private SrmDocument DeleteProteins(SrmDocument document, HashSet <IdentityPath> identityPathsToDelete)
{
var newProteins = new List <PeptideGroupDocNode>();
foreach (var protein in document.PeptideGroups)
{
if (identityPathsToDelete.Contains(new IdentityPath(protein.Id)))
{
continue;
}
if (protein.Children.Count != 0)
{
var newProtein = DeletePeptides(protein, identityPathsToDelete);
if (newProtein.Children.Count == 0)
{
continue;
}
newProteins.Add(newProtein);
}
else
{
newProteins.Add(protein);
}
}
return((SrmDocument)document.ChangeChildren(newProteins.Cast <DocNode>().ToArray()));
}
protected SrmDocument DeleteNodes(SrmDocument document, HashSet <IdentityPath> identityPathsToDelete)
{
var newDocument = (SrmDocument)DeleteChildren(document, IdentityPath.ROOT, identityPathsToDelete);
if (newDocument != null)
{
return(newDocument);
}
return((SrmDocument)document.ChangeChildren(new DocNode[0]));
}
private static SrmDocument DeleteNodes(SrmDocument document, HashSet <IdentityPath> identityPathsToDelete, out List <IdentityPath> deletedPaths)
{
var newDocument = (SrmDocument)DeleteChildren(document, IdentityPath.ROOT, identityPathsToDelete, out deletedPaths);
if (newDocument != null)
{
return(newDocument);
}
return((SrmDocument)document.ChangeChildren(new DocNode[0]));
}
private SrmDocument AddSmallMolecules(SrmDocument document)
{
var newChildren = new List <PeptideGroupDocNode>(document.MoleculeGroups);
newChildren.AddRange(new RefinementSettings().ConvertToSmallMolecules(document, TestContext.TestRunDirectory, RefinementSettings.ConvertToSmallMoleculesMode.masses_and_names).MoleculeGroups);
newChildren.AddRange(new RefinementSettings().ConvertToSmallMolecules(document, TestContext.TestRunDirectory, RefinementSettings.ConvertToSmallMoleculesMode.masses_only).MoleculeGroups);
newChildren.AddRange(new RefinementSettings().ConvertToSmallMolecules(document, TestContext.TestRunDirectory).MoleculeGroups); // Do this last for fullest library translation
document = (SrmDocument)document.ChangeChildren(newChildren.ToArray());
return(document);
}
public PeptideDocNode PermuteModificationsOnPeptide(SrmDocument document, PeptideGroupDocNode peptideGroupDocNode,
PeptideDocNode peptideDocNode, List <IsotopeLabelType> partialLabelTypes)
{
if (SkipPeptide(peptideDocNode))
{
return(peptideDocNode);
}
var potentiallyModifiedResidues = PotentiallyModifiedResidues(peptideDocNode, IsotopeModification);
if (potentiallyModifiedResidues.Count == 0)
{
return(peptideDocNode);
}
// Create a document containing only one peptide so that "ChangePeptideMods" does not have to walk
// over a long list of peptides to see which modifications are in use.
var smallDocument = (SrmDocument)document.ChangeChildren(new DocNode[]
{ peptideGroupDocNode.ChangeChildren(new DocNode[] { peptideDocNode }) });
var newTypedExplicitModifications = PermuteTypedExplicitModifications(partialLabelTypes, peptideDocNode, potentiallyModifiedResidues);
var newExplicitMods = new ExplicitMods(peptideDocNode.Peptide, peptideDocNode.ExplicitMods?.StaticModifications, newTypedExplicitModifications);
var identityPath = new IdentityPath(peptideGroupDocNode.PeptideGroup, peptideDocNode.Peptide);
smallDocument = smallDocument.ChangePeptideMods(identityPath, newExplicitMods, false, GlobalStaticMods,
GlobalIsotopeMods);
peptideDocNode = (PeptideDocNode)smallDocument.FindPeptideGroup(peptideGroupDocNode.PeptideGroup).FindNode(peptideDocNode.Peptide);
var lightChargeStates = peptideDocNode.TransitionGroups.Where(tg => tg.IsLight).Select(tg => tg.PrecursorCharge).Distinct().ToList();
var chargeStatesByLabel =
peptideDocNode.TransitionGroups.ToLookup(tg => tg.LabelType, tg => tg.PrecursorCharge);
var transitionGroupsToAdd = new List <TransitionGroupDocNode>();
foreach (var typedExplicitModifications in newExplicitMods.GetHeavyModifications())
{
var labelType = typedExplicitModifications.LabelType;
foreach (var chargeState in lightChargeStates.Except(chargeStatesByLabel[labelType]))
{
var tranGroup = new TransitionGroup(peptideDocNode.Peptide, Adduct.FromChargeProtonated(chargeState), labelType);
TransitionDocNode[] transitions = peptideDocNode.GetMatchingTransitions(tranGroup, smallDocument.Settings, newExplicitMods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(smallDocument.Settings, peptideDocNode, newExplicitMods, SrmSettingsDiff.ALL);
transitionGroupsToAdd.Add(nodeGroup);
}
}
if (transitionGroupsToAdd.Any())
{
var newChildren = peptideDocNode.TransitionGroups.Concat(transitionGroupsToAdd).ToList();
newChildren.Sort(Peptide.CompareGroups);
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren.Cast <DocNode>().ToList());
}
return(peptideDocNode);
}
public SrmDocument UpdateDocument(SrmDocument document)
{
if (document.Settings.HasResults && _annotationUpdaters.ContainsKey(AnnotationDef.AnnotationTarget.replicate))
{
var newMeasuredResults = UpdateReplicateAnnotations(document.MeasuredResults);
document = document.ChangeMeasuredResults(newMeasuredResults);
}
var newChildren = document.MoleculeGroups.Select(UpdateMoleculeGroup).ToArray();
document = (SrmDocument)document.ChangeChildren(newChildren);
return(document);
}
public void ThermoMixedPeptidesTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument docMixed = InitMixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
SrmDocument docUnmixed = InitUnmixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
new ChromatogramSet("rep05", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_05" + extRaw))
