private static TransitionGroupDocNode PickTransitionGroup(SrmDocument doc, PeptideTreeNode nodePepTree, int resultsIndex)
{
// Determine which transition group to use
var nodeTranGroups = nodePepTree.DocNode.TransitionGroups.ToArray();
if (!nodeTranGroups.Any())
{
return(null);
}
if (nodeTranGroups.Length == 1)
{
return(nodeTranGroups.First());
}
var standards = doc.Settings.PeptideSettings.Modifications.InternalStandardTypes;
var standardList = nodeTranGroups.Where(tranGroup => standards.Contains(tranGroup.TransitionGroup.LabelType)).ToArray();
if (standardList.Length == 1)
{
return(standardList.First());
}
if (standardList.Length > 1)
{
nodeTranGroups = standardList;
}
// Still not sure, pick the one with the most peak area
TransitionGroupDocNode best = null;
float mzMatchTolerance = (float)doc.Settings.TransitionSettings.Instrument.MzMatchTolerance;
float highestAreaSum = 0;
foreach (var tranGroup in nodeTranGroups)
{
ChromatogramSet chromSet = doc.Settings.MeasuredResults.Chromatograms[resultsIndex];
ChromatogramGroupInfo[] chromGroupInfos;
if (!doc.Settings.MeasuredResults.TryLoadChromatogram(chromSet, nodePepTree.DocNode, tranGroup, mzMatchTolerance, false, out chromGroupInfos))
{
continue;
}
float areaSum = chromGroupInfos.Where(info => info != null && info.TransitionPointSets != null)
.Sum(chromGroupInfo => chromGroupInfo.TransitionPointSets.Sum(chromInfo => chromInfo.Peaks.Sum(peak => peak.Area)));
if (areaSum > highestAreaSum)
{
best = tranGroup;
highestAreaSum = areaSum;
}
}
return(best);
}
public void TestNeutralLossTextSequences()
{
var document =
(SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(
new StringReader(NEUTRAL_LOSS_DOCUMENT));
var peptideDocNode = document.Molecules.First();
var modFontHolder = new ModFontHolder(new Control());
var textSequences = PeptideTreeNode.CreateTextSequences(peptideDocNode, document.Settings, "MGFGGTLEIK", null, modFontHolder);
VerifyTextSequences(textSequences,
Tuple.Create("M", FontStyle.Bold | FontStyle.Underline, Color.Black),
Tuple.Create("GFGGTLEIK", FontStyle.Regular, Color.Black)
);
}
private void AdjustModifications(string peptideSeq, bool removeCTerminalMod, char aa13C, double expectedPrecursorMz)
{
FindNode(peptideSeq);
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
string sequence = string.Empty;
bool modsContainLabel13C = false;
RunUI(() =>
{
PeptideTreeNode selNode = ((PeptideTreeNode)SkylineWindow.SequenceTree.SelectedNode);
sequence = selNode.DocNode.Peptide.Sequence;
if (removeCTerminalMod)
{
editPepModsDlg.SelectModification(IsotopeLabelType.heavy, sequence.Length - 1, string.Empty);
}
// Only access Settings.Default on the UI thread
modsContainLabel13C = Settings.Default.HeavyModList.Contains(mod => Equals(mod.Name, "Label:13C"));
});
if (modsContainLabel13C) // Not L10N
{
RunUI(() => editPepModsDlg.SelectModification(IsotopeLabelType.heavy, sequence.IndexOf(aa13C), "Label:13C")); // Not L10N
}
else
{
var editStaticModDlg = ShowDialog <EditStaticModDlg>(() => editPepModsDlg.AddNewModification(sequence.IndexOf(aa13C), IsotopeLabelType.heavy));
RunUI(() => editStaticModDlg.Modification = new StaticMod("Label:13C", null, null, LabelAtoms.C13)); // Not L10N
PauseForScreenShot <EditStaticModDlg.IsotopeModView>("Edit Isotope Modification form", 21);
OkDialog(editStaticModDlg, editStaticModDlg.OkDialog);
// Make sure the right combo has the focus for the screen shot
RunUI(() => editPepModsDlg.SelectModification(IsotopeLabelType.heavy, sequence.IndexOf(aa13C), "Label:13C")); // Not L10N
PauseForScreenShot <EditPepModsDlg>("Edit Modifications form", 21);
}
var doc = SkylineWindow.Document;
RunUI(editPepModsDlg.OkDialog);
WaitForDocumentChange(doc);
RunUI(() =>
{
PeptideTreeNode selNode = ((PeptideTreeNode)SkylineWindow.SequenceTree.SelectedNode);
DocNode[] choices = selNode.GetChoices(true).ToArray();
Assert.IsTrue(choices.Contains(node =>
((TransitionGroupDocNode)node).PrecursorMz.Value.ToString(LocalizationHelper.CurrentCulture)
.Contains(expectedPrecursorMz.ToString(LocalizationHelper.CurrentCulture))));
selNode.Pick(choices, false, false);
});
}
public void TestStaticAndHeavyTextSequences()
{
var document =
(SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(
new StringReader(STATIC_AND_HEAVY_MODIFICATIONS_DOCUMENT));
var modFontHolder = new ModFontHolder(new Control());
var oxidizedPeptide = document.Molecules.First();
VerifyTextSequences(PeptideTreeNode.CreateTextSequences(oxidizedPeptide, document.Settings, "MPEPTIDE", null, modFontHolder),
Tuple.Create("M", FontStyle.Bold | FontStyle.Underline, Color.Blue),
Tuple.Create("PEPTIDE", FontStyle.Bold, Color.Blue)
);
var peptide = document.Molecules.Skip(1).First();
VerifyTextSequences(PeptideTreeNode.CreateTextSequences(peptide, document.Settings, "MPEPTIDE", null, modFontHolder),
Tuple.Create("MPEPTIDE", FontStyle.Bold, Color.Blue));
}
private bool TryGetSelectedPeptide(out PeptideGroupDocNode peptideGroup, out PeptideDocNode peptide)
{
peptide = null;
peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType<PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType<PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
return peptide != null;
}
// ReSharper disable SuggestBaseTypeForParameter
private static TransitionGroupDocNode[] GetLibraryInfoChargeGroups(PeptideTreeNode nodeTree)
// ReSharper restore SuggestBaseTypeForParameter
{
// Return the first group of each charge stat that has library info.
