private void TestHistogramRatios <T>(Action showHistogram, int statsStartIndex) where T : SummaryGraphPane
{
RunUI(() =>
{
showHistogram();
SkylineWindow.SetAreaCVPointsType(PointsTypePeakArea.targets);
SkylineWindow.SetNormalizationMethod(NormalizeOption.RatioToFirstStandard(SkylineWindow.Document.Settings));
});
WaitForGraphs();
var graph = SkylineWindow.GraphPeakArea;
var toolbar = graph.Toolbar as AreaCVToolbar;
Assert.IsNotNull(toolbar);
RunUI(() => toolbar.SetMinimumDetections(2));
OpenAndChangeAreaCVProperties(graph, p => p.QValueCutoff = double.NaN);
// Make sure toolbar is there, combo box items are correct and data is correct
T pane;
Assert.IsTrue(graph.TryGetGraphPane(out pane));
Assert.IsTrue(pane.HasToolbar);
CollectionAssert.AreEqual(new[] { NormalizeOption.DEFAULT.Caption, "Light", "Heavy", "All 15N", NormalizationMethod.EQUALIZE_MEDIANS.NormalizeToCaption, NormalizationMethod.NONE.NormalizeToCaption }, toolbar.NormalizationMethods.ToArray());
AssertDataCorrect(pane, statsStartIndex++); // Light
RunUI(() => SkylineWindow.SetNormalizationMethod(NormalizeOption.FromIsotopeLabelType(SkylineWindow.Document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[1])));
WaitForGraphs();
AssertDataCorrect(pane, statsStartIndex++); // Heavy
RunUI(() => SkylineWindow.SetNormalizationMethod(NormalizeOption.FromIsotopeLabelType(SkylineWindow.Document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[2])));
WaitForGraphs();
AssertDataCorrect(pane, statsStartIndex++, allowInvalid: true); // All 15N
}
public GraphDataProperties(ReplicateValue group, NormalizeOption normalizeOption, object annotation, int minimumDetections)
{
Group = group;
NormalizeOption = normalizeOption;
Annotation = annotation;
MinimumDetections = minimumDetections;
}
public override int GetHashCode()
{
unchecked
{
var hashCode = (Group != null ? Group.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ NormalizeOption.GetHashCode();
hashCode = (hashCode * 397) ^ (Annotation != null ? Annotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ MinimumDetections;
return(hashCode);
}
}
public AreaCVRefinementSettings(double cvCutoff, double qValueCutoff, int minimumDetections, NormalizeOption normalizeOption,
AreaCVTransitions transitions, int countTransitions, AreaCVMsLevel msLevel)
{
CVCutoff = cvCutoff;
QValueCutoff = qValueCutoff;
MinimumDetections = minimumDetections;
NormalizeOption = normalizeOption;
MsLevel = msLevel;
Transitions = transitions;
CountTransitions = countTransitions;
Annotation = null;
Group = null;
}
public AreaCVGraphSettings(GraphTypeSummary graphType, NormalizeOption normalizeOption, ReplicateValue group, object annotation, PointsTypePeakArea pointsType, double qValueCutoff,
double cvCutoff, int minimumDetections, double binwidth, AreaCVMsLevel msLevel, AreaCVTransitions transitions, int countTransitions)
{
GraphType = graphType;
NormalizeOption = normalizeOption;
Group = group;
Annotation = annotation;
PointsType = pointsType;
QValueCutoff = qValueCutoff;
CVCutoff = cvCutoff;
MinimumDetections = minimumDetections;
BinWidth = binwidth;
MsLevel = msLevel;
Transitions = transitions;
CountTransitions = countTransitions;
}
public override int GetHashCode()
{
unchecked
{
var hashCode = MsLevel.GetHashCode();
hashCode = (hashCode * 397) ^ (int)Transitions;
hashCode = (hashCode * 397) ^ CountTransitions;
hashCode = (hashCode * 397) ^ NormalizeOption.GetHashCode();
