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 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);
}
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;
}
}