var listGroups = new List <TransitionGroupDocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodeTree.ChildDocNodes)
{
if (!nodeGroup.HasLibInfo)
{
continue;
}
var precursorCharge = nodeGroup.TransitionGroup.PrecursorAdduct;
if (!listGroups.Contains(g => g.TransitionGroup.PrecursorAdduct == precursorCharge))
{
listGroups.Add(nodeGroup);
}
}
return(listGroups.ToArray());
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, ChromFileInfoId resultsFile, bool subsequent, ReplicateValue groupBy, object groupByValue, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out var referenceTarget, out var referenceMatchData, out var runTime);
var annotationCalculator = new AnnotationCalculator(doc);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (var i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
if (groupBy != null)
{
if (!Equals(groupByValue, groupBy.GetValue(annotationCalculator, chromSet)))
{
continue;
}
}
for (var j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (resultsFile == null || ReferenceEquals(resultsFile, fileInfo.FileId))) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
{
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return(doc);
}
public UniquePeptideSettings(UniquePeptidesDlg dlg)
{
ProteinPeptideSelections = new Dictionary <int, ProteinPeptideSelection>();
for (var i = 0; i < dlg.dataGridView1.Rows.Count; ++i)
{
var row = dlg.dataGridView1.Rows[i];
var rowTag = (Tuple <IdentityPath, PeptideDocNode>)row.Tag;
if (!(bool)row.Cells[dlg.PeptideIncludedColumn.Name].Value)
{
var id = rowTag.Item1.GetIdentity(0);
if (!ProteinPeptideSelections.ContainsKey(id.GlobalIndex))
{
var node = (PeptideGroupDocNode)dlg.SrmDocument.FindNode(id);
ProteinPeptideSelections.Add(id.GlobalIndex, new ProteinPeptideSelection(node.ProteinMetadata.Name, new List <string>()));
}
var item = ProteinPeptideSelections[id.GlobalIndex];
item.Peptides.Add(PeptideTreeNode.GetLabel(rowTag.Item2, string.Empty));
++_excludedCount;
}
}
}
public static SrmDocument ApplyPeak(SrmDocument doc, PeptideTreeNode nodePepTree, ref TransitionGroupDocNode nodeTranGroup,
int resultsIndex, int?resultsFile, bool subsequent, ILongWaitBroker longWaitBroker)
{
nodeTranGroup = nodeTranGroup ?? PickTransitionGroup(doc, nodePepTree, resultsIndex);
PeakMatchData referenceTarget;
PeakMatchData[] referenceMatchData;
DateTime? runTime;
GetReferenceData(doc, nodePepTree.DocNode, nodeTranGroup, resultsIndex, resultsFile, out referenceTarget, out referenceMatchData, out runTime);
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromSet = chromatograms[i];
for (int j = 0; j < chromSet.MSDataFileInfos.Count; j++)
{
var fileInfo = chromSet.MSDataFileInfos[j];
if ((i == resultsIndex && (!resultsFile.HasValue || resultsFile.Value == j)) ||
(subsequent && runTime != null && fileInfo.RunStartTime < runTime))
{
continue;
}
var bestMatch = GetPeakMatch(doc, chromSet, fileInfo, nodeTranGroup, referenceTarget, referenceMatchData);
if (bestMatch != null)
{
doc = bestMatch.ChangePeak(doc, nodePepTree, nodeTranGroup, chromSet.Name, fileInfo.FilePath);
}
}
longWaitBroker.SetProgressCheckCancel(i + 1, chromatograms.Count);
}
return(doc);
}
private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 15
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13,
RelativeRT.Matching, null, null, null);
AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 17);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new[] { "" };
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 18.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
{
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(SkylineWindow.Paste);
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 18);
OkDialog(messageDlg, messageDlg.CancelDialog);
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
SkylineWindow.Paste();
SkylineWindow.CollapsePeptides();
});
PauseForScreenShot("Targets tree (selected from main window)", 19);
// Adjusting Modifications Manually, p. 19.
AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348);
PauseForScreenShot("Target tree clipped from main window", 22);
AdjustModifications("IVGGWECEK", true, 'V', 541.763);
AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky")));
// Importing Data from a Multiple Sample WIFF file, p. 23.
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7"));
openDataSourceDialog1.SelectAllFileType(IsFullData ? ".wiff" : ExtensionTestContext.ExtAbWiff); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 23);
RunUI(() =>
{
if (IsFullData)
{
importResultsSamplesDlg.CheckAll(true);
importResultsSamplesDlg.ExcludeSample(0); // Blank
importResultsSamplesDlg.ExcludeSample(25); // QC
importResultsSamplesDlg.ExcludeSample(26);
importResultsSamplesDlg.ExcludeSample(27);
importResultsSamplesDlg.ExcludeSample(28);
importResultsSamplesDlg.ExcludeSample(45); // A2
importResultsSamplesDlg.ExcludeSample(46);
importResultsSamplesDlg.ExcludeSample(47);
importResultsSamplesDlg.ExcludeSample(48);
importResultsSamplesDlg.ExcludeSample(49); // gradientwash
importResultsSamplesDlg.ExcludeSample(50);
importResultsSamplesDlg.ExcludeSample(51);
importResultsSamplesDlg.ExcludeSample(52);
importResultsSamplesDlg.ExcludeSample(53); // A3
importResultsSamplesDlg.ExcludeSample(54);
importResultsSamplesDlg.ExcludeSample(55);
importResultsSamplesDlg.ExcludeSample(56);
}
else
{
importResultsSamplesDlg.CheckAll(false);
importResultsSamplesDlg.IncludeSample(1);
importResultsSamplesDlg.IncludeSample(2);
importResultsSamplesDlg.IncludeSample(11);
importResultsSamplesDlg.IncludeSample(12);
}
});
OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog);
}
else
{
RunUI(openDataSourceDialog1.Open);
}
{
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportDocResultsDlg>("Import Results Common prefix form", 24);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(25);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 25);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
RunUI(SkylineWindow.EditDelete);
FindNode("IVGGWECEK"); // Not L10N
TransitionGroupTreeNode selNodeGroup = null;
RunUI(() =>
{
selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1];
Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank);
});
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.MZMatchTolerance = 0.065;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex);
SkylineWindow.ToggleIntegrateAll();
});
RunUI(() =>
{
foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules)
{
string sequence = nodePep.Peptide.Sequence;
int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree);
if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N
{
Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex,
string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else if (sequence != null)
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex,
string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else // Custom Ion
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex,
string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex));
}
}
});
PauseForScreenShot("Main window", 27);
// Data Inspection with Peak Areas View, p. 27.