hashCode = (hashCode * 397) ^ (Group != null ? Group.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Annotation != null ? Annotation.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (int)PointsType;
hashCode = (hashCode * 397) ^ QValueCutoff.GetHashCode();
hashCode = (hashCode * 397) ^ CVCutoff.GetHashCode();
hashCode = (hashCode * 397) ^ MinimumDetections;
return(hashCode);
}
}
private void TestNormalizeToHeavyHistogram()
{
RunUI(SkylineWindow.ShowPeakAreaCVHistogram);
ResetHistogramSettings();
AreaCVHistogramGraphPane pane;
Assert.IsTrue(SkylineWindow.GraphPeakArea.TryGetGraphPane(out pane));
Assert.IsInstanceOfType(pane, typeof(IAreaCVHistogramInfo));
int startIndex = HISTOGRAM_HEAVY_START;
AssertDataCorrect(pane, startIndex++);
RunUI(() => SkylineWindow.SetNormalizationMethod(NormalizeOption.RatioToFirstStandard(SkylineWindow.Document.Settings)));
AssertDataCorrect(pane, startIndex);
}
public void OnUpdateGraph()
{
// CONSIDER: Need a better guarantee that this ratio index matches the
// one in the sequence tree, but at least this will keep the UI
// from crashing with IndexOutOfBoundsException.
var settings = GraphSummary.DocumentUIContainer.DocumentUI.Settings;
GraphSummary.NormalizeOption = NormalizeOption.Constrain(settings, GraphSummary.NormalizeOption);
var pane = GraphSummary.GraphPanes.FirstOrDefault();
switch (GraphSummary.Type)
{
case GraphTypeSummary.replicate:
case GraphTypeSummary.peptide:
GraphSummary.DoUpdateGraph(this, GraphSummary.Type);
break;
case GraphTypeSummary.histogram:
if (!(pane is AreaCVHistogramGraphPane))
{
GraphSummary.GraphPanes = new[] { new AreaCVHistogramGraphPane(GraphSummary) }
}
;
break;
case GraphTypeSummary.histogram2d:
if (!(pane is AreaCVHistogram2DGraphPane))
{
GraphSummary.GraphPanes = new[] { new AreaCVHistogram2DGraphPane(GraphSummary) }
}
;
break;
}
if (!ReferenceEquals(GraphSummary.GraphPanes.FirstOrDefault(), pane))
{
var disposable = pane as IDisposable;
if (disposable != null)
{
disposable.Dispose();
}
}
}
private IEnumerable <GraphDataProperties> GetPropertyVariants(AreaCVGraphSettings graphSettings)
{
SrmDocument document;
lock (_cacheInfo)
{
document = _cacheInfo.Document;
}
var annotationsArray = AnnotationHelper.GetPossibleAnnotations(document, graphSettings.Group);
// Add an entry for All
var annotations = annotationsArray.Concat(new string[] { null }).ToList();
var normalizationMethods = new List <NormalizeOption>(NormalizeOption.AvailableNormalizeOptions(document).Prepend(NormalizeOption.NONE));
// First cache the histograms for the current annotation
if (annotations.Remove(graphSettings.Annotation))
{
annotations.Insert(0, graphSettings.Annotation);
}
foreach (var n in normalizationMethods)
{
if (n.IsRatioToLabel && !document.Settings.PeptideSettings.Modifications.HasHeavyModifications)
{
continue;
}
foreach (var a in annotations)
{
var minDetections = GetMinDetectionsForAnnotation(document, graphSettings, a);
for (var i = 2; i <= minDetections; ++i)
{
yield return(new GraphDataProperties(graphSettings.Group, n, a, i));
}
}
}
}
public void RunTestFindNode(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = asSmallMolecules.ToString();
}
SrmDocument doc = CreateStudy7Doc();
doc = new RefinementSettings().ConvertToSmallMolecules(doc, TestDirectoryName, asSmallMolecules);
var displaySettings = new DisplaySettings(new NormalizedValueCalculator(doc), null, false, 0, NormalizeOption.RatioToFirstStandard(doc.Settings)); //, ProteinDisplayMode.ByName);
// Find every other transition, searching down.