})
};
var docResults = docMixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerMixed = new ResultsTestDocumentContainer(docMixed, docPath);
Assert.IsTrue(docContainerMixed.SetDocument(docResults, docMixed, true));
docContainerMixed.AssertComplete();
docMixed = docContainerMixed.Document;
SrmDocument docMixedUnmixed = (SrmDocument)docMixed.ChangeChildren(new DocNode[0]);
IdentityPath tempPath;
docMixedUnmixed = docMixedUnmixed.AddPeptideGroups(docUnmixed.PeptideGroups, true, IdentityPath.ROOT,
out tempPath, out tempPath);
docResults = docUnmixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerUnmixed = new ResultsTestDocumentContainer(docUnmixed, docPath);
Assert.IsTrue(docContainerUnmixed.SetDocument(docResults, docUnmixed, true));
docContainerUnmixed.AssertComplete();
docUnmixed = docContainerUnmixed.Document;
AssertEx.DocumentCloned(docMixedUnmixed, docUnmixed);
docContainerMixed.Release();
docContainerUnmixed.Release();
}
public void TestSerializePeptides()
{
var srmDocument = new SrmDocument(SrmSettingsList.GetDefault());
string strProteinSequence = string.Join(string.Empty,
"MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVL",
"ASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLEN",
"LRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLP",
"QRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAF",
"TFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT",
"DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKS",
"SAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK");
var fastaSequence = new FastaSequence("YCR012W", "PGK1", null, strProteinSequence);
var peptideGroup = new PeptideGroupDocNode(fastaSequence, fastaSequence.Name, fastaSequence.Description, new PeptideDocNode[0]);
Assert.AreEqual(true, peptideGroup.AutoManageChildren);
peptideGroup = peptideGroup.ChangeSettings(srmDocument.Settings, SrmSettingsDiff.ALL);
srmDocument = (SrmDocument)srmDocument.ChangeChildren(new DocNode[] { peptideGroup });
Assert.AreNotEqual(0, srmDocument.PeptideCount);
Assert.AreNotEqual(0, srmDocument.MoleculeTransitionCount);
Assert.IsFalse(CompactFormatOption.NEVER.UseCompactFormat(srmDocument));
Assert.IsTrue(CompactFormatOption.ALWAYS.UseCompactFormat(srmDocument));
VerifyRoundTrips(srmDocument);
VerifyRoundTrips(AddSmallMolecules(srmDocument));
}
private SrmDocument ReplaceTransitionGroups(
SrmDocument document, Func <TransitionGroupDocNode, TransitionGroupDocNode> transitionGroupTransformFunc)
{
var newMoleculeGroups = new List <PeptideGroupDocNode>();
foreach (var moleculeGroup in document.MoleculeGroups)
{
var newMolecules = new List <PeptideDocNode>();
foreach (var molecule in moleculeGroup.Molecules)
{
var newTransitionGroups = new List <TransitionGroupDocNode>();
foreach (var transitionGroup in molecule.TransitionGroups)
{
var newTransitionGroup = transitionGroupTransformFunc(transitionGroup);
newTransitionGroups.Add(newTransitionGroup);
}
var newMolecule = (PeptideDocNode)molecule.ChangeChildren(
newTransitionGroups.ToArray());
newMolecules.Add(newMolecule);
}
newMoleculeGroups.Add((PeptideGroupDocNode)moleculeGroup.ChangeChildren(newMolecules.ToArray()));
}
return((SrmDocument)document.ChangeChildren(newMoleculeGroups.ToArray()));
}
protected override void DoTest()
{
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-1_Settings.pdf";
//Tutorial 1
string fastaFile = GetTestPath("Tutorial-1_Settings/TubercuList_v2-6.fasta.txt");
WaitForCondition(() => File.Exists(fastaFile));
var pepSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
SkylineWindow.Size = new Size(1600, 800);
pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest;
pepSettings.ComboEnzymeSelected = "Trypsin [KR | P]";
pepSettings.MaxMissedCleavages = 0;
});
var backProteomeDlg = ShowDialog <BuildBackgroundProteomeDlg>(pepSettings.AddBackgroundProteome);
RunUI(() =>
{
backProteomeDlg.BackgroundProteomePath = GetTestPath("Skyline");
backProteomeDlg.BackgroundProteomeName = "TubercuList_v2-6";
backProteomeDlg.AddFastaFile(fastaFile);
WaitForCondition(() => backProteomeDlg.StatusText.Length > 10);
Assert.IsTrue(backProteomeDlg.StatusText.Contains("3982".ToString(CultureInfo.CurrentCulture)));
});
OkDialog(backProteomeDlg, backProteomeDlg.OkDialog);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction);
RunUI(() =>
{
pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter;
pepSettings.TextMinLength = 7;
pepSettings.TextMaxLength = 25;
pepSettings.TextExcludeAAs = 0;
pepSettings.AutoSelectMatchingPeptides = true;
});
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library);
var editListDlg =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(pepSettings.EditLibraryList);
var editLibraryDlg = ShowDialog <EditLibraryDlg>(editListDlg.AddItem);
RunUI(() =>
{
editLibraryDlg.LibraryName = "Mtb_proteome_library";
editLibraryDlg.LibraryPath = GetTestPath("Skyline\\Mtb_DirtyPeptides_QT_filtered_cons.sptxt");
});
OkDialog(editLibraryDlg, editLibraryDlg.OkDialog);
OkDialog(editListDlg, editListDlg.OkDialog);
RunUI(() => pepSettings.SetLibraryChecked(0, true));
RunUI(() => { pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications; });
var editHeavyModListDlg =
ShowDialog <EditListDlg <SettingsListBase <StaticMod>, StaticMod> >(pepSettings.EditHeavyMods);
var addDlgOne = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem);
RunUI(() => addDlgOne.SetModification("Label:13C(6)15N(2) (C-term K)"));
PauseForScreenShot("Isotope modification 1", 3);
OkDialog(addDlgOne, addDlgOne.OkDialog);
