private static ViewInfo CreateAuditLogViewInfo(SkylineDataSchema dataSchema, string name, params string[] columnNames)
{
var columnDescriptor = ColumnDescriptor.RootColumn(dataSchema, typeof(AuditLogRow));
var viewSpec = new ViewSpec().SetName(name).SetRowType(columnDescriptor.PropertyType);
var columns = columnNames.Select(c => new ColumnSpec(PropertyPath.Parse(c)));
viewSpec = viewSpec.SetSublistId(PropertyPath.Root.Property(@"Details").LookupAllItems());
viewSpec = viewSpec.SetColumns(columns);
return(new ViewInfo(columnDescriptor, viewSpec).ChangeViewGroup(ViewGroup.BUILT_IN));
}
public void SetPivotReplicate(bool pivot)
{
if (pivot)
{
ViewSpec = ViewSpec.SetSublistId(PropertyPath.Root);
}
else
{
ViewSpec = ViewSpec.SetSublistId(SkylineViewContext.GetReplicateSublist(ViewInfo.ParentColumn.PropertyType));
}
}
private void comboSublist_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeView)
{
return;
}
var sublistItem = comboSublist.SelectedItem as SublistItem;
if (sublistItem != null)
{
ViewSpec = _viewSpec.SetSublistId(sublistItem.IdentifierPath);
}
}
// ReSharper disable NonLocalizedString
public static ViewInfo GetDefaultViewInfo(ColumnDescriptor columnDescriptor)
{
ViewSpec viewSpec = GetDefaultViewSpec(columnDescriptor);
bool addAnnotations = false;
if (columnDescriptor.PropertyType == typeof(TransitionResult))
{
viewSpec = viewSpec.SetColumns(new[]
{
new ColumnSpec().SetName("PrecursorResult.PeptideResult.ResultFile.Replicate"),
new ColumnSpec().SetName("Note"),
new ColumnSpec().SetName("RetentionTime"),
new ColumnSpec().SetName("Fwhm"),
new ColumnSpec().SetName("StartTime"),
new ColumnSpec().SetName("EndTime"),
new ColumnSpec().SetName("Area"),
new ColumnSpec().SetName("Background"),
new ColumnSpec().SetName("AreaRatio"),
new ColumnSpec().SetName("Height"),
new ColumnSpec().SetName("PeakRank"),
});
addAnnotations = true;
}
else if (columnDescriptor.PropertyType == typeof(PrecursorResult))
{
viewSpec = viewSpec.SetColumns(new[]
{
new ColumnSpec().SetName("PeptideResult.ResultFile.Replicate"),
new ColumnSpec().SetName("Note"),
new ColumnSpec().SetName("PrecursorPeakFoundRatio"),
new ColumnSpec().SetName("BestRetentionTime"),
new ColumnSpec().SetName("MaxFwhm"),
new ColumnSpec().SetName("MinStartTime"),
new ColumnSpec().SetName("MaxEndTime"),
new ColumnSpec().SetName("TotalArea"),
new ColumnSpec().SetName("TotalBackground"),
new ColumnSpec().SetName("TotalAreaRatio"),
new ColumnSpec().SetName("MaxHeight"),
new ColumnSpec().SetName("LibraryDotProduct"),
new ColumnSpec().SetName("IsotopeDotProduct"),
});
addAnnotations = true;
}
else if (columnDescriptor.PropertyType == typeof(PeptideResult))
{
viewSpec = viewSpec.SetColumns(new[]
{
new ColumnSpec().SetName("ResultFile.Replicate"),
new ColumnSpec().SetName("PeptidePeakFoundRatio"),
new ColumnSpec().SetName("PeptideRetentionTime"),
new ColumnSpec().SetName("RatioToStandard"),
});
var skylineDataSchema = (SkylineDataSchema)columnDescriptor.DataSchema;
PropertyPath propertyPathReplicate = PropertyPath.Parse("ResultFile.Replicate");
viewSpec = viewSpec.SetColumns(viewSpec.Columns.Concat(
skylineDataSchema.GetAnnotations(typeof(Replicate))
