/// <inheritdoc />
public void RegisterTipProvider(ITipProvider provider)
{
lock (this.lockObject)
{
this.tipsByProvider.Add(provider, null);
}
}
/// <inheritdoc />
public void CommitTipPersisted(ITipProvider provider, ChainedHeader tip)
{
lock (this.lockObject)
{
this.tipsByProvider[provider] = tip;
// Get lowest tip out of all tips commited.
ChainedHeader lowestTip = null;
foreach (ChainedHeader chainedHeader in this.tipsByProvider.Values)
{
// Do nothing if there is at least 1 component that didn't commit it's tip yet.
if (chainedHeader == null)
{
this.logger.LogTrace("(-)[NOT_ALL_TIPS_COMMITED]");
return;
}
if ((lowestTip == null) || (chainedHeader.Height < lowestTip.Height))
{
lowestTip = chainedHeader;
}
}
// Last common tip can't be changed because lowest tip is equal to it already.
if (this.lastCommonTip == lowestTip)
{
this.logger.LogTrace("(-)[ALREADY_PERSISTED]");
return;
}
// Make sure all tips are on the same chain.
bool tipsOnSameChain = true;
foreach (ChainedHeader chainedHeader in this.tipsByProvider.Values)
{
if (chainedHeader.GetAncestor(lowestTip.Height) != lowestTip)
{
tipsOnSameChain = false;
break;
}
}
if (!tipsOnSameChain)
{
this.logger.LogDebug("Tips are not on the same chain, finding last common fork between them.");
lowestTip = this.FindCommonFork(this.tipsByProvider.Values.ToList());
}
this.lastCommonTip = lowestTip;
this.newCommonTipSetEvent.Set();
}
}
private void pickListMulti_MouseMove(object sender, MouseEventArgs e)
{
Point pt = e.Location;
if (!_moveThreshold.Moved(pt))
{
return;
}
_moveThreshold.Location = null;
ITipProvider tipProvider = null;
int i = GetIndexAtPoint(pt);
// Make sure it is in the text portion of the item
if (i != -1 && !GetItemTextRectangle(i).Contains(pt))
{
i = -1;
}
if (i == -1)
{
_lastTipNode = null;
_lastTipProvider = null;
}
else
{
var nodeDoc = GetVisibleChoice(i).Choice;
if (!ReferenceEquals(nodeDoc, _lastTipNode))
{
_lastTipNode = nodeDoc;
_lastTipProvider = _picker.GetPickTip(nodeDoc);
}
tipProvider = _lastTipProvider;
}
if (tipProvider == null || !tipProvider.HasTip)
{
_nodeTip.HideTip();
}
else
{
_nodeTip.SetTipProvider(tipProvider, GetItemTextRectangle(i), pt);
}
}
private IEnumerable <Tip> GetTips(ITipProvider tipsProvider, string productText)
{
return(tipsProvider.GetTips(productText));
}
protected override void DoTest()
{
// Creating a MS/MS Spectral Library, p. 1
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg <BuildLibraryDlg>(peptideSettingsUI.ShowBuildLibraryDlg, buildLibraryDlg =>
{
buildLibraryDlg.LibraryPath = TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\"); // Not L10N
buildLibraryDlg.LibraryName = YEAST_ATLAS;
buildLibraryDlg.LibraryCutoff = 0.95;
buildLibraryDlg.LibraryAuthority = "peptideatlas.org"; // Not L10N
buildLibraryDlg.OkWizardPage();
IList <string> inputPaths = new List <string>
{
TestFilesDirs[0].GetTestPath(@"MethodEdit\Yeast_atlas\interact-prob.pep.xml") // Not L10N
};
buildLibraryDlg.AddInputFiles(inputPaths);
buildLibraryDlg.OkWizardPage();
});
PeptideSettingsUI peptideSettingsUI1 = peptideSettingsUI;
RunUI(() =>
{
peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI1.PickedLibraries = new[] { YEAST_ATLAS };
});
WaitForOpenForm <PeptideSettingsUI>(); // To show Library tab for Forms testing
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 4); // Not L10N
RunUI(() => peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Digest);
WaitForOpenForm <PeptideSettingsUI>(); // To show Digestion tab for Forms testing
// Creating a Background Proteome File, p. 3
FileEx.SafeDelete(TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast" + ProteomeDb.EXT_PROTDB)); // Not L10N
var buildBackgroundProteomeDlg =
ShowDialog <BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg);
RunUI(() =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath =
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast"); // Not L10N
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast"; // Not L10N
buildBackgroundProteomeDlg.AddFastaFile(