var addDlgTwo = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem);
RunUI(() => addDlgTwo.SetModification("Label:13C(6)15N(4) (C-term R)"));
PauseForScreenShot("Isotope modification 2", 3);
OkDialog(addDlgTwo, addDlgTwo.OkDialog);
OkDialog(editHeavyModListDlg, editHeavyModListDlg.OkDialog);
RunUI(() =>
{
pepSettings.SetIsotopeModifications(0, true);
pepSettings.SetIsotopeModifications(1, true);
});
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest);
PauseForScreenShot("Digestion tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction);
PauseForScreenShot("Prediction tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter);
PauseForScreenShot("Filter tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library);
PauseForScreenShot("Library tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot("Modifications tab", 4);
OkDialog(pepSettings, pepSettings.OkDialog);
WaitForCondition(
() => SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('{').First()) &&
SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('}').Last()));
WaitForCondition(
() => SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('{').First()) &&
SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('}').Last()));
WaitForCondition(() => SkylineWindow.Status.Contains(Resources.SkylineWindow_UpdateProgressUI_Ready));
WaitForDocumentLoaded();
var transitionDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionDlg.PrecursorMassType = MassType.Monoisotopic;
transitionDlg.FragmentMassType = MassType.Monoisotopic;
transitionDlg.RegressionCEName = "ABI 5500 QTrap";
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionDlg.PrecursorCharges = "2,3".ToString(CultureInfo.CurrentCulture);
transitionDlg.ProductCharges = "1,2".ToString(CultureInfo.CurrentCulture);
transitionDlg.FragmentTypes = "y";
transitionDlg.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_1;
transitionDlg.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion;
transitionDlg.SetListAlwaysAdd(0, false);
transitionDlg.ExclusionWindow = 5;
transitionDlg.SetAutoSelect = true;
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionDlg.IonMatchTolerance = 1.0;
transitionDlg.UseLibraryPick = true;
transitionDlg.IonCount = 5;
transitionDlg.Filtered = true;
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionDlg.MinMz = 300;
transitionDlg.MaxMz = 1250;
});
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction);
PauseForScreenShot("Prediction Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter);
PauseForScreenShot("Filter Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library);
PauseForScreenShot("Library Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument);
PauseForScreenShot("Instrument Tab", 7);
OkDialog(transitionDlg, transitionDlg.OkDialog);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Tutorial-1_Settings\\SRMcourse_20140210_Settings.sky")));
//Tutorial 2
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-2_TransitionList.pdf";
RunUI(() => { });
SetExcelFileClipboardText(GetTestPath(@"Tutorial-2_TransitionList\\target_peptides.xlsx"), "Sheet1", 1,
false);
var peptidePasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
var matchingDlg = ShowDialog <FilterMatchedPeptidesDlg>(peptidePasteDlg.PastePeptides);
PauseForScreenShot("Filter Peptides", 1);
OkDialog(matchingDlg, matchingDlg.OkDialog);
OkDialog(peptidePasteDlg, peptidePasteDlg.OkDialog);
int expectedTrans = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 306 : 313;
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 68, expectedTrans);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
});
PauseForScreenShot("Skyline Window", 2);
var exportDlg = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg.InstrumentType = "AB SCIEX";
exportDlg.ExportStrategy = ExportStrategy.Single;
exportDlg.DwellTime = 20;
});
PauseForScreenShot("Export Transition List", 3);
var declusteringWarningDlg = ShowDialog <MultiButtonMsgDlg>(
() => exportDlg.OkDialog(GetTestPath("Tutorial-2_TransitionList\\SRMcourse_20140210_MtbProteomeLib_TransList.csv")));
PauseForScreenShot("Decluster Window", 3);
OkDialog(declusteringWarningDlg, declusteringWarningDlg.Btn1Click);
WaitForClosedForm(exportDlg);
//Tutorial 3
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-3_Library.pdf";
var pepSettings2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => pepSettings2.SelectedTab = PeptideSettingsUI.TABS.Library);
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(pepSettings2.ShowBuildLibraryDlg);
RunUI(() =>
{
buildLibraryDlg.LibraryPath = GetTestPath("Skyline");
buildLibraryDlg.LibraryName = "Mtb_hDP_20140210";
buildLibraryDlg.LibraryCutoff = 0.9;
buildLibraryDlg.LibraryAuthority = "SRMcourse";
});
PauseForScreenShot("Build Library Window", 2);
RunUI(() =>
{
buildLibraryDlg.OkWizardPage();
buildLibraryDlg.AddDirectory(GetTestPath("Tutorial-3_Library"));
});
PauseForScreenShot("Build Library Window Next", 2);
OkDialog(buildLibraryDlg, buildLibraryDlg.OkWizardPage);
RunUI(() =>
{
pepSettings2.SetLibraryChecked(0, true);
pepSettings2.SetLibraryChecked(1, true);
});
OkDialog(pepSettings2, pepSettings2.OkDialog);
WaitForLibrary(20213);
WaitForCondition(() => SkylineWindow.Document.PeptideTransitionCount != expectedTrans);
int expectedTransAfter = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 444 : 450;
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 96, expectedTransAfter);
var libraryExpl = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