List <TransitionDocNode> listTransitions = doc.MoleculeTransitions.ToList();
var pathFound = doc.GetPathTo(0, 0);
int i;
for (i = 0; i < doc.MoleculeTransitionCount; i += 2)
{
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[i].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, i), pathFound);
}
// Test wrapping in search down.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[0].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, 0), pathFound);
// Find every other peptide searching up while for each finding one of its children searching down.
pathFound = doc.LastNodePath;
List <PeptideDocNode> listPeptides = new List <PeptideDocNode>();
listPeptides.AddRange(doc.Molecules);
List <TransitionGroupDocNode> listTransitionGroups = new List <TransitionGroupDocNode>();
listTransitionGroups.AddRange(doc.MoleculeTransitionGroups);
for (int x = doc.MoleculeCount; x > 0; x -= 2)
{
// Test case insensitivity.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
// Test parents can find children.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[x * 2 - 1].PrecursorMz.Value), displaySettings,
false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, x * 2 - 1), pathFound);
// Test Children can find parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
}
// Test wrapping in search up.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[listTransitionGroups.Count - 1].PrecursorMz.Value),
displaySettings, false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, listTransitionGroups.Count - 1), pathFound);
// Test children can find other parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[0].ToString().ToLowerInvariant(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, 0), pathFound);
// Test forward and backward searching in succession
const string heavyText = "heavy";
int countHeavyForward = CountOccurrances(doc, heavyText, displaySettings, false, true);
Assert.IsTrue(countHeavyForward > 0);
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText, displaySettings, true, true));
// More tests of case insensitive searching
Assert.AreEqual(0, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, true));
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, false));
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
Assert.AreEqual(1, CountOccurrances(doc, "hgflpr", displaySettings, true, false));
}
// Test mismatched transitions finder
var missmatchFinder = new FindOptions().ChangeCustomFinders(new[] { new MismatchedIsotopeTransitionsFinder() });
Assert.AreEqual(4, CountOccurrances(doc, missmatchFinder, displaySettings));
var docRemoved = (SrmDocument)doc.RemoveChild(doc.Children[1]).RemoveChild(doc.Children[2]);
Assert.AreEqual(0, CountOccurrances(docRemoved, missmatchFinder, displaySettings));
var refineRemoveHeavy = new RefinementSettings {
RefineLabelType = IsotopeLabelType.heavy
};
var docLight = refineRemoveHeavy.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docLight, missmatchFinder, displaySettings));
var refineRemoveLight = new RefinementSettings {
RefineLabelType = IsotopeLabelType.light
};
var docHeavy = refineRemoveLight.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docHeavy, missmatchFinder, displaySettings));
var docMulti = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
docMulti = (new RefinementSettings()).ConvertToSmallMolecules(docMulti, TestContext.TestDir, asSmallMolecules);
Assert.AreEqual(0, CountOccurrances(docMulti, missmatchFinder, displaySettings));
var pathTranMultiRemove = docMulti.GetPathTo((int)SrmDocument.Level.Transitions, 7);
var tranMultiRemove = docMulti.FindNode(pathTranMultiRemove);
var docMultiRemoved = (SrmDocument)docMulti.RemoveChild(pathTranMultiRemove.Parent, tranMultiRemove);
Assert.AreEqual(2, CountOccurrances(docMultiRemoved, missmatchFinder, displaySettings));
var tranGroupMultiRemove = docMulti.FindNode(pathTranMultiRemove.Parent);
var docMultiGroupRemoved = (SrmDocument)
docMulti.RemoveChild(pathTranMultiRemove.Parent.Parent, tranGroupMultiRemove);
Assert.AreEqual(0, CountOccurrances(docMultiGroupRemoved, missmatchFinder, displaySettings));
}
public AreaCVGraphData Get(ReplicateValue group, object annotation, int minimumDetections, NormalizeOption normalizeOption)
{
lock (_cacheInfo)
{
// Linear search, but very short list
return(_cacheInfo.Data.FirstOrDefault(d => Equals(d._graphSettings.Group, group) &&
Equals(d._graphSettings.Annotation, annotation) &&
d._graphSettings.MinimumDetections ==
minimumDetections &&
d._graphSettings.NormalizeOption == normalizeOption));
}
}
// Returns true if a normalizer was added.