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
RestoreViewOnScreen(28);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 28);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_03"));
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(true));
RunUI(() =>
{
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowTotalTransitions();
SkylineWindow.ShowCVValues(true);
SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 32);
// Annotating replicates with concentration values
var chooseAnnotationsDlg = ShowDialog <DocumentSettingsDlg>(SkylineWindow.ShowDocumentSettingsDialog);
var editListDlg = ShowDialog <EditListDlg <SettingsListBase <AnnotationDef>, AnnotationDef> >(chooseAnnotationsDlg.EditAnnotationList);
RunUI(editListDlg.ResetList);
var defineAnnotationDlg = ShowDialog <DefineAnnotationDlg>(editListDlg.AddItem);
RunUI(() =>
{
defineAnnotationDlg.AnnotationName = "Concentration";
defineAnnotationDlg.AnnotationType = AnnotationDef.AnnotationType.number;
defineAnnotationDlg.AnnotationTargets = AnnotationDef.AnnotationTargetSet.Singleton(AnnotationDef.AnnotationTarget.replicate);
});
PauseForScreenShot <DefineAnnotationDlg>("Define Annotation form", 33);
OkDialog(defineAnnotationDlg, defineAnnotationDlg.OkDialog);
OkDialog(editListDlg, () => editListDlg.DialogResult = DialogResult.OK);
RunUI(() => chooseAnnotationsDlg.AnnotationsCheckedListBox.SetItemChecked(0, true));
PauseForScreenShot <DocumentSettingsDlg>("Annotation Settings form", 34);
OkDialog(chooseAnnotationsDlg, chooseAnnotationsDlg.OkDialog);
RunUI(() => SkylineWindow.ShowResultsGrid(true));
RunUI(() =>
{
SkylineWindow.SelectedPath =
SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0);
});
WaitForGraphs();
WaitForConditionUI(() => FindOpenForm <LiveResultsGrid>().IsComplete);
RunUI(() =>
{
Settings.Default.ResultsGridSynchSelection = false;
var resultsGrid = FindOpenForm <LiveResultsGrid>().DataGridView;
var colConcentration =
// ReSharper disable LocalizableElement
resultsGrid.Columns.Cast <DataGridViewColumn>().First(col => "Concentration" == col.HeaderText); // Not L10N
// ReSharper restore LocalizableElement
if (IsFullData)
{
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
SetCellValue(resultsGrid, j, colConcentration.Index, concentrations[i]);
}
}
}
else
{
SetCellValue(resultsGrid, 0, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 1, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 2, colConcentration.Index, 175f);
SetCellValue(resultsGrid, 3, colConcentration.Index, 175f);
}
});
WaitForGraphs();
PauseForScreenShot <LiveResultsGrid>("Results grid with annotations (scrolled to the end)", 35);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.GroupByReplicateAnnotation("Concentration");
NormalizeGraphToHeavy();
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36);
RunUI(() => SkylineWindow.ShowCVValues(false));
RunUI(() => SkylineWindow.SaveDocument());
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 36);
PauseForAuditLog();
// Further Exploration, p. 33.
RunUI(() =>
{
SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowCVValues(true);
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 37);
FindNode("LSEPAELTDAVK");
RunUI(SkylineWindow.ShowRTReplicateGraph);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38);
FindNode("INDISHTQSVSAK");
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 38);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 39);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 40);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 40);
}
public ToolStripMenuItem MakeExcludeStandardMenuItem(int replicateIndex)
{
var document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
return(null);
}
ChromatogramSet chromatogramSet = null;
if (replicateIndex >= 0 &&
replicateIndex < document.Settings.MeasuredResults.Chromatograms.Count)
{
chromatogramSet = document.Settings.MeasuredResults.Chromatograms[replicateIndex];
}
if (chromatogramSet == null)
{
return(null);
}
if (!chromatogramSet.SampleType.AllowExclude)
{
return(null);
}
PeptideDocNode peptideDocNode;
PeptideGroupDocNode peptideGroupDocNode;
if (!TryGetSelectedPeptide(out peptideGroupDocNode, out peptideDocNode))
{
return(null);
}
bool isExcluded = peptideDocNode.IsExcludeFromCalibration(replicateIndex);
var menuItemText = isExcluded ? QuantificationStrings.CalibrationForm_MakeExcludeStandardMenuItem_Include_Standard
: QuantificationStrings.CalibrationForm_MakeExcludeStandardMenuItem_Exclude_Standard;
var peptideIdPath = new IdentityPath(peptideGroupDocNode.Id, peptideDocNode.Id);
var menuItem = new ToolStripMenuItem(menuItemText, null, (sender, args) =>
{
_skylineWindow.ModifyDocument(menuItemText,
doc => SetExcludeStandard(doc, peptideIdPath, replicateIndex, !isExcluded), docPair =>
{
var msgType = isExcluded
? MessageType.set_included_standard
: MessageType.set_excluded_standard;
return(AuditLogEntry.CreateSingleMessageEntry(new MessageInfo(msgType, docPair.NewDocumentType, PeptideTreeNode.GetLabel(peptideDocNode, string.Empty), chromatogramSet.Name)));
});
});
return(menuItem);
}
private void MainTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Check using libkey with small molecules
var adduct = Adduct.FromStringAssumeProtonated("M+3Na");
var z = adduct.AdductCharge;
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const string caffeineInChi = "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3";
const string caffeineCAS = "58-08-2";
const string caffeineSMILES = "Cn1cnc2n(C)c(=O)n(C)c(=O)c12";
const string caffeineKEGG = "C07481";
var mId = new MoleculeAccessionNumbers(string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS, MoleculeAccessionNumbers.TagInChiKey + ":" + caffeineInChiKey,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
Assert.AreEqual(caffeineInChiKey, mId.GetInChiKey());