var messageWarning = WaitForOpenForm <MultiButtonMsgDlg>();
OkDialog(messageWarning, messageWarning.Btn1Click);
PauseForScreenShot("Spectral Library Explorer Window", 3);
OkDialog(libraryExpl, libraryExpl.Close);
var exportDlg2 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg2.InstrumentType = "AB SCIEX";
exportDlg2.ExportStrategy = ExportStrategy.Buckets;
exportDlg2.MaxTransitions = 150;
exportDlg2.DwellTime = 20;
exportDlg2.IgnoreProteins = true;
});
var declusteringWarningDlg2 = ShowDialog <MultiButtonMsgDlg>(() =>
exportDlg2.OkDialog(GetTestPath("Tutorial-3_Library\\SRMcourse_20140210_MtbProteomeLib_hDP_TransList.csv")));
OkDialog(declusteringWarningDlg2, declusteringWarningDlg2.Btn1Click);
WaitForClosedForm(exportDlg2);
//Tutorial 4-A
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-4_Parameters.pdf";
SrmDocument smallDocument = SkylineWindow.Document;
PeptideGroupDocNode[] newProteins = smallDocument.PeptideGroups.Take(0).ToArray();
smallDocument = (SrmDocument)smallDocument.ChangeChildren(newProteins);
Assert.IsTrue(SkylineWindow.SetDocument(smallDocument, SkylineWindow.Document)); // TODO: Must be a better way to do this
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettings.RegressionCEName = "ABI QTrap 4000";
});
var editCollisionEnergy = ShowDialog <EditCEDlg>(() =>
transitionSettings.RegressionCEName = Resources.SettingsListComboDriver_Edit_current);
RunUI(() =>
{
editCollisionEnergy.StepSize = 2;
editCollisionEnergy.StepCount = 5;
});
PauseForScreenShot("Edit Collision Energy Equation Window", 2);
OkDialog(editCollisionEnergy, editCollisionEnergy.OkDialog);
OkDialog(transitionSettings, transitionSettings.OkDialog);
SetExcelFileClipboardText(GetTestPath("Tutorial-4_Parameters\\transition_list_for_CEO.xlsx"), "Sheet1", 3,
false);
var insertTransitionDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() => insertTransitionDlg.IsMolecule = false); // Make sure it's ready to accept peptides, not small molecules
RunUI(insertTransitionDlg.PasteTransitions);
OkDialog(insertTransitionDlg, insertTransitionDlg.OkDialog);
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 30, 143);
var exportDlg3 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg3.InstrumentType = "AB SCIEX";
exportDlg3.ExportStrategy = ExportStrategy.Single;
exportDlg3.OptimizeType = ExportOptimize.CE;
exportDlg3.MethodType = ExportMethodType.Standard;
exportDlg2.DwellTime = 20;
});
PauseForScreenShot("Export Transition List", 3);
var defaultWaringDlg = ShowDialog <MultiButtonMsgDlg>(
() => exportDlg3.OkDialog(GetTestPath("Tutorial-4_Parameters\\SRMcourse_20140211_Parameters_CEO.csv")));
OkDialog(defaultWaringDlg, defaultWaringDlg.Btn1Click);
WaitForClosedForm(exportDlg3);
var paths = new string[4];
for (int i = 0; i < paths.Length; i++)
{
paths[i] = GetTestPath("Tutorial-4_Parameters\\CEO_" + (i + 1) + ".wiff");
}
ImportResults("CEO", paths, ExportOptimize.CE);
RestoreViewOnScreen(43);
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Skyline Window", 3);
ImportResults("", new[]
{
GetTestPath("Tutorial-4_Parameters\\CE_plus10.wiff"),
GetTestPath("Tutorial-4_Parameters\\CE_minus10.wiff")
}, ExportOptimize.NONE, false);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_maximum_view);
});
RestoreViewOnScreen(44);
PauseForScreenShot("Skyline Window", 4);
var transitionSettings2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => { transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Prediction; });
var addCollisionEnergyDlg = ShowDialog <EditCEDlg>(transitionSettings2.AddToCEList);
RunUI(() =>
{
addCollisionEnergyDlg.UseCurrentData();
addCollisionEnergyDlg.RegressionName = "SRMcourse_20140211_Parameters_custom-CE-equation";
});
var equationGraphDlg = ShowDialog <GraphRegression>(addCollisionEnergyDlg.ShowGraph);
PauseForScreenShot("Collision Energy Equation Graph", 6);
OkDialog(equationGraphDlg, equationGraphDlg.CloseDialog);
OkDialog(addCollisionEnergyDlg, addCollisionEnergyDlg.OkDialog);
RunUI(() =>
{
transitionSettings2.RegressionCEName = "SRMcourse_20140211_Parameters_custom-CE-equation";
transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings2.MZMatchTolerance = 0.01;
});
PauseForScreenShot("Instrument Tab", 7);
OkDialog(transitionSettings2, transitionSettings2.OkDialog);
//Tutorial 4-B
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RunUI(manageResultsDlg.RemoveAllReplicates);
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
string[] paths2 =
{
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 10)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 20)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 40)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 60)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 100))
};
ImportResults("", paths2, null, false);
RestoreViewOnScreen(48);
RunUI(() => SkylineWindow.AutoZoomBestPeak());
PauseForScreenShot("Skyline Window", 8);
}
public void TestPaste()
{
ClearDefaultModifications();
_yeastDoc = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMaxMz(1600)));
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new MeasuredIon[0])));
IdentityPath path;
_yeastDocReadOnly = _yeastDoc = _yeastDoc.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB),
false, IdentityPath.ROOT, out path);
_study7DocReadOnly = _study7Doc = CreateStudy7Doc();
IdentityPath pathRoot = IdentityPath.ROOT;
// Test pasting into document with same implicit modifications does not create any extra explicit modifications.