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\sgd_yeast.fasta")); // Not L10N
});
PauseForScreenShot <BuildBackgroundProteomeDlg>("Edit Background Proteome form", 5); // Not L10N
OkDialog(buildBackgroundProteomeDlg, buildBackgroundProteomeDlg.OkDialog);
PauseForScreenShot <PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 6); // Not L10N
var docB = SkylineWindow.Document;
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChange(docB);
if (!TryWaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0))
{
Assert.Fail("Timed out loading libraries: libCount={0}, NotLoadedExplained={1}",
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count,
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsNotLoadedExplained ?? "<null>");
}
WaitForCondition(() =>
{
var peptideSettings = SkylineWindow.Document.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
return(backgroundProteome.HasDigestion(peptideSettings));
}, "backgroundProteome.HasDigestion");
// Wait a bit in case web access is turned on and backgroundProteome is actually resolving protein metadata
int millis = (AllowInternetAccess ? 300 : 60) * 1000;
WaitForCondition(millis, () => !SkylineWindow.Document.Settings.PeptideSettings.BackgroundProteome.NeedsProteinMetadataSearch, "backgroundProteome.NeedsProteinMetadataSearch");
// Pasting FASTA Sequences, p. 5
RunUI(() => SetClipboardFileText(@"MethodEdit\FASTA\fasta.txt")); // Not L10N
// New in v0.7 : Skyline asks about removing empty proteins.
using (new CheckDocumentState(35, 25, 25, 75))
{
var emptyProteinsDlg = ShowDialog <EmptyProteinsDlg>(SkylineWindow.Paste);
RunUI(() => emptyProteinsDlg.IsKeepEmptyProteins = true);
OkDialog(emptyProteinsDlg, emptyProteinsDlg.OkDialog);
WaitForCondition(millis, () => SkylineWindow.SequenceTree.Nodes.Count > 4);
}
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[3].Nodes[0];
});
RestoreViewOnScreen(07);
PauseForScreenShot("Main window", 7); // Not L10N
RunUI(() =>
{
Settings.Default.ShowBIons = true;
SkylineWindow.SequenceTree.SelectedNode.Expand();
SkylineWindow.SequenceTree.SelectedNode =
SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[1];
});
PauseForScreenShot("Main window showing effect of selection on Library Match graph", 8); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 3); // Not L10N
using (new CheckDocumentState(35, 28, 31, 155))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2, 3"; // Not L10N
transitionSettingsUI.ProductCharges = "1"; // Not L10N
transitionSettingsUI.FragmentTypes = "y, b"; // Not L10N
});
WaitForOpenForm <TransitionSettingsUI>(); // To show Filter tab for Forms testing
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9); // Not L10N
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonCount = 5;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 10); // Not L10N
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
PauseForScreenShot("Targets tree clipped from main window", 11); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 5); // Not L10N
// Using a Public Spectral Library, p. 9
peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList);
var addLibUI = ShowDialog <EditLibraryDlg>(editListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(YEAST_GPM, TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\yeast_cmp_20.hlf"))); // Not L10N
OkDialog(addLibUI, addLibUI.OkDialog);
WaitForClosedForm(addLibUI);
OkDialog(editListUI, editListUI.OkDialog);
// Limiting Peptides per Protein, p. 11
using (new CheckDocumentState(35, 182, 219, 1058))
{
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI.PickedLibraries = new[] { YEAST_ATLAS, YEAST_GPM };
});
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 12); // Not L10N
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
Assert.IsTrue(WaitForCondition(
() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
}
using (new CheckDocumentState(35, 47, 47, 223, 2, true)) // Wait for change loaded, and expect 2 document revisions.