Assert.AreEqual(caffeineCAS, mId.GetCAS());
Assert.AreEqual(caffeineSMILES, mId.GetSMILES());
Assert.AreEqual(caffeineKEGG, mId.GetKEGG());
var moleculeName = "caffeine";
var smallMolAttributes = SmallMoleculeLibraryAttributes.Create(moleculeName, caffeineFormula, caffeineInChiKey,
string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
LibKey key;
for (var loop = 0; loop++ < 2;)
{
key = new LibKey(smallMolAttributes, adduct);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsFalse(key.IsProteomicKey);
Assert.IsTrue(key.IsSmallMoleculeKey);
Assert.IsFalse(key.IsModified);
Assert.AreEqual(0, key.ModificationCount);
Assert.AreEqual(z, key.Charge);
Assert.AreEqual(adduct, key.Adduct);
Assert.AreEqual(caffeineInChiKey, key.Target.ToString());
var viewLibPepInfo = new ViewLibraryPepInfo(key);
Assert.AreEqual(key, viewLibPepInfo.Key);
var smallMolInfo = viewLibPepInfo.GetSmallMoleculeLibraryAttributes();
Assert.AreEqual(moleculeName, smallMolInfo.MoleculeName);
Assert.AreEqual(caffeineInChiKey, smallMolInfo.InChiKey);
Assert.AreEqual(caffeineFormula, smallMolInfo.ChemicalFormula);
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineCAS));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineInChi));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineHMDB));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineSMILES));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineKEGG));
adduct = Adduct.FromString("M+3Si", Adduct.ADDUCT_TYPE.non_proteomic, z = -17); // Not realistic, but let's see if it's handled consistently
}
// Check general libkey operation
var seq = "YTQSNSVC[+57.0]YAK";
key = new LibKey(seq, Adduct.DOUBLY_PROTONATED);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsTrue(key.IsProteomicKey);
Assert.IsFalse(key.IsSmallMoleculeKey);
Assert.IsTrue(key.IsModified);
Assert.AreEqual(2, key.Charge);
Assert.AreEqual(1, key.ModificationCount);
Assert.AreEqual(Adduct.DOUBLY_PROTONATED, key.Adduct);
Assert.AreEqual(seq, key.Target.ToString());
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath);
BuildLibraryError("non_int_charge.pep.XML", null);
BuildLibraryError("zero_charge.pep.XML", null);
BuildLibraryError("truncated.pep.XML", null);
BuildLibraryError("no_such_file.pep.XML", null, "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", null, "Could not find spectrum file");
// Check for proper handling of labeled addducts in small molecule files
// (formerly this would throw on a null object, fixed with the use of ExplicitMods.EMPTY)
BuildLibraryValid("heavy_adduct.ssl", true, false, false, 1);
// Make sure explorer handles this adduct type
var viewLibUI = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
RunUI(() => AssertEx.IsTrue(viewLibUI.GraphItem.IonLabels.Any()));
RunUI(viewLibUI.CancelDialog);
// Barbara added code to ProteoWizard to rebuild a missing or invalid mzXML index
// BuildLibraryError("bad_mzxml.pep.XML", "<index> not found");
BuildLibraryValid(TestFilesDir.GetTestPath("library_errors"), new[] { "bad_mzxml.pep.XML" }, false, false, false, 1);
string libraryBaseName = _libraryName;
// Test mascot parser
_libraryName = libraryBaseName + "mascot";
string libraryMascot = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("mascot"), new[] { "F027319.dat" },
true, false, false, 121, 4);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryMascot)));
// Test successful builds
_libraryName = libraryBaseName + "a";
string libraryA = _libraryName + BiblioSpecLiteSpec.EXT;
string libraryARedundant = _libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT;
BuildLibraryValid("CPTAC_Set4_725_091509.pep.XML", true, false, false, 1);
BuildLibraryValid("CPTAC_Set4_610_080509.pep.XML", true, false, true, 2);
_libraryName = libraryBaseName + "b";
string libraryB = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid("CPTAC_Set4_624_072409.pep.XML", false, false, false, 6);
_libraryName = libraryBaseName + "c";
string libraryC = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.FullPath, new[] { libraryA, libraryB },
false, false, false, 8);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryA)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryARedundant)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryB)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryC)));
// Test peptide filter
const string filterList = "ACARPIISVYSEK\n" +
// TODO: Having the modified sequence as the first line causes an error with European number formats
"ADRDESSPYAAM[+{0:F01}]IAAQDVAQR\n" +
"ADAIQAGASQFETSAAK";
PastePeptideList(string.Format(filterList, 16.0), true, 0, 3, true);
_libraryName = libraryBaseName + "filter";
string libraryFilter = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("maxquant"), new[] { "test.msms.txt" },
false, true, false, 2);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryFilter)));
RunUI(SkylineWindow.Undo);
RunUI(SkylineWindow.Undo);
// Test AddPathsDlg (file not found)
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
string[] invalidPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.xml"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, invalidPaths, true);
// Test AddPathsDlg (file invalid type)
string[] invalidTypes =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "mqpar.xml")
};
TestAddPaths(buildLibraryDlg, invalidTypes, true);
// Test AddPathsDlg (valid files)
string[] goodPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, goodPaths, false);
OkDialog(buildLibraryDlg, buildLibraryDlg.CancelDialog);
const string heavyRPeptide = "TPAQFDADELR";
const string oxidizedMPeptide = "LVGNMHGDETVSR";
const string peptideList = heavyRPeptide + "\n" +
oxidizedMPeptide + "\n" +
"ALSIGFETCR\n" +
"GNMHGDETVSR\n" +
"VGNMHGDETVSR";
PastePeptideList(peptideList, true, 0, 1);
// Set modifications on peptides to verify they connect with library spectra.
