public TransitionLoss(StaticMod precursorMod, FragmentLoss loss, MassType massType)
: this()
{
PrecursorMod = precursorMod;
Loss = loss;
Mass = Loss.GetMass(massType);
}
public TransitionLoss(StaticMod precursorMod, FragmentLoss loss, MassType massType)
: this()
{
PrecursorMod = precursorMod;
Loss = loss;
Mass = Loss.GetMass(massType);
}
public bool Equals(FragmentLoss other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Equals(other.Formula, Formula) &&
other.MonoisotopicMass.Equals(MonoisotopicMass) &&
other.AverageMass.Equals(AverageMass) &&
other.Inclusion.Equals(Inclusion));
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string formulaLoss = _formulaBox.Formula;
double? monoLoss = null;
double? avgLoss = null;
if (!string.IsNullOrEmpty(formulaLoss))
{
try
{
double massMono = SequenceMassCalc.ParseModMass(BioMassCalc.MONOISOTOPIC, formulaLoss);
double massAverage = SequenceMassCalc.ParseModMass(BioMassCalc.AVERAGE, formulaLoss);
if (FragmentLoss.MIN_LOSS_MASS > massMono || FragmentLoss.MIN_LOSS_MASS > massAverage)
{
_formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditFragmentLossDlg_OkDialog_Neutral_loss_masses_must_be_greater_than_or_equal_to__0__,
FragmentLoss.MIN_LOSS_MASS));
return;
}
if (massMono > FragmentLoss.MAX_LOSS_MASS || massAverage > FragmentLoss.MAX_LOSS_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper, string.Format(Resources.EditFragmentLossDlg_OkDialog_Neutral_loss_masses_must_be_less_than_or_equal_to__0__,
FragmentLoss.MAX_LOSS_MASS));
return;
}
}
catch (ArgumentException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else if (_formulaBox.MonoMass != null ||
_formulaBox.AverageMass != null)
{
formulaLoss = null;
double mass;
if (!_formulaBox.ValidateMonoText(helper, FragmentLoss.MIN_LOSS_MASS, FragmentLoss.MAX_LOSS_MASS, out mass))
return;
monoLoss = mass;
if (!_formulaBox.ValidateAverageText(helper, FragmentLoss.MIN_LOSS_MASS, FragmentLoss.MAX_LOSS_MASS, out mass))
return;
avgLoss = mass;
}
else
{
_formulaBox.ShowTextBoxErrorFormula(helper,Resources.EditFragmentLossDlg_OkDialog_Please_specify_a_formula_or_constant_masses);
return;
}
// Make sure the new loss does not already exist.
var loss = new FragmentLoss(formulaLoss, monoLoss, avgLoss, Inclusion);
if (_existing.Contains(loss))
{
MessageDlg.Show(this, string.Format(Resources.EditFragmentLossDlg_OkDialog_The_loss__0__already_exists, loss));
return;
}
Loss = loss;
DialogResult = DialogResult.OK;
}
public StaticMod MatchVariableAndLossInclusion(StaticMod mod)
{
// Only allowed if the mods are equivalent
Assume.IsTrue(Equivalent(mod));
var result = this;
if (!Equals(result.IsVariable, mod.IsVariable))
result = result.ChangeVariable(mod.IsVariable);
if (result.Losses != null && !ArrayUtil.EqualsDeep(result.Losses, mod.Losses))
{
int len = result.Losses.Count;
var newLosses = new FragmentLoss[len];
for (int i = 0; i < len; i++)
{
newLosses[i] = result.Losses[i].ChangeInclusion(mod.Losses[i].Inclusion);
}
result = result.ChangeLosses(newLosses);
}
return result;
}
private bool EquivalentFormulas(FragmentLoss loss1, FragmentLoss loss2)
{
return ArrayUtil.EqualsDeep(GetFormulaCounts(loss1.Formula).ToArray(),
GetFormulaCounts(loss2.Formula).ToArray());
}
public bool Equals(FragmentLoss other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other.Formula, Formula) &&