var study7EmptyDoc = (SrmDocument) _study7Doc.ChangeChildren(new DocNode[0]);
var study7PasteDoc = CopyPaste(_study7Doc, null, study7EmptyDoc, pathRoot);
var arrayPeptides = _study7Doc.Peptides.ToArray();
var arrayPastePeptides = study7PasteDoc.Peptides.ToArray();
Assert.AreEqual(arrayPeptides.Length, arrayPastePeptides.Length);
AssertEx.DocsEqual(_study7Doc, study7PasteDoc); // DocsEqual gives a more verbose failure message using XML output
// Test implicit mods in source document become explicit mods in target document.
ResetDocuments();
_yeastDoc = (SrmDocument) _yeastDoc.ChangeChildren(new DocNode[0]);
var settings = _yeastDoc.Settings;
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0])));
_yeastDoc = CopyPaste(_study7Doc, null, _yeastDoc, pathRoot);
var pepMods = _yeastDoc.Settings.PeptideSettings.Modifications;
Assert.IsTrue(pepMods.StaticModifications != null);
Assert.IsTrue(pepMods.HasHeavyModifications);
Assert.IsFalse(pepMods.StaticModifications.Contains(mod => !mod.IsExplicit));
Assert.IsFalse(pepMods.HeavyModifications.Contains(mod => !mod.IsExplicit));
// Test explicit mods are dropped if the target document has matching implicit modifications.
study7PasteDoc = CopyPaste(_yeastDoc, null, study7EmptyDoc, pathRoot);
Assert.AreEqual(_study7Doc, study7PasteDoc);
// Add new label type to source document.
ResetDocuments();
const string labelTypeName13C = "heavy 13C";
var labelType13C = new IsotopeLabelType(labelTypeName13C, IsotopeLabelType.light.SortOrder + 1);
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] {new TypedModifications(labelType13C, HEAVY_MODS_13_C)});
Assert.IsTrue(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
Equals(nodeGroup.TransitionGroup.LabelType, labelType13C)));
// Test pasting into the same document with new label type.
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
// Check all transition have correct label type references.
Assert.IsFalse(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
{
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
return !ReferenceEquals(labelType,
_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelType.Name).LabelType);
}));
// Check new document still serializes correctly.
AssertEx.Serializable(_yeastDoc, AssertEx.DocumentCloned);
// Test pasting into new document drops label types from source document that are not found in the target document.
_yeastDoc = CopyPaste(_yeastDoc, null, new SrmDocument(SrmSettingsList.GetDefault()), pathRoot);
Assert.IsNull(_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelTypeName13C));
// If only specific children are selected, test that only these children get copied.
ResetDocuments();
var arrayTrans = _study7Doc.PeptideTransitions.ToArray();
IList<DocNode> selNodes = new List<DocNode>();
for (int i = 0; i < arrayTrans.Length; i += 2)
{
selNodes.Add(arrayTrans[i]);
}
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
Assert.AreEqual(arrayTrans.Length + selNodes.Count, _study7Doc.PeptideTransitionCount);
// Test after pasting to a peptide list, all children have been updated to point to the correct parent.
ResetDocuments();
_study7Doc = CopyPaste(_yeastDoc, new[] { _yeastDoc.Peptides.ToArray()[0] }, _study7Doc,
_study7Doc.GetPathTo((int) SrmDocument.Level.MoleculeGroups, 0));
Assert.AreEqual(_yeastDoc.Peptides.ToArray()[0].Peptide, _study7Doc.Peptides.ToArray()[0].Peptide);
Assert.AreEqual(_study7Doc.Peptides.ToArray()[0].Peptide,
_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup.Peptide);
Assert.AreEqual(_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup,
_study7Doc.PeptideTransitions.ToArray()[0].Transition.Group);
// If only specific transition are selected for a peptide, but all transition groups are included, test AutoManageChildren is true.
ResetDocuments();
selNodes = new List<DocNode>();
foreach (TransitionGroupDocNode transGroup in _study7Doc.PeptideTransitionGroups)
{
selNodes.Add(transGroup.Children[0]);
}
// TODO: Fix this and make it pass
// var emptyDoc = (SrmDocument)_study7Doc.ChangeChildren(new List<DocNode>());
// _study7Doc = CopyPaste(_study7Doc, selNodes, emptyDoc, pathRoot);
_study7Doc = (SrmDocument)_study7Doc.ChangeChildren(new List<DocNode>());
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
foreach (PeptideDocNode peptide in _study7Doc.Peptides)
Assert.IsTrue(peptide.AutoManageChildren);
// Test pasting in modifications with the same name as but different definition from existing modifications not allowed.