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
const string heavyR = "Heavy R";
Settings.Default.HeavyModList.Add(new StaticMod(heavyR, "R", ModTerminus.C, null, labelAtoms, null, null));
const string oMeth = "Oxidized Methionine";
Settings.Default.StaticModList.Add(new StaticMod(oMeth, "M", null, "O"));
var sequenceTree = SkylineWindow.SequenceTree;
var docCurrent = SkylineWindow.Document;
// Select the heavyR peptide
PeptideTreeNode nodePepTree = null;
IdentityPath pathPep = docCurrent.GetPathTo((int)SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
sequenceTree.SelectedPath = pathPep;
nodePepTree = sequenceTree.SelectedNode as PeptideTreeNode;
});
Assert.IsNotNull(nodePepTree);
Assert.AreEqual(heavyRPeptide, nodePepTree.DocNode.Peptide.Sequence);
// Set the Heavy R modification explicitly
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
RunUI(() =>
{
editPepModsDlg.SetModification(heavyRPeptide.Length - 1, IsotopeLabelType.heavy, heavyR);
editPepModsDlg.OkDialog();
});
WaitForCondition(() => (SkylineWindow.Document.Molecules.First().TransitionGroupCount == 2));
// The peptide should now match the spectrum in the library, and have
// both heavy and light precursors, with ranked transitions
PeptideDocNode nodePep = null;
RunUI(() => nodePep = nodePepTree.DocNode);
Assert.IsNotNull(nodePep);
Debug.Assert(nodePep != null);
Assert.AreEqual(2, nodePep.Children.Count, "Missing precursor for heavy R peptide.");
docCurrent = SkylineWindow.Document;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// Which means all transition groups should now have spectrum info
foreach (var nodeGroup in docCurrent.PeptideTransitionGroups)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// New document
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
var docNewCopy = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy, null));
const string idpList3 = "FHYKTDQGIK\n" +
"WCAIGHQER\n" +
"WCTISTHEANK";
int idpCount3 = idpList3.Split('\n').Length;
const string idpList = "ADVTLGGGAK\n" +
"AGFAGDDAPR\n" +
"ALEFAKK\n" +
"CCTESLVNR\n" +
"DSYVGDEAQSK\n" +
"YICDNQDTISSK\n" +
// charge 3 peptides all have 2 also
idpList3;
int idpCount = idpList.Split('\n').Length;
_libraryName = libraryBaseName + "_idp";
string libraryIdp = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("idp_xml"), new[] { "orbi-small-eg.idpXML" },
false, false, false, idpCount + idpCount3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryIdp)));
// Add peptides expected to have charge 2 spectra in the library
PastePeptideList(idpList, true, 0, 0);
// Undo the paste
RunUI(SkylineWindow.Undo);
// Try filtering for only charge 3 spectra
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.PrecursorCharges = "3";
transitionSettingsUI.OkDialog();
});
PastePeptideList(idpList, false, idpCount - idpCount3 + 1 /* missing cleavage*/, 0);
// New document
var docNewCopy2 = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy2, null));
_libraryName = libraryBaseName + "_cpas1";
string libraryCpas1 = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryCpas1)));
// These are very poor searches, so repeat with no filter
Settings.Default.LibraryResultCutOff = 0;
_libraryName = libraryBaseName + "_cpas2";
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 100, 100);
// And, since the spectra are really poor, allow lots of
// possibilities for fragment ions.
var transitionSettingsCpas = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsCpas.PrecursorCharges =
transitionSettingsCpas.ProductCharges = "1,2,3";
transitionSettingsCpas.FragmentTypes = "y,b";
transitionSettingsCpas.InstrumentMaxMz = 2000;
transitionSettingsCpas.OkDialog();
});
EnsurePeptideSettings();
RunUI(() =>
{
// Turn off carbamidomethyl cys, since not in these searches
PeptideSettingsUI.PickedStaticMods = new string[0];
PeptideSettingsUI.OkDialog();
});
// Get the set of peptides to paste from the library, since there
// are a lot.
var setPeptides = new HashSet <Target>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Target);
}
}
string cpasPeptides = string.Join("\n", setPeptides.Select(p => p.ToString()).ToArray());
var pasteFilteredPeptideDlg = ShowDialog <PasteFilteredPeptidesDlg>(
() => SkylineWindow.Paste(cpasPeptides));
RunUI(pasteFilteredPeptideDlg.NoDialog);
Assert.IsTrue(WaitForCondition(() => SkylineWindow.Document.PeptideCount == setPeptides.Count),
string.Format("Expecting {0} peptides, found {1}.", setPeptides.Count, SkylineWindow.Document.PeptideCount));
Assert.AreEqual(setPeptides.Count, SkylineWindow.Document.PeptideTransitionGroupCount,
"Expecting precursors for peptides matched to library spectrum.");
// New document
docNew = new SrmDocument(SrmSettingsList.GetDefault());
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
// Tests for adding iRTs to spectral library after building
// 1. ask to recalibrate iRTs
// 2. ask to add iRTs
// 3. if added iRTs, ask to add RT predictor
// no recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt1"; // library_test_irt1
BuildLibraryIrt(true, false, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime == null));
// no recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt2"; // library_test_irt2
BuildLibraryIrt(true, false, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg2 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg2.IrtStandards, IrtStandard.BIOGNOSYS_10)));
OkDialog(editIrtDlg2, editIrtDlg2.CancelDialog);
// recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt3"; // library_test_irt3
BuildLibraryIrt(true, true, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(libraryBaseName + "_irt2")));
// recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt4"; // library_test_irt4
BuildLibraryIrt(true, true, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg4 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg4.IrtStandards, IrtStandard.EMPTY)));
OkDialog(editIrtDlg4, editIrtDlg4.CancelDialog);
OkDialog(PeptideSettingsUI, PeptideSettingsUI.CancelDialog);
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath, "uw.edu");
BuildLibraryError("non_int_charge.pep.XML");
BuildLibraryError("zero_charge.pep.XML");
BuildLibraryError("truncated.pep.XML");
BuildLibraryError("no_such_file.pep.XML", "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", "Could not find spectrum file");
// Barbara added code to ProteoWizard to rebuild a missing or invalid mzXML index
// BuildLibraryError("bad_mzxml.pep.XML", "<index> not found");
BuildLibraryValid(TestFilesDir.GetTestPath("library_errors"), new[] { "bad_mzxml.pep.XML" }, false, false, false, 1);
