private void TestModificationMatching()
{
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.Add(phosphoLossMod.ChangeExplicit(false));
var phosphoNotVariable = SkylineWindow.Document.Settings.ChangePeptideModifications(
mods => mods.ChangeStaticModifications(new[] { phosphoLossMod.ChangeExplicit(false) }));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods",
doc => doc.ChangeSettings(phosphoNotVariable)));
RelaunchLibExplorer(false, PHOSPHO_LIB);
// Test doesn't find variable match if implicit match exists in doc
WaitForConditionUI(() => !_viewLibUI.HasUnmatchedPeptides);
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 4, 4, 12))
{
RunDlg <MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides, msgDlg => msgDlg.Btn1Click());
}
Assert.IsTrue(SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications
.Contains(mod => mod.Equivalent(phosphoLossMod)));
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications
.Contains(mod => mod.Equivalent(phosphoLossMod) && mod.IsVariable));
RunUI(SkylineWindow.Undo);
// Test creates variable mod if implicit match exists in globals
var pepModsNoMods1 =
SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0]));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsNoMods1)));
RelaunchLibExplorer(false, PHOSPHO_LIB);
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 4, 4, 12))
{
RunDlg <MultiButtonMsgDlg>(_viewLibUI.AddAllPeptides, msgDlg => msgDlg.Btn1Click());
}
Assert.IsTrue(SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications
.Contains(mod => mod.Equivalent(phosphoLossMod) && mod.IsVariable));
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications
.Contains(mod => mod.Equivalent(phosphoLossMod) && !mod.IsVariable));
// Test implicit mods only created if safe to do so
RunUI(() => SkylineWindow.Undo());
RunDlg <MultiButtonMsgDlg>(() => _libComboBox.SelectedIndex = 4, msgDlg => msgDlg.Btn1Click());
WaitForConditionUI(() => _pepList.SelectedIndex != -1);
WaitForConditionUI(() => _viewLibUI.HasMatches);
RunDlg <MultiButtonMsgDlg>(() => _viewLibUI.CheckLibraryInSettings(),
msgDlg => msgDlg.Btn0Click());
var fmpDlg0 = ShowDialog <FilterMatchedPeptidesDlg>(() => _viewLibUI.AddAllPeptides());
RunUI(() => fmpDlg0.AddFiltered = true);
using (new CheckDocumentStateWithPossibleProteinMetadataBackgroundUpdate(1, 82, 96,
TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 279 : 282))
{
RunDlg <MultiButtonMsgDlg>(fmpDlg0.OkDialog, msgDlg => msgDlg.Btn1Click());
}
// Implicit mod is created because there are no conflicting peptides in the current document.
Assert.IsTrue(
SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications.Contains(mod =>
!mod.IsExplicit && !mod.IsVariable));
var nodeRemoved = "";
RunUI(() =>
{
Settings.Default.EditFindText = "C";
SkylineWindow.FindNext(false);
nodeRemoved = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence;
SkylineWindow.EditDelete();
});
Assert.IsFalse(
SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications.Contains(mod =>
mod.IsExplicit));
var pepModsNoMods2 =
SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0]));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsNoMods2)));
RelaunchLibExplorer(false, YEAST);
RunUI(() =>
{
_viewLibUI.ChangeSelectedPeptide(nodeRemoved.Replace("C", "C[+57.0]"));
_viewLibUI.AddPeptide();
});
// Explicit mod is created because an implicit mod conflicts with current document settings.
Assert.IsFalse(
SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications.Contains(mod =>
!mod.IsExplicit));
Assert.IsTrue(SkylineWindow.Document.Peptides.Contains(nodePep =>
nodePep.Peptide.Sequence == nodeRemoved && nodePep.HasExplicitMods));
// Implicit modifications only added to document if they apply to the added peptide
RunUI(() =>
{
SkylineWindow.SelectAll();
SkylineWindow.EditDelete();
});
var pepModsNoMods3 =
SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0]));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsNoMods3)));
Settings.Default.StaticModList.Clear();
RelaunchLibExplorer(true, ANL_COMBINED);
RunUI(() => _viewLibUI.AddPeptide());
Assert.AreEqual(0, Settings.Default.StaticModList.Count);
// Variable mods not added if conflict with existing peptides.
RunUI(() =>
{
_pepList.SelectedIndex = 1;
_viewLibUI.AddPeptide();
});
Assert.IsFalse(SkylineWindow.Document.Peptides.Contains(nodePep =>
nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods));
// Test removing mod from globals affects matches
var pepModsNoMods4 = SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(Settings.Default.StaticModList.GetDefaults().ToArray()));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsNoMods4)));
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(Settings.Default.StaticModList.GetDefaults());
RelaunchLibExplorer(false, YEAST);
Assert.IsFalse(_viewLibUI.HasUnmatchedPeptides);
// Test removing mod from doc does not remove matches
Settings.Default.StaticModList.Clear();
var pepModsNone = SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0]));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsNone)));
RunUI(SkylineWindow.Activate);
RunUI(_viewLibUI.Activate);
WaitForConditionUI(() => _pepList.Items.Count == 96);
WaitForConditionUI(() => _pepList.SelectedIndex != -1);
Assert.IsFalse(_viewLibUI.HasUnmatchedPeptides);
// Relaunch explorer without modification matching
RunUI(() => _viewLibUI.CancelDialog());
WaitForClosedForm(_viewLibUI);
_viewLibUI = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(YEAST));
var matchedPepModsDlg = WaitForOpenForm <MultiButtonMsgDlg>();
RunUI(matchedPepModsDlg.BtnCancelClick);
WaitForConditionUI(() => _pepList.Items.Count == 96);
WaitForConditionUI(() => _pepList.SelectedIndex != -1);
Assert.IsTrue(_viewLibUI.HasUnmatchedPeptides);
// Test adding mod to doc affects matches
Settings.Default.StaticModList.AddRange(Settings.Default.StaticModList.GetDefaults());
var pepModsDefault = SkylineWindow.Document.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(Settings.Default.StaticModList.Select(mod =>
mod.ChangeExplicit(false)).ToArray()));
RunUI(() => SkylineWindow.ModifyDocument("Change static mods", doc =>
doc.ChangeSettings(pepModsDefault)));
RunUI(SkylineWindow.Activate);
RunUI(_viewLibUI.Activate);
WaitForConditionUI(() => _pepList.Items.Count == 96);
WaitForConditionUI(() => _pepList.SelectedIndex != -1);
Assert.IsFalse(_viewLibUI.HasUnmatchedPeptides);
RunUI(() => _viewLibUI.CancelDialog());
WaitForClosedForm(_viewLibUI);
}