public static bool AddNormalizerIfNeeded(IHostEnvironment env, IChannel ch, ITrainer trainer, ref IDataView view, string featureColumn, NormalizeOption autoNorm)
{
Contracts.CheckValue(env, nameof(env));
env.CheckValue(ch, nameof(ch));
ch.CheckValue(trainer, nameof(trainer));
ch.CheckValue(view, nameof(view));
ch.CheckValueOrNull(featureColumn);
ch.CheckUserArg(Enum.IsDefined(typeof(NormalizeOption), autoNorm), nameof(TrainCommand.Arguments.NormalizeFeatures),
"Normalize option is invalid. Specify one of 'norm=No', 'norm=Warn', 'norm=Auto', or 'norm=Yes'.");
if (autoNorm == NormalizeOption.No)
{
ch.Info("Not adding a normalizer.");
return(false);
}
if (string.IsNullOrEmpty(featureColumn))
{
return(false);
}
int featCol;
var schema = view.Schema;
if (schema.TryGetColumnIndex(featureColumn, out featCol))
{
if (autoNorm != NormalizeOption.Yes)
{
var nn = trainer as ITrainerEx;
DvBool isNormalized = DvBool.False;
if (nn == null || !nn.NeedNormalization ||
(schema.TryGetMetadata(BoolType.Instance, MetadataUtils.Kinds.IsNormalized, featCol, ref isNormalized) &&
isNormalized.IsTrue))
{
ch.Info("Not adding a normalizer.");
return(false);
}
if (autoNorm == NormalizeOption.Warn)
{
ch.Warning("A normalizer is needed for this trainer. Either add a normalizing transform or use the 'norm=Auto', 'norm=Yes' or 'norm=No' options.");
return(false);
}
}
ch.Info("Automatically adding a MinMax normalization transform, use 'norm=Warn' or 'norm=No' to turn this behavior off.");
// Quote the feature column name
string quotedFeatureColumnName = featureColumn;
StringBuilder sb = new StringBuilder();
if (CmdQuoter.QuoteValue(quotedFeatureColumnName, sb))
{
quotedFeatureColumnName = sb.ToString();
}
var component = new SubComponent <IDataTransform, SignatureDataTransform>("MinMax", string.Format("col={{ name={0} source={0} }}", quotedFeatureColumnName));
var loader = view as IDataLoader;
if (loader != null)
{
view = CompositeDataLoader.Create(env, loader,
new KeyValuePair <string, SubComponent <IDataTransform, SignatureDataTransform> >(null, component));
}
else
{
view = component.CreateInstance(env, view);
}
return(true);
}
return(false);
}
private static void NormalizeGraphToHeavy()
{
AreaGraphController.AreaNormalizeOption = NormalizeOption.FromIsotopeLabelType(IsotopeLabelType.heavy);
Settings.Default.AreaLogScale = false;
SkylineWindow.UpdatePeakAreaGraph();
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 5, 6
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Prediction Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 5);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 6);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 7, 8
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null,
LabelAtoms.C13 | LabelAtoms.N15, RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi, "Edit Isotope Modification over Transition Settings", 7);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 8);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Inserting a peptide sequence p. 9
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
RunUI(() => pasteDlg.Size = new Size(700, 210));
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 9);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
RunUI(() => SkylineWindow.Size = new Size(840, 410));
PauseForScreenShot("Main window with Targets view", 9);
// Exporting a transition list p. 10
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 10);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 11, 12
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 11);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
RunUI(() =>
{ //resize the window and activate the first standard chromatogram pane.