string libraryBaseName = _libraryName;
// Test mascot parser
_libraryName = libraryBaseName + "mascot";
string libraryMascot = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("mascot"), new[] { "F027319.dat" },
true, false, false, 121, 4);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryMascot)));
// Test successful builds
_libraryName = libraryBaseName + "a";
string libraryA = _libraryName + BiblioSpecLiteSpec.EXT;
string libraryARedundant = _libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT;
BuildLibraryValid("CPTAC_Set4_725_091509.pep.XML", true, false, false, 1);
BuildLibraryValid("CPTAC_Set4_610_080509.pep.XML", true, false, true, 2);
_libraryName = libraryBaseName + "b";
string libraryB = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid("CPTAC_Set4_624_072409.pep.XML", false, false, false, 6);
_libraryName = libraryBaseName + "c";
string libraryC = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.FullPath, new[] { libraryA, libraryB },
false, false, false, 8);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryA)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryARedundant)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryB)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryC)));
// Test peptide filter
const string filterList = "ACARPIISVYSEK\n" +
// TODO: Having the modified sequence as the first line causes an error with European number formats
"ADRDESSPYAAM[+{0:F01}]IAAQDVAQR\n" +
"ADAIQAGASQFETSAAK";
PastePeptideList(string.Format(filterList, 16.0), true, 0, 3, true);
_libraryName = libraryBaseName + "filter";
string libraryFilter = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("maxquant"), new[] { "test.msms.txt" },
false, true, false, 2);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryFilter)));
RunUI(SkylineWindow.Undo);
RunUI(SkylineWindow.Undo);
// Test AddPathsDlg (file not found)
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
string[] invalidPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.xml"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, invalidPaths, true);
// Test AddPathsDlg (file invalid type)
string[] invalidTypes =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "mqpar.xml")
};
TestAddPaths(buildLibraryDlg, invalidTypes, true);
// Test AddPathsDlg (valid files)
string[] goodPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, goodPaths, false);
OkDialog(buildLibraryDlg, buildLibraryDlg.CancelDialog);
const string heavyRPeptide = "TPAQFDADELR";
const string oxidizedMPeptide = "LVGNMHGDETVSR";
const string peptideList = heavyRPeptide + "\n" +
oxidizedMPeptide + "\n" +
"ALSIGFETCR\n" +
"GNMHGDETVSR\n" +
"VGNMHGDETVSR";
PastePeptideList(peptideList, true, 0, 1);
// Set modifications on peptides to verify they connect with library spectra.
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
const string heavyR = "Heavy R";
Settings.Default.HeavyModList.Add(new StaticMod(heavyR, "R", ModTerminus.C, null, labelAtoms, null, null));
const string oMeth = "Oxidized Methionine";
Settings.Default.StaticModList.Add(new StaticMod(oMeth, "M", null, "O"));
var sequenceTree = SkylineWindow.SequenceTree;
var docCurrent = SkylineWindow.Document;
// Select the heavyR peptide
PeptideTreeNode nodePepTree = null;
IdentityPath pathPep = docCurrent.GetPathTo((int)SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
sequenceTree.SelectedPath = pathPep;
nodePepTree = sequenceTree.SelectedNode as PeptideTreeNode;
});
Assert.IsNotNull(nodePepTree);
Assert.AreEqual(heavyRPeptide, nodePepTree.DocNode.Peptide.Sequence);
// Set the Heavy R modification explicitly
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
RunUI(() =>
{
editPepModsDlg.SetModification(heavyRPeptide.Length - 1, IsotopeLabelType.heavy, heavyR);
editPepModsDlg.OkDialog();
});
WaitForCondition(() => (SkylineWindow.Document.Molecules.First().TransitionGroupCount == 2));
// The peptide should now match the spectrum in the library, and have
// both heavy and light precursors, with ranked transitions
PeptideDocNode nodePep = null;
RunUI(() => nodePep = nodePepTree.DocNode);
Assert.IsNotNull(nodePep);
Debug.Assert(nodePep != null);
Assert.AreEqual(2, nodePep.Children.Count, "Missing precursor for heavy R peptide.");
docCurrent = SkylineWindow.Document;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// Which means all transition groups should now have spectrum info
foreach (var nodeGroup in docCurrent.PeptideTransitionGroups)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// New document
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
const string idpList3 = "FHYKTDQGIK\n" +
"WCAIGHQER\n" +
"WCTISTHEANK";
int idpCount3 = idpList3.Split('\n').Length;
const string idpList = "ADVTLGGGAK\n" +
"AGFAGDDAPR\n" +
"ALEFAKK\n" +
"CCTESLVNR\n" +
"DSYVGDEAQSK\n" +
"YICDNQDTISSK\n" +
// charge 3 peptides all have 2 also
idpList3;
int idpCount = idpList.Split('\n').Length;
_libraryName = libraryBaseName + "_idp";
string libraryIdp = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("idp_xml"), new[] { "orbi-small-eg.idpXML" },
false, false, false, idpCount + idpCount3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryIdp)));
// Add peptides expected to have charge 2 spectra in the library
PastePeptideList(idpList, true, 0, 0);
// Undo the paste
RunUI(SkylineWindow.Undo);
// Try filtering for only charge 3 spectra
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.PrecursorCharges = "3";
transitionSettingsUI.OkDialog();
});
PastePeptideList(idpList, false, idpCount - idpCount3 + 1 /* missing cleavage*/, 0);
// New document
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
_libraryName = libraryBaseName + "_cpas1";
string libraryCpas1 = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryCpas1)));
// These are very poor searches, so repeat with no filter
Settings.Default.LibraryResultCutOff = 0;
_libraryName = libraryBaseName + "_cpas2";
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 100, 100);
// And, since the spectra are really poor, allow lots of
// possibilities for fragment ions.
var transitionSettingsCpas = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsCpas.PrecursorCharges =
transitionSettingsCpas.ProductCharges = "1,2,3";
transitionSettingsCpas.FragmentTypes = "y,b";
transitionSettingsCpas.InstrumentMaxMz = 2000;
transitionSettingsCpas.OkDialog();
});
EnsurePeptideSettings();
RunUI(() =>
{
// Turn off carbamidomethyl cys, since not in these searches
PeptideSettingsUI.PickedStaticMods = new string[0];
PeptideSettingsUI.OkDialog();
});
// Get the set of peptides to paste from the library, since there
// are a lot.
