private static void TestAddingSmallMolecule()
{
RunUI(() => SkylineWindow.SelectedPath = new IdentityPath(SkylineWindow.Document.MoleculeGroups.ElementAt(0).Id));
var doc = SkylineWindow.Document;
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 = WaitForDocumentChange(doc);
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));
}
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);
});
}
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;
}
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);
}
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);
}