other.MonoisotopicMass.Equals(MonoisotopicMass) &&
other.AverageMass.Equals(AverageMass) &&
other.Inclusion.Equals(Inclusion);
}
protected override void DoTest()
{
// Create modifications used in this test
var aquaMod = new StaticMod("Aqua 13C", "K, R", ModTerminus.C, null, LabelAtoms.C13|LabelAtoms.N15, null, null);
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var multipleLossMod = new StaticMod("Multiple Loss-only", "A", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("NH3"), new FragmentLoss("H2O") });
var explicitMassesLossMod = new StaticMod("Explicit Mass Loss", "N", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss(null, 5, 10) });
var variableLossMod = new StaticMod("Methionine Oxidized Loss", "M", null, true, "O",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("CH3O") });
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.Add(aquaMod);
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
Settings.Default.StaticModList.Add(variableLossMod);
// Bump up the max mz a bit
var transitionSettingsUI = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettingsUI.MaxMz = 1510;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
// Bring up add modification dialog
var peptideSettingsUI = ShowDialog<PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlg = ShowEditStaticModsDlg(peptideSettingsUI);
var addModDlg = ShowAddModDlg(editModsDlg);
// Try a few things with new loss UI on the phospho loss modification
RunUI(() =>
{
addModDlg.Modification = phosphoLossMod;
Assert.IsTrue(addModDlg.GetLossText(0).EndsWith(phosphoLossMod.Losses[0].Formula));
addModDlg.LossSelectedIndex = 0;
addModDlg.DeleteLoss();
});
// Add back the original loss with the new loss editor dialog
RunDlg<EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = phosphoLossMod.Losses[0];
dlg.OkDialog();
});
// Add a smaller formula loss with the new loss editor dialog
var fragmentLossWater = new FragmentLoss("H2O");
RunDlg<EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossWater;
dlg.OkDialog();
});
// Add an explicit mass loss with the new loss editor dialog
var fragmentLossConstants = new FragmentLoss(null, 20, 25);
RunDlg<EditFragmentLossDlg>(addModDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossConstants;
dlg.OkDialog();
});
// Check the added losses, and remove all but the original loss
RunUI(() =>
{
VerifyLossText(addModDlg.GetLossText(0), fragmentLossWater);
VerifyLossText(addModDlg.GetLossText(1), fragmentLossConstants);
VerifyLossText(addModDlg.GetLossText(2), phosphoLossMod.Losses[0]);
addModDlg.LossSelectedIndex = 0;
addModDlg.DeleteLoss();
addModDlg.DeleteLoss();
});
OkDialog(addModDlg, addModDlg.OkDialog);
// Add a loss modification with 2 losses and no formula
RunDlg<EditStaticModDlg>(editModsDlg.AddItem, dlg =>
{
dlg.Modification = multipleLossMod;
VerifyLossText(dlg.GetLossText(0), multipleLossMod.Losses[0]);
VerifyLossText(dlg.GetLossText(1), multipleLossMod.Losses[1]);
dlg.OkDialog();
});
// Add a loss modification with explicit numeric losses and no formula
// starting with no losses
var addExplicitLossDlg = ShowAddModDlg(editModsDlg);
RunUI(() =>
{
addExplicitLossDlg.Modification = explicitMassesLossMod;
addExplicitLossDlg.ShowLoss = true;