ResetDocuments();
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] { new TypedModifications(IsotopeLabelType.heavy, HEAVY_C_K_DIFDEF) });
SetDefaultModifications(_study7Doc);
AssertEx.ThrowsException<Exception>(() => _yeastDoc.Settings.UpdateDefaultModifications(false));
// Test variable modifications kept if target document has matching variable modifications turned on.
ResetDocuments();
settings = _yeastDoc.Settings;
var modsDefault = settings.PeptideSettings.Modifications;
var listVariableMods = new List<StaticMod>(modsDefault.StaticModifications) { VAR_MET_OXIDIZED };
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listVariableMods.ToArray())));
// Make sure there is an implicitly modified peptide in the yeast document
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.Peptide.Sequence.Contains("C")));
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods && !nodePep.HasVariableMods));
// Otherwise the variable modifications become only explicit modifications.
var yeastDocVar = _yeastDoc;
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangePeptideModifications(mods => modsDefault));
_yeastDoc = CopyPaste(yeastDocVar, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Settings.PeptideSettings.Modifications.HasVariableModifications);
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods));
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
}
public SrmDocument AddAnnotationTestValues(SrmDocument document)
{
_counter = 0;
_elementCount = 0;
document = document.ChangeSettings(document.Settings.ChangeDataSettings(
document.Settings.DataSettings.ChangeAnnotationDefs(ImmutableList.ValueOf(GetTestAnnotations()))));
var measuredResults = document.MeasuredResults;
if (measuredResults != null)
{
var chromatograms = measuredResults.Chromatograms.ToArray();
for (int i = 0; i < chromatograms.Length; i++)
{
_elementCount++;
chromatograms[i] = chromatograms[i].ChangeAnnotations(
AddAnnotations(chromatograms[i].Annotations, AnnotationDef.AnnotationTarget.replicate));
}
document = document.ChangeMeasuredResults(measuredResults.ChangeChromatograms(chromatograms));
}
var proteins = document.MoleculeGroups.ToArray();
for (int iProtein = 0; iProtein < proteins.Length; iProtein++)
{
var protein = proteins[iProtein];
_elementCount++;
protein = (PeptideGroupDocNode)protein.ChangeAnnotations(AddAnnotations(protein.Annotations,
AnnotationDef.AnnotationTarget.protein));
var peptides = protein.Molecules.ToArray();
for (int iPeptide = 0; iPeptide < peptides.Length; iPeptide++)
{
var peptide = peptides[iPeptide];
_elementCount++;
peptide = (PeptideDocNode)peptide.ChangeAnnotations(AddAnnotations(peptide.Annotations,
AnnotationDef.AnnotationTarget.peptide));
var precursors = peptide.TransitionGroups.ToArray();
for (int iPrecursor = 0; iPrecursor < precursors.Length; iPrecursor++)
{
var precursor = precursors[iPrecursor];
precursor = (TransitionGroupDocNode)precursor.ChangeAnnotations(
AddAnnotations(precursor.Annotations,
AnnotationDef.AnnotationTarget.precursor));
_elementCount++;
var transitions = precursor.Transitions.ToArray();
for (int iTransition = 0; iTransition < transitions.Length; iTransition++)
{
var transition = transitions[iTransition];
_elementCount++;
transition = (TransitionDocNode)transition.ChangeAnnotations(
AddAnnotations(transition.Annotations,
AnnotationDef.AnnotationTarget.transition));
if (transition.Results != null)
{
var results = transition.Results.ToArray();
for (int replicateIndex = 0; replicateIndex < results.Length; replicateIndex++)
{
_elementCount += results[replicateIndex].Count;
results[replicateIndex] = new ChromInfoList <TransitionChromInfo>(
results[replicateIndex]
.Select(chromInfo => chromInfo.ChangeAnnotations(AddAnnotations(
chromInfo.Annotations,
AnnotationDef.AnnotationTarget.transition_result))));
}
transition = transition.ChangeResults(new Results <TransitionChromInfo>(results));
}
transitions[iTransition] = transition;
}
if (precursor.Results != null)
{
var results = precursor.Results.ToArray();
for (int replicateIndex = 0; replicateIndex < results.Length; replicateIndex++)
{
_elementCount += results[replicateIndex].Count;
results[replicateIndex] = new ChromInfoList <TransitionGroupChromInfo>(
results[replicateIndex].Select(chromInfo =>
chromInfo.ChangeAnnotations(AddAnnotations(chromInfo.Annotations,
AnnotationDef.AnnotationTarget.precursor_result))));
}
precursor = precursor.ChangeResults(new Results <TransitionGroupChromInfo>(results));
}
precursor = (TransitionGroupDocNode)precursor.ChangeChildren(transitions);
precursors[iPrecursor] = precursor;
}
peptide = (PeptideDocNode)peptide.ChangeChildren(precursors);
peptides[iPeptide] = peptide;
}
protein = (PeptideGroupDocNode)protein.ChangeChildren(peptides);
proteins[iProtein] = protein;
}
return((SrmDocument)document.ChangeChildren(proteins));
}
public SrmDocument PermuteIsotopeModifications(IProgressMonitor progressMonitor, SrmDocument document)
{
var progressStatus = new ProgressStatus(Resources.IsotopeModificationPermuter_PermuteIsotopeModifications_Permuting_isotope_modifications);
progressMonitor.UpdateProgress(progressStatus.ChangePercentComplete(0));
int maxPermutationCount = 0;
foreach (var peptide in document.Peptides)
{
if (SkipPeptide(peptide))
{
continue;
}