HashSet <string> setPeptides = new HashSet <string>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Sequence);
}
}
string cpasPeptides = string.Join("\n", setPeptides.ToArray());
var pasteFilteredPeptideDlg = ShowDialog <PasteFilteredPeptidesDlg>(
() => SkylineWindow.Paste(cpasPeptides));
RunUI(pasteFilteredPeptideDlg.NoDialog);
Assert.IsTrue(WaitForCondition(() => SkylineWindow.Document.PeptideCount == setPeptides.Count),
string.Format("Expecting {0} peptides, found {1}.", setPeptides.Count, SkylineWindow.Document.PeptideCount));
Assert.AreEqual(setPeptides.Count, SkylineWindow.Document.PeptideTransitionGroupCount,
"Expecting precursors for peptides matched to library spectrum.");
}
private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 18
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
if (IsCoverShotMode)
{
var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI1, "Edit Isotope Modification form", 6);
}
var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13,
RelativeRT.Matching, null, null, null);
AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 18);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new string[0];
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 19.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
// We expect this to fail due to instrument settings rather than format issues eg "The product m/z 1519.78 is out of range for the instrument settings, in the peptide sequence YEVQGEVFTKPQLWP. Check the Instrument tab in the Transition Settings."
{
var transitionSelectdgl = ShowDialog <ImportTransitionListColumnSelectDlg>(SkylineWindow.Paste);
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(transitionSelectdgl.AcceptButton.PerformClick);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
messageDlg.ErrorList[0].ErrorMessage,
2);
RunUI(() => messageDlg.Size = new Size(838, 192));
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 19);
OkDialog(messageDlg, messageDlg.CancelButton.PerformClick); // Acknowledge the error but decline to proceed with import
RunUI(() => transitionSelectdgl.DialogResult = DialogResult.Cancel); // Cancel the import
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
PasteTransitionListSkipColumnSelect();
RunUI(SkylineWindow.CollapsePeptides);
PauseForScreenShot("Targets tree (selected from main window)", 20);
// Adjusting Modifications Manually, p. 19.
AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348);
PauseForScreenShot("Target tree clipped from main window", 22);
AdjustModifications("IVGGWECEK", true, 'V', 541.763);
AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky")));
// Importing Data from a Multiple Sample WIFF file, p. 23.
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7"));
openDataSourceDialog1.SelectAllFileType(UseRawFilesOrFullData ? ".wiff" : ".mzML"); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 24);
RunUI(() =>
{
if (IsFullData)
{
importResultsSamplesDlg.CheckAll(true);
importResultsSamplesDlg.ExcludeSample(0); // Blank
importResultsSamplesDlg.ExcludeSample(25); // QC
importResultsSamplesDlg.ExcludeSample(26);
importResultsSamplesDlg.ExcludeSample(27);
importResultsSamplesDlg.ExcludeSample(28);
importResultsSamplesDlg.ExcludeSample(45); // A2
importResultsSamplesDlg.ExcludeSample(46);
importResultsSamplesDlg.ExcludeSample(47);
importResultsSamplesDlg.ExcludeSample(48);
importResultsSamplesDlg.ExcludeSample(49); // gradientwash
importResultsSamplesDlg.ExcludeSample(50);
importResultsSamplesDlg.ExcludeSample(51);
importResultsSamplesDlg.ExcludeSample(52);
importResultsSamplesDlg.ExcludeSample(53); // A3
importResultsSamplesDlg.ExcludeSample(54);
importResultsSamplesDlg.ExcludeSample(55);
importResultsSamplesDlg.ExcludeSample(56);
}
else
{
importResultsSamplesDlg.CheckAll(false);
importResultsSamplesDlg.IncludeSample(1);
importResultsSamplesDlg.IncludeSample(2);
importResultsSamplesDlg.IncludeSample(11);
importResultsSamplesDlg.IncludeSample(12);
}
});
OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog);
}
else
{
RunUI(openDataSourceDialog1.Open);
}
{
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results Common prefix form", 25);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(26);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
SkylineWindow.Size = new Size(1029, 659);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 26);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
RunUI(SkylineWindow.EditDelete);
FindNode("IVGGWECEK"); // Not L10N
TransitionGroupTreeNode selNodeGroup = null;
RunUI(() =>
{
selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1];
Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank);
});
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.MZMatchTolerance = 0.065;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex);
SkylineWindow.ToggleIntegrateAll();
});
RunUI(() =>
{
foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules)
{
string sequence = nodePep.Peptide.Sequence;
int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree);
if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N
{
Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex,
string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else if (sequence != null)
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex,
string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else // Custom Ion
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex,
string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex));
}
}
});
PauseForScreenShot("Main window", 27);
// Data Inspection with Peak Areas View, p. 29.
RestoreViewOnScreen(28);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 31);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 32);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.ActivateReplicate("E_03");
SkylineWindow.Size = new Size(757, 655);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 32);
RunUI(() => SkylineWindow.ShowGraphPeakArea(true));
RunUI(() =>
{
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowTotalTransitions();
SkylineWindow.ShowCVValues(true);
SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 33);
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
var pathConcentration = PropertyPath.Parse("AnalyteConcentration");
var pathSampleType = PropertyPath.Parse("SampleType");
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
WaitForConditionUI(() => documentGrid.RowCount == (IsFullData ? concentrations.Length * 4 : 4) &&
documentGrid.FindColumn(pathConcentration) != null &&
documentGrid.FindColumn(pathSampleType) != null); // Let it initialize
RunUI(() =>
{
// Parent is a DocPane and Parent.Parent is the floating window
documentGrid.Parent.Parent.Size = new Size(585, 325);
var documentGridView = documentGrid.DataGridView;
var colConcentration = documentGrid.FindColumn(pathConcentration);
var colStandardType = documentGrid.FindColumn(pathSampleType);
if (IsFullData)
{
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
double?concentration = concentrations[i];
SetCellValue(documentGridView, j, colConcentration.Index, concentration);
SetCellValue(documentGridView, j, colStandardType.Index,
concentration == 0 ? SampleType.BLANK : SampleType.STANDARD);
}
}
}
else
{
SetCellValue(documentGridView, 0, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 0, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 1, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 1, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 2, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 2, colStandardType.Index, SampleType.STANDARD);
SetCellValue(documentGridView, 3, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 3, colStandardType.Index, SampleType.STANDARD);
}
});
WaitForGraphs();
PauseForScreenShot <DocumentGridForm>("Document grid filled (scrolled to the end)", 35);
RunUI(() => documentGrid.Close());
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
var settings = SkylineWindow.DocumentUI.Settings;
var valConcentration = ReplicateValue.GetAllReplicateValues(settings).Skip(1).First();
SkylineWindow.GroupByReplicateValue(valConcentration);
NormalizeGraphToHeavy();
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36);
RunUI(() => SkylineWindow.ShowCVValues(false));
RunUI(() => SkylineWindow.SaveDocument());
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 37);
PauseForAuditLog();
// Further Exploration, p. 33.