RunUI(() => SkylineWindow.Size = new Size(1330, 720));
var chrom = SkylineWindow.GraphChromatograms.First();
chrom.Select();
});
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 13);
// Analyzing SRM Data from FOXN1-GST Sample p. 14
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
RunUI(() => SkylineWindow.Size = new Size(1470, 656));
RestoreViewOnScreen(14);
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 14);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 14);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.FromIsotopeLabelType(IsotopeLabelType.heavy)));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 15);
// Peptide Quantitification Settings p. 16
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 16);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
var documentGridForm = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
for (int iRow = 0; iRow < concentrations.Length; iRow++)
{
// ReSharper disable AccessToModifiedClosure
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.Rows[iRow].Cells[colSampleType.Index].Value = SampleType.STANDARD;
});
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var colAnalyteConcentration =
documentGridForm.FindColumn(PropertyPath.Root.Property("AnalyteConcentration"));
var cell = documentGridForm.DataGridView.Rows[iRow].Cells[colAnalyteConcentration.Index];
documentGridForm.DataGridView.CurrentCell = cell;
cell.Value = concentrations[iRow];
});
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
}
if (IsPauseForScreenShots)
{
RunUI(() =>
{
SkylineWindow.Width = 500;
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Top;
gridFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot("Document grid with concentrations filled in", 17);
}
// View the calibration curve p. 18
RunUI(() => SkylineWindow.ShowDocumentGrid(false));
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowPeakAreaLegend(false);
SkylineWindow.ShowRTLegend(false);
});
RestoreCoverViewOnScreen();
RunUI(() =>
{
var calibrationOpenForm = WaitForOpenForm <CalibrationForm>();
var calibrationFloatingWindow = calibrationOpenForm.Parent.Parent;
calibrationFloatingWindow.Top = SkylineWindow.Bottom - calibrationFloatingWindow.Height - 35;
calibrationFloatingWindow.Left = SkylineWindow.Left + 15;
});
TakeCoverShot();
return;
}
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
if (IsPauseForScreenShots)
{
RunUI(() =>
{
var calibrationFloatingWindow = calibrationForm.Parent.Parent;
calibrationFloatingWindow.Width = 565;
calibrationFloatingWindow.Top = SkylineWindow.Top;
calibrationFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot("View calibration curve", 18);
}
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
}
public RefineDlg(IDocumentUIContainer documentContainer)
{
_document = documentContainer.DocumentUI;
_settings = documentContainer.DocumentUI.Settings;
DocumentContainer = documentContainer;
InitializeComponent();
Icon = Resources.Skyline;
// Save text for later use
_removeLabelText = labelLabelType.Text;
_removeTipText = helpTip.GetToolTip(comboRefineLabelType);
// Fill label type comb_o box
comboRefineLabelType.Items.Add(string.Empty);
comboRefineLabelType.Items.Add(IsotopeLabelType.LIGHT_NAME);
foreach (var typedMods in _settings.PeptideSettings.Modifications.GetHeavyModifications())
{
comboRefineLabelType.Items.Add(typedMods.LabelType.Name);