int residueCount = PotentiallyModifiedResidues(peptide, IsotopeModification).Count;
int permutationCount = SimplePermutation ? residueCount + 1 : 1 << residueCount;
maxPermutationCount = Math.Max(permutationCount, maxPermutationCount);
}
var partialLabelTypes = new List <IsotopeLabelType>(maxPermutationCount);
document = EnsureLabelTypes(progressMonitor, document, maxPermutationCount, partialLabelTypes);
int totalPeptideCount = document.PeptideCount;
int processedPeptideCount = 0;
var newMoleculeGroups = new List <PeptideGroupDocNode>();
foreach (var peptideGroup in document.MoleculeGroups)
{
if (!peptideGroup.IsProteomic)
{
newMoleculeGroups.Add(peptideGroup);
continue;
}
var newPeptides = new List <PeptideDocNode>();
foreach (var peptideDocNode in peptideGroup.Peptides)
{
if (progressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
progressMonitor.UpdateProgress(
progressStatus.ChangePercentComplete(100 * processedPeptideCount++ / totalPeptideCount));
var newPeptide = PermuteModificationsOnPeptide(document, peptideGroup, peptideDocNode, partialLabelTypes);
newPeptides.Add(newPeptide);
}
var newChildren = ImmutableList.ValueOf(newPeptides.Cast <DocNode>());
if (ArrayUtil.ReferencesEqual(newChildren, peptideGroup.Children))
{
newMoleculeGroups.Add(peptideGroup);
}
else
{
newMoleculeGroups.Add((PeptideGroupDocNode)peptideGroup.ChangeChildren(newChildren));
}
}
document = (SrmDocument)document.ChangeChildren(ImmutableList.ValueOf(newMoleculeGroups.Cast <DocNode>()));
var pepModsNew = document.Settings.PeptideSettings.Modifications;
pepModsNew = pepModsNew.DeclareExplicitMods(document, GlobalStaticMods, GlobalIsotopeMods);
if (!Equals(pepModsNew, document.Settings.PeptideSettings.Modifications))
{
var newSettings = document.Settings.ChangePeptideModifications(m => pepModsNew);
document = document.ChangeSettings(newSettings);
}
return(document);
}
public string GenerateDocumentXml(SrmDocument doc, string oldXml)
{
if (doc == null)
{
return(null);
}
// Minimize document to only the peptides we need
var minimalPeptides = StandardPeptides.ToHashSet();
var oldPeptides = new Dictionary <Target, PeptideDocNode>();
if (!string.IsNullOrEmpty(oldXml))
{
try
{
using (var reader = new StringReader(oldXml))
{
var oldDoc = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(reader);
oldPeptides = oldDoc.Molecules.Where(pep => minimalPeptides.Contains(pep.Target)).ToDictionary(pep => pep.Target, pep => pep);
}
}
catch
{
// ignored
}
}
var addPeptides = new List <PeptideDocNode>();
foreach (var nodePep in doc.Molecules.Where(pep => minimalPeptides.Contains(pep.Target)))
{
if (oldPeptides.TryGetValue(nodePep.Target, out var nodePepOld))
{
addPeptides.Add(nodePep.Merge(nodePepOld));
oldPeptides.Remove(nodePep.Target);
}
else
{
addPeptides.Add(nodePep);
}
}
addPeptides.AddRange(oldPeptides.Values);
var peptides = new List <PeptideDocNode>();
foreach (var nodePep in addPeptides)
{
var precursors = new List <DocNode>();
foreach (TransitionGroupDocNode nodeTranGroup in nodePep.Children)
{
var transitions = nodeTranGroup.Transitions.Where(tran => tran.ResultsRank.HasValue).OrderBy(tran => tran.ResultsRank.Value).Cast <DocNode>().ToList();
if (transitions.Count > 0)
{
precursors.Add(nodeTranGroup.ChangeChildren(transitions));
}
}
if (precursors.Count > 0)
{
peptides.Add((PeptideDocNode)nodePep.ChangeChildren(precursors));
}
}
if (peptides.Count == 0)
{
return(null);
}
peptides.Sort((nodePep1, nodePep2) => nodePep1.ModifiedTarget.CompareTo(nodePep2.ModifiedTarget));
doc = (SrmDocument)doc.ChangeChildren(new[] { new PeptideGroupDocNode(new PeptideGroup(), Resources.IrtDb_MakeDocumentXml_iRT_standards, string.Empty, peptides.ToArray()) });
// Clear some settings to make the document smaller and so that they won't get imported into a document
// TODO: Convert all modifications to explicit?
doc = doc.ChangeMeasuredResults(null);
doc = doc.ChangeSettings(doc.Settings.ChangePeptideLibraries(libs => libs.ChangeLibraries(new List <LibrarySpec>(), new List <Library>())));
using (var writer = new StringWriter())
using (var writer2 = new XmlTextWriter(writer))
{
doc.Serialize(writer2, null, SkylineVersion.CURRENT, null);
return(writer.ToString());
}
}
public void TestPaste()
{
ClearDefaultModifications();
_yeastDoc = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMaxMz(1600)));
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new MeasuredIon[0])));
IdentityPath path;
_yeastDocReadOnly = _yeastDoc = _yeastDoc.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB),
false, IdentityPath.ROOT, out path);
_study7DocReadOnly = _study7Doc = CreateStudy7Doc();
IdentityPath pathRoot = IdentityPath.ROOT;
// Test pasting into document with same implicit modifications does not create any extra explicit modifications.
var study7EmptyDoc = (SrmDocument)_study7Doc.ChangeChildren(new DocNode[0]);
var study7PasteDoc = CopyPaste(_study7Doc, null, study7EmptyDoc, pathRoot);
var arrayPeptides = _study7Doc.Peptides.ToArray();
var arrayPastePeptides = study7PasteDoc.Peptides.ToArray();
Assert.AreEqual(arrayPeptides.Length, arrayPastePeptides.Length);
AssertEx.DocsEqual(_study7Doc, study7PasteDoc); // DocsEqual gives a more verbose failure message using XML output
// Test implicit mods in source document become explicit mods in target document.