VerifyLossText(addExplicitLossDlg.GetLossText(0), explicitMassesLossMod.Losses[0]);
addExplicitLossDlg.LossSelectedIndex = 0;
addExplicitLossDlg.DeleteLoss();
});
// Add the explicit numeric loss
RunDlg<EditFragmentLossDlg>(addExplicitLossDlg.AddLoss, dlg =>
{
dlg.Loss = fragmentLossConstants;
dlg.OkDialog();
});
OkDialog(addExplicitLossDlg, addExplicitLossDlg.OkDialog);
OkDialog(editModsDlg, editModsDlg.OkDialog);
// Check the phospho loss modification
RunUI(() => peptideSettingsUI.PickedStaticMods =
new List<string>(peptideSettingsUI.PickedStaticMods) { phosphoLossMod.Name }.ToArray());
WaitForOpenForm<PeptideSettingsUI>(); // Show Modifications tab for form testing
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_YEAST_7));
// Losses not added by default without a library
Assert.AreEqual(0, GetLossCount(SkylineWindow.Document, 1));
// Make sure setting losses as included Always works
{
var docBeforeAlways = SkylineWindow.Document;
var peptideSettingsUIAlways = ShowDialog<PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlgAlways = ShowEditStaticModsDlg(peptideSettingsUIAlways);
RunUI(() => editModsDlgAlways.SelectItem(phosphoLossMod.Name));
var editModDlgAlways = ShowDialog<EditStaticModDlg>(editModsDlgAlways.EditItem);
RunUI(() => editModDlgAlways.LossSelectedIndex = 0);
RunDlg<EditFragmentLossDlg>(editModDlgAlways.EditLoss, dlg =>
{
dlg.Inclusion = LossInclusion.Always;
dlg.OkDialog();
});
OkDialog(editModDlgAlways, editModDlgAlways.OkDialog);
OkDialog(editModsDlgAlways, editModsDlgAlways.OkDialog);
OkDialog(peptideSettingsUIAlways, peptideSettingsUIAlways.OkDialog);
var docAfterAlways = WaitForDocumentChange(docBeforeAlways);
Assert.AreEqual(5, GetLossCount(docAfterAlways, 1));
AssertEx.Serializable(docAfterAlways);
// Undo and revert to original phospo loss modification definition
RunUI(SkylineWindow.Undo);
Settings.Default.StaticModList.SetValue(phosphoLossMod);
}
// Show losses in the pick list
var docFasta = WaitForProteinMetadataBackgroundLoaderCompletedUI();
SelectNode(SrmDocument.Level.TransitionGroups, 0);
RunDlg<PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(1, losses.Length);
VerifyLossGroup(losses, 0, 98, 124);
dlg.ToggleFind();
dlg.SearchString = "-98";
dlg.ToggleItem(0);
dlg.ToggleItem(1);
dlg.OnOk();
});
var docLoss = WaitForDocumentChange(docFasta);
// Make sure two losses were added
Assert.AreEqual(2, GetLossCount(docLoss, 1));
// Allow 2 neutral losses per fragment
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.MaxNeutralLosses = 2;
dlg.OkDialog();
});
var docLoss2 = WaitForDocumentChange(docLoss);
// Make sure 2 phospho losses are now possible
IGrouping<double, string>[] losses1 = null;
RunDlg<PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
losses1 = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(2, losses1.Length);
VerifyLossGroup(losses1, 0, 98, 124);
VerifyLossGroup(losses1, 1, 196, 109);
dlg.OnCancel();
});
// Add a modification with multiple possible losses
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new List<string>(dlg.PickedStaticMods)
{ multipleLossMod.Name }.ToArray();
dlg.OkDialog();
});
var docLossMulti = WaitForDocumentChange(docLoss2);
// Make sure all combinations of 2 except 2 of the multiple
// losses are possible, since only one amino acid A exists in this
// peptide.