{
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUI2 =>
{
peptideSettingsUI2.PickedLibraries = new[] { YEAST_GPM };
peptideSettingsUI2.LimitPeptides = true;
peptideSettingsUI2.RankID = XHunterLibSpec.PEP_RANK_EXPECT;
peptideSettingsUI2.PeptidesPerProtein = 3;
peptideSettingsUI2.OkDialog();
});
}
using (new CheckDocumentState(19, 47, 47, 223))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {
MinPeptidesPerProtein = 1
};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Protein List, p. 11
using (new CheckDocumentState(36, 58, 58, 278))
{
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = node;
SetClipboardFileText(@"MethodEdit\FASTA\Protein list.txt"); // Not L10N
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
PauseForScreenShot <PasteDlg.ProteinListTab>("Insert Protein List - For Screenshot, select last (empty) item in list", 14); // Not L10N
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
}
using (new CheckDocumentState(24, 58, 58, 278))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {
MinPeptidesPerProtein = 1
};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Peptide List, p. 13
using (new CheckDocumentState(25, 70, 70, 338))
{
RunUI(() =>
{
SetClipboardFileText(@"MethodEdit\FASTA\Peptide list.txt"); // Not L10N
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.Paste();
// ReSharper disable LocalizableElement
SkylineWindow.SequenceTree.Nodes[0].Text = "Primary Peptides"; // Not L10N
// ReSharper restore LocalizableElement
});
FindNode("TLTAQSMQNSTQSAPNK"); // Not L10N
PauseForScreenShot("Main window", 16); // Not L10N
}
using (new CheckDocumentState(35, 70, 70, 338))
{
RunUI(() => SkylineWindow.Undo());
PasteDlg pastePeptidesDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pastePeptidesDlg.PastePeptides);
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List - For screenshot, select last (empty) line in list", 17); // Not L10N
OkDialog(pastePeptidesDlg, pastePeptidesDlg.OkDialog);
}
// Simple Refinement, p. 16
var findPeptideDlg = ShowDialog <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() => findPeptideDlg.SearchString = "IPEE"); // Not L10N
OkDialog(findPeptideDlg, () =>
{
findPeptideDlg.FindNext();
findPeptideDlg.Close();
});
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile", 18); // Not L10N
using (new CheckDocumentState(35, 64, 64, 320))
{
RefineDlg refineDlg = ShowDialog <RefineDlg>(SkylineWindow.ShowRefineDlg);
RunUI(() => refineDlg.MinTransitions = 5);
OkDialog(refineDlg, refineDlg.OkDialog);
PauseForScreenShot("29/35 prot 50/64 pep 50/64 prec 246/320 tran", 18); // Not L10N
}
// Checking Peptide Uniqueness, p. 18
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 3 : 2)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
using (new CheckDocumentState(34, 63, 63, 315))
{
var uniquePeptidesDlg = ShowDialog <UniquePeptidesDlg>(SkylineWindow.ShowUniquePeptidesDlg);
WaitForConditionUI(() => uniquePeptidesDlg.GetDataGridView().RowCount == 1);
RunUI(() =>
{
Assert.AreEqual(1, uniquePeptidesDlg.GetDataGridView().RowCount);
Assert.AreEqual(7, uniquePeptidesDlg.GetDataGridView().ColumnCount);
});
PauseForScreenShot <UniquePeptidesDlg>("Unique Peptides form", 19); // Not L10N
OkDialog(uniquePeptidesDlg, uniquePeptidesDlg.OkDialog);
RunUI(() => SkylineWindow.EditDelete());
}
// Protein Name Auto-Completion
PauseForScreenShot("(fig. 1): For screenshot, click at bottom of document tree, type 'ybl087' and see the autocomplete text. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("ybl087", 0); // Not L10N
var peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YBL087C", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Protein Description Auto-Completion
PauseForScreenShot("(fig. 2): For screenshot, click at bottom of document tree, type 'eft2' and see the autocomplete text, then down-arrow twice. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("eft2", 0); // Sorting logic puts this at the 0th entry in the list - Not L10N
peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YDR385W", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Peptide Sequence Auto-Completion, p. 21
TestAutoComplete("IQGP", 0); // Not L10N
var peptides = new List <PeptideDocNode>(Program.ActiveDocument.Peptides);