ResetDocuments();
_yeastDoc = (SrmDocument)_yeastDoc.ChangeChildren(new DocNode[0]);
var settings = _yeastDoc.Settings;
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0])));
_yeastDoc = CopyPaste(_study7Doc, null, _yeastDoc, pathRoot);
var pepMods = _yeastDoc.Settings.PeptideSettings.Modifications;
Assert.IsTrue(pepMods.StaticModifications != null);
Assert.IsTrue(pepMods.HasHeavyModifications);
Assert.IsFalse(pepMods.StaticModifications.Contains(mod => !mod.IsExplicit));
Assert.IsFalse(pepMods.HeavyModifications.Contains(mod => !mod.IsExplicit));
// Test explicit mods are dropped if the target document has matching implicit modifications.
study7PasteDoc = CopyPaste(_yeastDoc, null, study7EmptyDoc, pathRoot);
Assert.AreEqual(_study7Doc, study7PasteDoc);
// Add new label type to source document.
ResetDocuments();
const string labelTypeName13C = "heavy 13C";
var labelType13C = new IsotopeLabelType(labelTypeName13C, IsotopeLabelType.light.SortOrder + 1);
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] { new TypedModifications(labelType13C, HEAVY_MODS_13_C) });
Assert.IsTrue(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
Equals(nodeGroup.TransitionGroup.LabelType, labelType13C)));
// Test pasting into the same document with new label type.
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
// Check all transition have correct label type references.
Assert.IsFalse(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
{
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
return(!ReferenceEquals(labelType,
_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelType.Name).LabelType));
}));
// Check new document still serializes correctly.
AssertEx.Serializable(_yeastDoc, AssertEx.DocumentCloned);
// Test pasting into new document drops label types from source document that are not found in the target document.
_yeastDoc = CopyPaste(_yeastDoc, null, new SrmDocument(SrmSettingsList.GetDefault()), pathRoot);
Assert.IsNull(_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelTypeName13C));
// If only specific children are selected, test that only these children get copied.
ResetDocuments();
var arrayTrans = _study7Doc.PeptideTransitions.ToArray();
IList <DocNode> selNodes = new List <DocNode>();
for (int i = 0; i < arrayTrans.Length; i += 2)
{
selNodes.Add(arrayTrans[i]);
}
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
Assert.AreEqual(arrayTrans.Length + selNodes.Count, _study7Doc.PeptideTransitionCount);
// Test after pasting to a peptide list, all children have been updated to point to the correct parent.
ResetDocuments();
_study7Doc = CopyPaste(_yeastDoc, new[] { _yeastDoc.Peptides.ToArray()[0] }, _study7Doc,
_study7Doc.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0));
Assert.AreEqual(_yeastDoc.Peptides.ToArray()[0].Peptide, _study7Doc.Peptides.ToArray()[0].Peptide);
Assert.AreEqual(_study7Doc.Peptides.ToArray()[0].Peptide,
_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup.Peptide);
Assert.AreEqual(_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup,
_study7Doc.PeptideTransitions.ToArray()[0].Transition.Group);
// If only specific transition are selected for a peptide, but all transition groups are included, test AutoManageChildren is true.
ResetDocuments();
selNodes = new List <DocNode>();
foreach (TransitionGroupDocNode transGroup in _study7Doc.PeptideTransitionGroups)
{
selNodes.Add(transGroup.Children[0]);
}
// TODO: Fix this and make it pass
// var emptyDoc = (SrmDocument)_study7Doc.ChangeChildren(new List<DocNode>());
// _study7Doc = CopyPaste(_study7Doc, selNodes, emptyDoc, pathRoot);
_study7Doc = (SrmDocument)_study7Doc.ChangeChildren(new List <DocNode>());
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
foreach (PeptideDocNode peptide in _study7Doc.Peptides)
{
Assert.IsTrue(peptide.AutoManageChildren);
}
// Test pasting in modifications with the same name as but different definition from existing modifications not allowed.
ResetDocuments();
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] { new TypedModifications(IsotopeLabelType.heavy, HEAVY_C_K_DIFDEF) });
SetDefaultModifications(_study7Doc);
AssertEx.ThrowsException <Exception>(() => _yeastDoc.Settings.UpdateDefaultModifications(false));
// Test variable modifications kept if target document has matching variable modifications turned on.
ResetDocuments();
settings = _yeastDoc.Settings;
var modsDefault = settings.PeptideSettings.Modifications;
var listVariableMods = new List <StaticMod>(modsDefault.StaticModifications)
{
VAR_MET_OXIDIZED
};
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listVariableMods.ToArray())));
// Make sure there is an implicitly modified peptide in the yeast document
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.Peptide.Sequence.Contains("C")));
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods && !nodePep.HasVariableMods));
// Otherwise the variable modifications become only explicit modifications.
var yeastDocVar = _yeastDoc;
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangePeptideModifications(mods => modsDefault));
_yeastDoc = CopyPaste(yeastDocVar, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Settings.PeptideSettings.Modifications.HasVariableModifications);
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods));
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
}