RunDlg<PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(6, losses.Length);
VerifyLossGroup(losses, 0, 17, 66);
VerifyLossGroup(losses, 1, 18, 66);
VerifyLossGroup(losses, 2, 98, 124);
VerifyLossGroup(losses, 3, 115, 61);
VerifyLossGroup(losses, 4, 116, 61);
VerifyLossGroup(losses, 5, 196, 109);
AssertEx.NoDiff(TextUtil.LineSeparate(losses1[0].ToArray()), TextUtil.LineSeparate(losses[2].ToArray()));
AssertEx.NoDiff(TextUtil.LineSeparate(losses1[1].ToArray()), TextUtil.LineSeparate(losses[5].ToArray()));
// Add new neutral loss transitions to the document
dlg.ToggleFind();
dlg.SearchString = "-17]";
dlg.ToggleItem(0);
dlg.SearchString = "-115]";
dlg.ToggleItem(0);
dlg.OnOk();
});
var docLossMultiAdded = WaitForDocumentChange(docLossMulti);
Assert.AreEqual(1, GetLossCount(docLossMultiAdded, 2));
// Add heavy modifications and make sure transition group is added with losses
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedHeavyMods = new[] { aquaMod.Name };
dlg.OkDialog();
});
var docLossMultiHeavy = WaitForDocumentChange(docLossMultiAdded);
Assert.AreEqual(4, docLossMultiHeavy.PeptideTransitionGroupCount);
Assert.AreEqual(8, GetLossCount(docLossMultiHeavy, 1));
Assert.AreEqual(2, GetLossCount(docLossMultiHeavy, 2));
// Make sure this document is serializable
AssertEx.Serializable(docLossMultiHeavy, AssertEx.DocumentCloned);
// Reset to just 1 neutral loss per fragment, and turn off heavy mod
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedHeavyMods = new string[0];
dlg.MaxNeutralLosses = 1;
dlg.OkDialog();
});
var docLossMulti1 = WaitForDocumentChange(docLossMultiHeavy);
Assert.AreEqual(3, GetLossCount(docLossMulti1, 1));
Assert.AreEqual(0, GetLossCount(docLossMulti1, 2));
// Remove all neutral loss modifications currently on the document
// and add the constant numeric loss
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, dlg =>
{
dlg.PickedStaticMods = new[] { explicitMassesLossMod.Name };
dlg.OkDialog();
});
var docNoLoss2 = WaitForDocumentChange(docLossMulti1);
Assert.AreEqual(0, GetLossCount(docNoLoss2, 1));
// Add a neutral loss transition with constant numeric loss
RunDlg<PopupPickList>(SkylineWindow.ShowPickChildrenInTest, dlg =>
{
dlg.ApplyFilter(false);
var losses = GetLossGroups(dlg.ItemNames).ToArray();
Assert.AreEqual(1, losses.Length);
VerifyLossGroup(losses, 0, 20, 85);
// Add new neutral loss transitions to the document
dlg.ToggleFind();
dlg.SearchString = "-20";
dlg.ToggleItem(0);
dlg.OnOk();
});
// Verify that the expected loss was added to the document
var docConstantMono = WaitForDocumentChange(docNoLoss2);
Assert.AreEqual(1, GetLossCount(docConstantMono, 1));
var pathTranLoss = docConstantMono.GetPathTo((int) SrmDocument.Level.Transitions, 0);
var nodeTranLos = (TransitionDocNode) docConstantMono.FindNode(pathTranLoss);
Assert.AreEqual(IonType.precursor.GetLocalizedString() + " -20", nodeTranLos.FragmentIonName);
// Switch mass type to average
RunDlg<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, dlg =>
{
dlg.FragmentMassType = MassType.Average;
dlg.OkDialog();
});
// Make sure neutral loss changes as expected
var docConstantAverage = WaitForDocumentChange(docConstantMono);
Assert.AreEqual(1, GetLossCount(docConstantAverage, 1));
nodeTranLos = (TransitionDocNode)docConstantAverage.FindNode(pathTranLoss);
Assert.AreEqual(IonType.precursor.GetLocalizedString() + " -25", nodeTranLos.FragmentIonName);
// Make sure the resulting document is serializable
AssertEx.Serializable(docConstantAverage, AssertEx.DocumentCloned);
}
private static void VerifyLossText(string lossText, FragmentLoss loss)
{
if (loss.Formula != null)
Assert.IsTrue(lossText.EndsWith(loss.Formula));
Assert.IsTrue(lossText.StartsWith(string.Format("{0:F04}", loss.MonoisotopicMass)));
}