Assert.AreEqual("K.AYLPVNESFGFTGELR.Q [769, 784]", peptides[peptides.Count - 1].Peptide.ToString()); // Not L10N
PauseForScreenShot("(fig. 1) - For screenshot, click at the bottom of the document tree", 21); // Not L10N
// Pop-up Pick-Lists, p. 21
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 4 : 3)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(8, true);
pickList.AutoManageChildren = false; // TODO: Because calling SetItemChecked does not do this
});
PauseForScreenShot <PopupPickList>("(fig. 2) - YBL087C Peptides picklist", 21); // Not L10N
RunUI(pickList.OnOk);
}
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
SkylineWindow.SequenceTree.Nodes[34].ExpandAll();
var node =
SkylineWindow.SequenceTree.Nodes[34].Nodes[0].Nodes[0];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList1 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.SearchString = "y"; // Not L10N
pickList1.SetItemChecked(0, false);
pickList1.SetItemChecked(1, false);
pickList1.ApplyFilter(false);
pickList1.ToggleFind();
pickList1.SearchString = "b ++"; // Not L10N
pickList1.SetItemChecked(4, true);
pickList1.SetItemChecked(6, true);
});
PauseForScreenShot <PopupPickList>("b ++ filtered picklist", 22); // Not L10N
RunUI(pickList1.OnOk);
}
// Bigger Picture, p. 22. Drag and Drop, p. 23
RunUI(() =>
{
ITipProvider nodeTip = SkylineWindow.SequenceTree.SelectedNode as ITipProvider;
Assert.IsTrue(nodeTip != null && nodeTip.HasTip);
var nodeName = SkylineWindow.SequenceTree.Nodes[1].Name;
IdentityPath selectPath;
SkylineWindow.ModifyDocument("Drag and drop", // Not L10N
doc => doc.MoveNode(SkylineWindow.Document.GetPathTo(0, 1), SkylineWindow.Document.GetPathTo(0, 0), out selectPath));
Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Name == nodeName);
});
FindNode(string.Format("L [b5] - {0:F04}+", 484.3130)); // Not L10N - may be localized " (rank 3)"
PauseForScreenShot("For Screenshots, First hover over YBL087C, then over 672.671+++", 23); // Not L10N
// Preparing to Measure, p. 25
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction), transitionSettingsUI =>
{
transitionSettingsUI.RegressionCE = Settings.Default.GetCollisionEnergyByName("ABI 4000 QTrap"); // Not L10N
transitionSettingsUI.RegressionDP = Settings.Default.GetDeclusterPotentialByName("ABI"); // Not L10N
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument(TestFilesDirs[0].GetTestPath("MethodEdit Tutorial.sky"))); // Not L10N
var exportDialog = ShowDialog <ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportDialog.ExportStrategy = ExportStrategy.Buckets;
exportDialog.MethodType = ExportMethodType.Standard;
exportDialog.OptimizeType = ExportOptimize.NONE;
exportDialog.IgnoreProteins = true;
exportDialog.MaxTransitions = 75;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 25); // Not L10N
const string basename = "Yeast_list"; // Not L10N
OkDialog(exportDialog, () => exportDialog.OkDialog(TestFilesDirs[0].GetTestPath(basename))); // write Yeast_list_000n.csv
// check the output files
for (int n = 0; n++ < 5;)
{
var csvname = String.Format("{0}_{1}.csv", basename, n.ToString("D4")); // Not L10N
// AssertEx.FieldsEqual is hard-coded with CultureInfo.InvariantCulture, but so is transition list CSV export, so OK
using (TextReader actual = new StreamReader(TestFilesDirs[0].GetTestPath(csvname)))
using (TextReader target = new StreamReader(TestFilesDirs[1].GetTestPath(csvname)))
{
AssertEx.FieldsEqual(target, actual, 6, null, true, TestSmallMolecules ? 3 : 0);
}
}
}
private void pickListMulti_MouseMove(object sender, MouseEventArgs e)
{
Point pt = e.Location;
if (!_moveThreshold.Moved(pt))
return;
_moveThreshold.Location = null;
ITipProvider tipProvider = null;
int i = GetIndexAtPoint(pt);
// Make sure it is in the text portion of the item
if (i != -1 && !GetItemTextRectangle(i).Contains(pt))
i = -1;
if (i == -1)
{
_lastTipNode = null;
_lastTipProvider = null;
}
else
{
var nodeDoc = GetVisibleChoice(i).Choice;
if (!ReferenceEquals(nodeDoc, _lastTipNode))
{
_lastTipNode = nodeDoc;
_lastTipProvider = _picker.GetPickTip(nodeDoc);
}
tipProvider = _lastTipProvider;
}
if (tipProvider == null || !tipProvider.HasTip)
_nodeTip.HideTip();
else
_nodeTip.SetTipProvider(tipProvider, GetItemTextRectangle(i), pt);
}