}
comboRefineLabelType.SelectedIndex = 0;
comboReplicateUse.SelectedIndex = 0;
if (!_settings.HasResults)
{
FormUtil.RemoveTabPage(tabResults, helpTip);
}
if (!_settings.HasResults || _settings.MeasuredResults.Chromatograms.Count < 2)
{
FormUtil.RemoveTabPage(tabConsistency, helpTip);
}
else
{
// Consistency tab
textQVal.Enabled = _settings.PeptideSettings.Integration.PeakScoringModel.IsTrained;
numericUpDownDetections.Enabled = textQVal.Enabled;
if (numericUpDownDetections.Enabled)
{
numericUpDownDetections.Minimum = 1;
numericUpDownDetections.Maximum = _document.MeasuredResults.Chromatograms.Count;
numericUpDownDetections.Value = 1;
}
_normalizationMethods.Clear();
_normalizationMethods.Add(NormalizeOption.DEFAULT);
_normalizationMethods.AddRange(NormalizeOption.AvailableNormalizeOptions(_document));
_normalizationMethods.Add(NormalizeOption.NONE);
comboNormalizeTo.Items.Clear();
comboNormalizeTo.Items.AddRange(_normalizationMethods.Select(option => option.Caption).ToArray());
comboNormalizeTo.SelectedIndex = comboNormalizeTo.Items.Count - 1;
comboTransitions.Items.Add(Resources.RefineDlg_RefineDlg_all);
comboTransitions.Items.Add(Resources.RefineDlg_RefineDlg_best);
comboTransitions.SelectedIndex = 0;
var maxTrans = _document.MoleculeTransitionGroups.Select(g => g.TransitionCount).DefaultIfEmpty().Max();
for (int i = 1; i <= maxTrans; i++)
{
comboTransitions.Items.Add(i);
}
if (_document.MoleculeTransitions.Any(t => t.IsMs1))
{
comboTransType.Items.Add(Resources.RefineDlg_RefineDlg_Precursors);
comboTransType.SelectedIndex = comboTransType.Items.Count - 1;
}
if (_document.MoleculeTransitions.Any(t => !t.IsMs1))
{
comboTransType.Items.Add(Resources.RefineDlg_RefineDlg_Products);
comboTransType.SelectedIndex = comboTransType.Items.Count - 1;
}
if (comboTransType.Items.Count == 1)
{
comboTransType.Enabled = false;
}
}
if (_settings.PeptideSettings.Libraries.HasLibraries)
{
labelMinDotProduct.Enabled = textMinDotProduct.Enabled = groupLibCorr.Enabled = true;
}
if (_settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
labelMinIdotProduct.Enabled = textMinIdotProduct.Enabled = groupLibCorr.Enabled = true;
}
// Group Comparisons
_groupComparisonsListBoxDriver = new SettingsListBoxDriver <GroupComparisonDef>(
checkedListBoxGroupComparisons, Settings.Default.GroupComparisonDefList);
_groupComparisonsListBoxDriver.LoadList(
_document.Settings.DataSettings.GroupComparisonDefs);
if (_document.PeptideTransitions.Any(t => t.IsMs1))
{
comboMSGroupComparisons.Items.Add(Resources.RefineDlg_MSLevel_1);
comboMSGroupComparisons.SelectedIndex = comboMSGroupComparisons.Items.Count - 1;
}
if (_document.PeptideTransitions.Any(t => !t.IsMs1))
{
comboMSGroupComparisons.Items.Add(Resources.RefineDlg_MSLevel_2);
comboMSGroupComparisons.SelectedIndex = comboMSGroupComparisons.Items.Count - 1;
}
if (comboMSGroupComparisons.Items.Count == 1)
{
comboMSGroupComparisons.Enabled = false;
}
}
private static void ValidateIrtAndLibrary(SrmDocument docAfter)
{
int irtStandardCount = 0;
foreach (var nodePep in docAfter.Peptides) // We don't expect this to work for non-peptide molecules
{
if (nodePep.GlobalStandardType == PeptideDocNode.STANDARD_TYPE_IRT)
{
irtStandardCount++;
}
else
{
Assert.IsTrue(nodePep.HasLibInfo);
foreach (var nodeTran in nodePep.TransitionGroups.SelectMany(g => g.Transitions))
{
if (!nodeTran.HasLibInfo)
{
