protected override void UpdateSettings()
{
var groupComparisonDef = GroupComparisonModel.GroupComparisonDef;
ReplaceComboItems(comboControlAnnotation, ListReplicateAnnotations(), groupComparisonDef.ControlAnnotation);
string[] controlValues = ListControlValues();
ReplaceComboItems(comboControlValue, controlValues, groupComparisonDef.ControlValue ?? string.Empty);
var caseValues = new HashSet <string>(controlValues)
{
string.Empty
};
if (null != groupComparisonDef.ControlValue)
{
caseValues.Remove(groupComparisonDef.ControlValue);
}
var sortedCaseValues = caseValues.ToArray();
Array.Sort(sortedCaseValues);
ReplaceComboItems(comboCaseValue, sortedCaseValues, groupComparisonDef.CaseValue ?? string.Empty);
ReplaceComboItems(comboIdentityAnnotation, new[] { string.Empty }.Concat(ListReplicateAnnotations()),
groupComparisonDef.IdentityAnnotation);
ReplaceComboItems(comboNormalizationMethod, NormalizationMethod.ListNormalizationMethods(GroupComparisonModel.Document, true), groupComparisonDef.NormalizationMethod);
tbxConfidenceLevel.Text = groupComparisonDef.ConfidenceLevelTimes100.ToString(CultureInfo.CurrentCulture);
radioScopeProtein.Checked = groupComparisonDef.PerProtein;
radioScopePeptide.Checked = !groupComparisonDef.PerProtein;
}
protected override object[] GetDropdownItems()
{
var document = SkylineDataSchema.Document;
List <Tuple <string, NormalizationMethod> > normalizationMethods
= new List <Tuple <string, NormalizationMethod> >
{
new Tuple <string, NormalizationMethod>(string.Empty, null)
};
normalizationMethods.AddRange(NormalizationMethod.ListNormalizationMethods(document).Select(ToDropdownItem));
normalizationMethods.AddRange(NormalizationMethod.RatioToSurrogate.ListSurrogateNormalizationMethods(document).Select(ToDropdownItem));
// If there are any molecules that have a normalization method that is not in the list, add it to the end.
var normalizationMethodValues = new HashSet <NormalizationMethod>(normalizationMethods.Select(tuple => tuple.Item2)
.Where(normalizationMethod => null != normalizationMethod));
foreach (var molecule in document.Molecules)
{
if (molecule.NormalizationMethod != null &&
normalizationMethodValues.Add(molecule.NormalizationMethod))
{
normalizationMethods.Add(ToDropdownItem(molecule.NormalizationMethod));
}
}
return(normalizationMethods.Cast <object>().ToArray());
}
private IList <Tuple <string, NormalizationMethod> > GetDropdownItems(SrmDocument document)
{
List <Tuple <string, NormalizationMethod> > normalizationMethods
= new List <Tuple <string, NormalizationMethod> >
{
new Tuple <string, NormalizationMethod>(string.Empty, null)
};
if (null != document)
{
normalizationMethods.AddRange(NormalizationMethod.ListNormalizationMethods(document).Select(ToDropdownItem));
normalizationMethods.AddRange(NormalizationMethod.RatioToSurrogate.ListSurrogateNormalizationMethods(document).Select(ToDropdownItem));
// If there are any molecules that have a normalization method that is not in the list, add it to the end.
var normalizationMethodValues = new HashSet <NormalizationMethod>(normalizationMethods.Select(tuple => tuple.Item2)
.Where(normalizationMethod => null != normalizationMethod));
foreach (var molecule in document.Molecules)
{
if (molecule.NormalizationMethod != null &&
normalizationMethodValues.Add(molecule.NormalizationMethod))
{
normalizationMethods.Add(ToDropdownItem(molecule.NormalizationMethod));
}
}
}
return(normalizationMethods);
}
/// <summary>
/// Returns the normalization options that are appropriate for the document.
/// Note: never includes "Default", "None", "Total", or "Maximum".
/// </summary>
/// <param name="document"></param>
/// <returns></returns>
public static IEnumerable <NormalizeOption> AvailableNormalizeOptions(SrmDocument document)
{
foreach (var normalizationMethod in NormalizationMethod.ListNormalizationMethods(document)
.OrderBy(method => method is NormalizationMethod.RatioToLabel ? 0 : 1))
{
if (Equals(normalizationMethod, NormalizationMethod.NONE))
{
continue;
}
yield return(FromNormalizationMethod(normalizationMethod));
}
if (document.Settings.PeptideSettings.Quantification.RegressionFit != RegressionFit.NONE)
{
yield return(CALIBRATED);
}
}
protected void UpdateSettings()
{
var groupComparisonDef = GroupComparisonModel.GroupComparisonDef;
ReplaceComboItems(comboControlAnnotation, ListReplicateAnnotations(), groupComparisonDef.ControlAnnotation);
string[] controlValues = ListControlValues();
ReplaceComboItems(comboControlValue, controlValues, groupComparisonDef.ControlValue ?? string.Empty);
var caseValues = new HashSet <string>(controlValues)
{
string.Empty
};
if (null != groupComparisonDef.ControlValue)
{
caseValues.Remove(groupComparisonDef.ControlValue);
}
var sortedCaseValues = caseValues.ToArray();
Array.Sort(sortedCaseValues);
ReplaceComboItems(comboCaseValue, sortedCaseValues, groupComparisonDef.CaseValue ?? string.Empty);
ReplaceComboItems(comboIdentityAnnotation, new[] { string.Empty }.Concat(ListReplicateAnnotations()),
groupComparisonDef.IdentityAnnotation);
ReplaceComboItems(comboNormalizationMethod, NormalizationMethod.ListNormalizationMethods(GroupComparisonModel.Document), groupComparisonDef.NormalizationMethod);
ReplaceComboItems(comboSummaryMethod, SummarizationMethod.ListSummarizationMethods(), groupComparisonDef.SummarizationMethod);
tbxConfidenceLevel.Text = groupComparisonDef.ConfidenceLevelTimes100.ToString(CultureInfo.CurrentCulture);
radioScopeProtein.Checked = groupComparisonDef.PerProtein;
radioScopePeptide.Checked = !groupComparisonDef.PerProtein;
cbxUseZeroForMissingPeaks.Checked = groupComparisonDef.UseZeroForMissingPeaks;
cbxUseZeroForMissingPeaks.Visible = GroupComparisonModel.Document.Settings.PeptideSettings.Integration.PeakScoringModel != null;
if (GroupComparisonDef.QValueCutoff.HasValue)
{
tbxQValueCutoff.Text = groupComparisonDef.QValueCutoff.Value.ToString(CultureInfo.CurrentCulture);
groupBoxQValueCutoff.Visible = true;
}
else
{
tbxQValueCutoff.Text = string.Empty;
}
if (RequiresAdvanced(groupComparisonDef))
{
ShowAdvanced(true);
}
}