RunUI(() =>
{
SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowCVValues(true);
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 38);
FindNode("LSEPAELTDAVK");
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.Width = 920;
SkylineWindow.ShowRTReplicateGraph();
});
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38);
FindNode("INDISHTQSVSAK");
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 39);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.AutoZoomBestPeak();
});
RestoreCoverViewOnScreen();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Parent);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Nodes[0]);
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 40);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 41);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 41);
}
private void DisplayCalibrationCurve()
{
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = zedGraphControl.GraphPane.XAxis.Type
= options.LogPlot ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide = null;
PeptideGroupDocNode peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType <PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType <PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
if (null == peptide)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve;
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document.Settings, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (string.IsNullOrEmpty(
peptideQuantifier.QuantificationSettings.NormalizationMethod.IsotopeLabelTypeName))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_;
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
string.Format(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
double minX = double.MaxValue, maxX = double.MinValue;
_scatterPlots = new CurveList();
foreach (var sampleType in SampleType.ListSampleTypes())
{
if (!Options.DisplaySampleType(sampleType))
{
continue;
}
PointPairList pointPairList = new PointPairList();
for (int iReplicate = 0;
iReplicate < document.Settings.MeasuredResults.Chromatograms.Count;
iReplicate++)
{
ChromatogramSet chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
if (!Equals(sampleType, chromatogramSet.SampleType))
{
continue;
}
double?y = curveFitter.GetYValue(iReplicate);
double?x = curveFitter.GetSpecifiedXValue(iReplicate)
?? curveFitter.GetCalculatedXValue(CalibrationCurve, iReplicate);
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = iReplicate
};
pointPairList.Add(point);
if (!Options.LogPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
maxX = Math.Max(maxX, x.Value);
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!options.LogPlot)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, minX, maxX,
interpolatedLinePointCount, Options.LogPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
CalibrationCurve.RSquared.Value.ToString("0.####")); // Not L10N
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format("{0}: {1}", // Not L10N
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
}
if (options.ShowSelection)
{
double?ySelected = curveFitter.GetYValue(_skylineWindow.SelectedResultsIndex);
double?xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, _skylineWindow.SelectedResultsIndex);
if (xSelected.HasValue && ySelected.HasValue)
{
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
}
var quantificationResult = curveFitter.GetQuantificationResult(_skylineWindow.SelectedResultsIndex);
if (quantificationResult.CalculatedConcentration.HasValue)
{
labelLines.Add(string.Format("{0} = {1}", // Not L10N
QuantificationStrings.Calculated_Concentration, quantificationResult));
}
else if (!quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.OpenFile(TestFilesDir.GetTestPath("SimpleRatiosTest.sky"));
SkylineWindow.ExpandPrecursors();
});
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Quantification.SimpleRatios);
Assert.AreEqual(new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy),
SkylineWindow.Document.Settings.PeptideSettings.Quantification.NormalizationMethod);
PeptideTreeNode peptideTreeNode = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
TransitionGroupTreeNode lightTreeNode =
(TransitionGroupTreeNode)peptideTreeNode.Nodes[0];
TransitionGroupTreeNode heavyTreeNode = (TransitionGroupTreeNode)peptideTreeNode.Nodes[1];
var lightTransitionAreas =
lightTreeNode.DocNode.Transitions.Select(tran => tran.Results[0][0].Area).ToList();
Assert.AreEqual(4, lightTransitionAreas.Count);
var heavyTransitionAreas =
heavyTreeNode.DocNode.Transitions.Select(tran => tran.Results[0][0].Area).ToList();
Assert.AreEqual(2, heavyTransitionAreas.Count);
// Verify that only the first two transition areas in both precursors contribute to the displayed ratio
var expectedRatio = lightTransitionAreas.Take(2).Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
RunUI(() =>
{
SkylineWindow.ShowResultsGrid(true);
SkylineWindow.SelectedPath = peptideTreeNode.Path;
});
var resultsGridForm = FindOpenForm <LiveResultsGrid>();
WaitForConditionUI(() => resultsGridForm.IsComplete);
RunDlg <ViewEditor>(resultsGridForm.DataboundGridControl.NavBar.CustomizeView, viewEditor =>
{
viewEditor.ChooseColumnsTab.AddColumn(propertyPathNormalizedArea);
viewEditor.ViewName = "PeptideResultsWithNormalizedArea";
viewEditor.OkDialog();
});
VerifyExpectedRatio(resultsGridForm, expectedRatio);
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUi =>
{
peptideSettingsUi.SimpleRatios = true;
peptideSettingsUi.OkDialog();
});
Assert.IsTrue(SkylineWindow.Document.Settings.PeptideSettings.Quantification.SimpleRatios);
// When SimpleRatios is true, verify that all transitions contribute to the ratio
expectedRatio = lightTransitionAreas.Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
VerifyExpectedRatio(resultsGridForm, expectedRatio);
// Verify that deleting a transition from the light precursor does not affect the heavy precursor
Assert.AreEqual(4, lightTreeNode.DocNode.TransitionCount);
Assert.AreEqual(2, heavyTreeNode.DocNode.TransitionCount);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPaths = new[]
{ SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 0) };
SkylineWindow.EditDelete();
});
Assert.AreEqual(3, lightTreeNode.DocNode.TransitionCount);
Assert.AreEqual(2, heavyTreeNode.DocNode.TransitionCount);
expectedRatio = lightTransitionAreas.Skip(1).Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
RunUI(() => SkylineWindow.SelectedPath = peptideTreeNode.Path);
VerifyExpectedRatio(resultsGridForm, expectedRatio);
}