Assert.Fail("Missing library info from {0} - {1}", nodePep, nodeTran.GetDisplayText(new DisplaySettings(
new NormalizedValueCalculator(docAfter),
nodePep, false, 0, NormalizeOption.RatioToFirstStandard(docAfter.Settings))));
}
}
}
}
Assert.AreEqual(10, irtStandardCount);
}
public override void UpdateUI()
{
var document = _graphSummary.DocumentUIContainer.DocumentUI;
if (!document.Settings.HasResults)
{
return;
}
var groupsVisible = AreaGraphController.GroupByGroup != null;
toolStripLabel1.Visible = toolStripComboGroup.Visible = groupsVisible;
var detectionsVisiblePrev = toolStripLabel2.Visible && toolStripNumericDetections.Visible && toolStripLabel3.Visible;
var detectionsVisible = AreaGraphController.ShouldUseQValues(document);
toolStripLabel2.Visible = toolStripNumericDetections.Visible = toolStripLabel3.Visible = detectionsVisible;
if (detectionsVisible)
{
toolStripNumericDetections.NumericUpDownControl.Minimum = 2;
if (AreaGraphController.GroupByGroup == null || AreaGraphController.GroupByAnnotation == null)
{
toolStripNumericDetections.NumericUpDownControl.Maximum = document.MeasuredResults.Chromatograms.Count;
}
else
{
toolStripNumericDetections.NumericUpDownControl.Maximum = AnnotationHelper.GetReplicateIndices(document, ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup), AreaGraphController.GroupByAnnotation).Length;
}
if (!detectionsVisiblePrev)
{
toolStripNumericDetections.NumericUpDownControl.Value = 2;
}
}
if (groupsVisible)
{
var annotations = new[] { Resources.GraphSummary_UpdateToolbar_All }.Concat(
AnnotationHelper.GetPossibleAnnotations(document,
ReplicateValue.FromPersistedString(document.Settings, AreaGraphController.GroupByGroup))
.Except(new object[] { null })).ToArray();
toolStripComboGroup.Items.Clear();
// ReSharper disable once CoVariantArrayConversion
toolStripComboGroup.Items.AddRange(annotations);
if (AreaGraphController.GroupByAnnotation != null)
{
toolStripComboGroup.SelectedItem = AreaGraphController.GroupByAnnotation;
}
else
{
toolStripComboGroup.SelectedIndex = 0;
}
ComboHelper.AutoSizeDropDown(toolStripComboGroup);
}
toolStripComboNormalizedTo.Items.Clear();
_normalizationMethods.Clear();
_normalizationMethods.Add(NormalizeOption.DEFAULT);
_normalizationMethods.AddRange(NormalizeOption.AvailableNormalizeOptions(_graphSummary.DocumentUIContainer.DocumentUI));
_normalizationMethods.Add(NormalizeOption.NONE);
toolStripComboNormalizedTo.Items.AddRange(_normalizationMethods.Select(item => item.Caption).ToArray());
toolStripComboNormalizedTo.SelectedIndex = _normalizationMethods.IndexOf(AreaGraphController.AreaCVNormalizeOption);
ComboHelper.AutoSizeDropDown(toolStripComboNormalizedTo);
}
/// <summary>
/// Normalizes datetime.
/// </summary>
/// <param name="dateTime"><see cref="DateTime"/>.</param>
/// <param name="baseSpan"><see cref="TimeSpan"/> for normalization base.It will be better to use multiples or divisors of 60 secs, 60 mins.</param>
/// <param name="option"><see cref="NormalizeOption.Future"/> for nomalized future date.<see cref="NormalizeOption.Past"/> for normalized past date.</param>
/// <returns>Normalized <see cref="DateTime"/>.</returns>
public static DateTime Normalize(DateTime dateTime, TimeSpan baseSpan, NormalizeOption option = NormalizeOption.Future)
{
return(Normalize(dateTime, baseSpan, TimeSpan.Zero, option));
}
// Returns true if a normalizer was added.
