private void TestPreloadedMeasuredIons()
{
var ions = new[]
{
new MeasuredIon("Water", "H2O", null, null, 1),
new MeasuredIon("Carbon", "CO2", null, null, 1, true)
};
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)))));
TransitionSettingsUI tranSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
tranSettings.SelectedTab = TransitionSettingsUI.TABS.Filter;
Assert.IsTrue(tranSettings.ValidateIonCheckBoxes(new[] { CheckState.Checked, CheckState.Indeterminate }));
});
OkDialog(tranSettings, tranSettings.OkDialog);
}
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());
}
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());
}
private void TestPreloadedMeasuredIons()
{
var ions = new[]
{
new MeasuredIon("Water", "H2O", null, null, 1),
new MeasuredIon("Carbon", "CO2", null, null, 1, true)
};
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)))));
TransitionSettingsUI tranSettings = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
tranSettings.SelectedTab = TransitionSettingsUI.TABS.Filter;
Assert.IsTrue(tranSettings.ValidateIonCheckBoxes(new[] { CheckState.Checked, CheckState.Indeterminate }));
});
OkDialog(tranSettings, tranSettings.OkDialog);
}
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);
}