private bool Equals(GroupComparisonDef other)
{
return(base.Equals(other) &&
string.Equals(ControlAnnotation, other.ControlAnnotation) &&
string.Equals(ControlValue, other.ControlValue) &&
string.Equals(CaseValue, other.CaseValue) &&
string.Equals(IdentityAnnotation, other.IdentityAnnotation) &&
AverageTechnicalReplicates.Equals(other.AverageTechnicalReplicates) &&
SumTransitions.Equals(other.SumTransitions) &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
IncludeInteractionTransitions.Equals(other.IncludeInteractionTransitions) &&
Equals(SummarizationMethod, other.SummarizationMethod) &&
Equals(ConfidenceLevel, other.ConfidenceLevel) &&
Equals(PerProtein, other.PerProtein));
}
public GroupComparer(GroupComparisonDef comparisonDef, SrmDocument document, QrFactorizationCache qrFactorizationCache)
{
SrmDocument = document;
ComparisonDef = comparisonDef;
var annotationCalculator = new AnnotationCalculator(document);
_qrFactorizationCache = qrFactorizationCache;
List <KeyValuePair <int, ReplicateDetails> > replicateIndexes = new List <KeyValuePair <int, ReplicateDetails> >();
var controlGroupIdentifier = ComparisonDef.GetControlGroupIdentifier(SrmDocument.Settings);
if (SrmDocument.Settings.HasResults)
{
var chromatograms = SrmDocument.Settings.MeasuredResults.Chromatograms;
for (int i = 0; i < chromatograms.Count; i++)
{
var chromatogramSet = chromatograms[i];
ReplicateDetails replicateDetails = new ReplicateDetails()
{
GroupIdentifier = comparisonDef.GetGroupIdentifier(annotationCalculator, chromatogramSet)
};
if (Equals(controlGroupIdentifier, replicateDetails.GroupIdentifier))
{
replicateDetails.IsControl = true;
}
else
{
if (!string.IsNullOrEmpty(ComparisonDef.CaseValue))
{
var annotationValue = chromatogramSet.Annotations.GetAnnotation(ComparisonDef.ControlAnnotation);
if (!Equals(annotationValue, ComparisonDef.CaseValue))
{
continue;
}
}
}
if (null != ComparisonDef.IdentityAnnotation)
{
replicateDetails.BioReplicate =
chromatogramSet.Annotations.GetAnnotation(ComparisonDef.IdentityAnnotation);
}
replicateIndexes.Add(new KeyValuePair <int, ReplicateDetails>(i, replicateDetails));
}
}
_replicateIndexes = ImmutableList.ValueOf(replicateIndexes);
IsValid = _replicateIndexes.Any(keyValuePair => keyValuePair.Value.IsControl) &&
_replicateIndexes.Any(keyValuePair => !keyValuePair.Value.IsControl);
}
private bool Equals(GroupComparisonDef other)
{
return(base.Equals(other) &&
string.Equals(ControlAnnotation, other.ControlAnnotation) &&
string.Equals(ControlValue, other.ControlValue) &&
string.Equals(CaseValue, other.CaseValue) &&
string.Equals(IdentityAnnotation, other.IdentityAnnotation) &&
AverageTechnicalReplicates == other.AverageTechnicalReplicates &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
IncludeInteractionTransitions == other.IncludeInteractionTransitions &&
Equals(SummarizationMethod, other.SummarizationMethod) &&
ConfidenceLevelTimes100.Equals(other.ConfidenceLevelTimes100) &&
PerProtein == other.PerProtein &&
UseZeroForMissingPeaks == other.UseZeroForMissingPeaks &&
QValueCutoff.Equals(other.QValueCutoff) &&
ColorRows.SequenceEqual(other.ColorRows));
}
public SrmDocument ApplyChangesToDocument(SrmDocument doc, GroupComparisonDef groupDef)
{
var groupComparisons = doc.Settings.DataSettings.GroupComparisonDefs.ToList();
int index = groupComparisons.FindIndex(def => def.Name == GroupComparisonName);
if (index < 0 || Equals(groupDef, groupComparisons[index]))
{
return(doc);
}
groupComparisons[index] = groupDef;
doc =
doc.ChangeSettings(
doc.Settings.ChangeDataSettings(
doc.Settings.DataSettings.ChangeGroupComparisonDefs(groupComparisons)));
return(doc);
}
public EditGroupComparisonDlg(IDocumentContainer documentContainer,
GroupComparisonDef groupComparisonDef, IEnumerable<GroupComparisonDef> existingGroupComparisons)
: base(new GroupComparisonModel(documentContainer, null) { GroupComparisonDef = groupComparisonDef})
{
InitializeComponent();
Icon = Resources.Skyline;
_originalGroupComparisonDef = groupComparisonDef;
_existingGroupComparisons = existingGroupComparisons;
if (documentContainer == null)
{
btnPreview.Visible = false;
}
tbxName.Text = groupComparisonDef.Name ?? string.Empty;
tbxConfidenceLevel.TextChanged += tbxConfidenceLevel_TextChanged;
comboControlAnnotation.SelectedIndexChanged += comboControlAnnotation_SelectedIndexChanged;
comboCaseValue.SelectedIndexChanged += comboCaseValue_SelectedIndexChanged;
comboControlValue.SelectedIndexChanged += comboControlValue_SelectedIndexChanged;
comboIdentityAnnotation.SelectedIndexChanged += comboIdentityAnnotation_SelectedIndexChanged;
comboNormalizationMethod.SelectedIndexChanged += comboNormalizationMethod_SelectedIndexChanged;
radioScopeProtein.CheckedChanged += radioScope_CheckedChanged;
radioScopePeptide.CheckedChanged += radioScope_CheckedChanged;
}
private bool Equals(GroupComparisonDef other)
{
return base.Equals(other) &&
string.Equals(ControlAnnotation, other.ControlAnnotation) &&
string.Equals(ControlValue, other.ControlValue) &&
string.Equals(CaseValue, other.CaseValue) &&
string.Equals(IdentityAnnotation, other.IdentityAnnotation) &&
AverageTechnicalReplicates.Equals(other.AverageTechnicalReplicates) &&
SumTransitions.Equals(other.SumTransitions) &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
IncludeInteractionTransitions.Equals(other.IncludeInteractionTransitions) &&
Equals(SummarizationMethod, other.SummarizationMethod) &&
Equals(ConfidenceLevel, other.ConfidenceLevel) &&
Equals(PerProtein, other.PerProtein);
}
public DataSettings AddGroupComparisonDef(GroupComparisonDef groupComparisonDef)
{
var groupComparisonDefs = GroupComparisonDefs.ToList();
int index = GroupComparisonDefs.IndexOf(def => def.Name == groupComparisonDef.Name);
if (index < 0)
{
groupComparisonDefs.Add(groupComparisonDef);
}
else
{
groupComparisonDefs[index] = groupComparisonDef;
}
return ChangeGroupComparisonDefs(groupComparisonDefs);
}