public static bool AddNormalizerIfNeeded(IHostEnvironment env, IChannel ch, ITrainer trainer, ref IDataView view, string featureColumn, NormalizeOption autoNorm)
{
Contracts.CheckValue(env, nameof(env));
env.CheckValue(ch, nameof(ch));
ch.CheckValue(trainer, nameof(trainer));
ch.CheckValue(view, nameof(view));
ch.CheckValueOrNull(featureColumn);
ch.CheckUserArg(Enum.IsDefined(typeof(NormalizeOption), autoNorm), nameof(TrainCommand.Arguments.NormalizeFeatures),
"Normalize option is invalid. Specify one of 'norm=No', 'norm=Warn', 'norm=Auto', or 'norm=Yes'.");
if (autoNorm == NormalizeOption.No)
{
ch.Info("Not adding a normalizer.");
return(false);
}
if (string.IsNullOrEmpty(featureColumn))
{
return(false);
}
int featCol;
var schema = view.Schema;
if (schema.TryGetColumnIndex(featureColumn, out featCol))
{
if (autoNorm != NormalizeOption.Yes)
{
if (!trainer.Info.NeedNormalization || schema.IsNormalized(featCol))
{
ch.Info("Not adding a normalizer.");
return(false);
}
if (autoNorm == NormalizeOption.Warn)
{
ch.Warning("A normalizer is needed for this trainer. Either add a normalizing transform or use the 'norm=Auto', 'norm=Yes' or 'norm=No' options.");
return(false);
}
}
ch.Info("Automatically adding a MinMax normalization transform, use 'norm=Warn' or 'norm=No' to turn this behavior off.");
IDataView ApplyNormalizer(IHostEnvironment innerEnv, IDataView input)
=> NormalizeTransform.CreateMinMaxNormalizer(innerEnv, input, featureColumn);
if (view is IDataLoader loader)
{
view = CompositeDataLoader.ApplyTransform(env, loader, tag: null, creationArgs: null, ApplyNormalizer);
}
else
{
view = ApplyNormalizer(env, view);
}
return(true);
}
return(false);
}
/// <summary>
/// Normalizes datetime.
/// </summary>
/// <param name="dateTime"><see cref="DateTime"/>.</param>
/// <param name="baseSpan"><see cref="TimeSpan"/> for normalization base.It will be better to use multiples or divisors of 60 secs, 60 mins.</param>
/// <param name="minDiff">The minimal difference between source datetime and normalized datetime.</param>
/// <param name="option"><see cref="NormalizeOption.Future"/> for nomalized future date.<see cref="NormalizeOption.Past"/> for normalized past date.</param>
/// <returns>Normalized <see cref="DateTime"/>.</returns>
public static DateTime Normalize(DateTime dateTime, TimeSpan baseSpan, TimeSpan minDiff, NormalizeOption option = NormalizeOption.Future)
{
long baseSpanTicks = baseSpan.Ticks;
long minDiffTicks = minDiff.Ticks;
if (baseSpanTicks <= 0)
{
throw new ArgumentOutOfRangeException("baseSpan", ResourceMessage.ErrorMessages.BaseSpanLessThanOrEqualsZero);
}
if (minDiffTicks < 0)
{
throw new ArgumentOutOfRangeException("minDiff", ResourceMessage.ErrorMessages.MinDiffLessThanZero);
}
long ticks = dateTime.Ticks;
long direction = 1L;
long addition = baseSpanTicks;
if (option == NormalizeOption.Past)
{
if (DateTime.MinValue.Ticks + minDiffTicks > ticks)
{
throw new ArgumentOutOfRangeException("minDiff", ResourceMessage.ErrorMessages.MinDiffTooLarge);
}
direction = -1L;
addition = 0L;
}
else
{
if (DateTime.MaxValue.Ticks - minDiffTicks < ticks)
{
throw new ArgumentOutOfRangeException("minDiff", ResourceMessage.ErrorMessages.MinDiffTooLarge);
}
}
ticks = (((ticks + (minDiffTicks * direction)) / baseSpanTicks) * baseSpanTicks);
if (DateTime.MaxValue.Ticks - addition < ticks)
{
throw new ArgumentOutOfRangeException("minDiff", ResourceMessage.ErrorMessages.MinDiffTooLarge);
}
return(new DateTime((ticks + addition), dateTime.Kind));
}
