.ElementAt(0).Id));
var moleculeDlg = ShowDialog<EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
const int charge = 1;
RunUI(() =>
{
moleculeDlg.NameText = COOO13H;
moleculeDlg.FormulaBox.Formula = COOO13H;
moleculeDlg.Charge = charge;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var compareIon = new DocNodeCustomIon(COOO13H, COOO13H);
var newDoc = SkylineWindow.Document;
Assert.AreEqual(compareIon, newDoc.Molecules.ElementAt(0).CustomIon);
Assert.AreEqual(compareIon, newDoc.MoleculeTransitionGroups.ElementAt(0).CustomIon);
Assert.AreEqual(charge, newDoc.MoleculeTransitionGroups.ElementAt(0).PrecursorCharge);
var predictedMz = BioMassCalc.MONOISOTOPIC.CalculateIonMz(COOO13H, charge);
var actualMz = newDoc.MoleculeTransitionGroups.ElementAt(0).PrecursorMz;
Assert.AreEqual(predictedMz, actualMz, Math.Pow(10, -SequenceMassCalc.MassPrecision));
}