.Select(pd => new ColumnSpec(propertyPathReplicate.Property(pd.Name))))
);
}
else
{
var columnsToRemove = new HashSet <PropertyPath>();
bool addRoot = false;
bool docHasCustomIons = ((SkylineDataSchema)columnDescriptor.DataSchema).Document.CustomIonCount != 0;
bool docHasOnlyCustomIons = docHasCustomIons && ((SkylineDataSchema)columnDescriptor.DataSchema).Document.PeptideCount == 0;
if (columnDescriptor.PropertyType == typeof(Protein))
{
columnsToRemove.Add(PropertyPath.Root.Property("Name"));
if (docHasOnlyCustomIons)
{
// Peptide-oriented fields that make no sense in a small molecule context
columnsToRemove.Add(PropertyPath.Root.Property("Accession"));
columnsToRemove.Add(PropertyPath.Root.Property("PreferredName"));
columnsToRemove.Add(PropertyPath.Root.Property("Gene"));
columnsToRemove.Add(PropertyPath.Root.Property("Species"));
columnsToRemove.Add(PropertyPath.Root.Property("Sequence"));
}
addRoot = true;
}
else if (columnDescriptor.PropertyType == typeof(Entities.Peptide))
{
columnsToRemove.Add(PropertyPath.Root.Property("Sequence"));
columnsToRemove.Add(PropertyPath.Root.Property("PreviousAa"));
columnsToRemove.Add(PropertyPath.Root.Property("NextAa"));
columnsToRemove.Add(PropertyPath.Root.Property("RetentionTimeCalculatorScore"));
columnsToRemove.Add(PropertyPath.Root.Property("DocumentLocation"));
columnsToRemove.Add(PropertyPath.Root.Property("ConcentrationMultiplier"));
columnsToRemove.Add(PropertyPath.Root.Property("InternalStandardConcentration"));
columnsToRemove.Add(PropertyPath.Root.Property("CalibrationCurve"));
if (docHasOnlyCustomIons)
{
// Peptide-oriented fields that make no sense in a small molecule context
columnsToRemove.Add(PropertyPath.Root.Property("ModifiedSequence"));
columnsToRemove.Add(PropertyPath.Root.Property("BeginPos"));
columnsToRemove.Add(PropertyPath.Root.Property("EndPos"));
columnsToRemove.Add(PropertyPath.Root.Property("MissedCleavages"));
}
if (!docHasCustomIons)
{
columnsToRemove.Add(PropertyPath.Root.Property("IonName"));
columnsToRemove.Add(PropertyPath.Root.Property("IonFormula"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitRetentionTime"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitRetentionTimeWindow"));
}
addRoot = true;
}
else if (columnDescriptor.PropertyType == typeof(Precursor))
{
if (docHasOnlyCustomIons)
{
columnsToRemove.Add(PropertyPath.Root.Property("ModifiedSequence"));
columnsToRemove.Add(PropertyPath.Root.Property("IsDecoy"));
}
if (!docHasCustomIons)
{
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitCollisionEnergy"));
columnsToRemove.Add(PropertyPath.Root.Property("IonName"));
columnsToRemove.Add(PropertyPath.Root.Property("IonFormula"));
}
columnsToRemove.Add(PropertyPath.Root.Property("TransitionCount"));
columnsToRemove.Add(PropertyPath.Root.Property("DeclusteringPotential"));
columnsToRemove.Add(PropertyPath.Root.Property("LibraryScore1"));
columnsToRemove.Add(PropertyPath.Root.Property("LibraryScore2"));
columnsToRemove.Add(PropertyPath.Root.Property("LibraryScore3"));
columnsToRemove.Add(PropertyPath.Root.Property("IsDecoy"));
columnsToRemove.Add(PropertyPath.Root.Property("DecoyMzShift"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitDriftTimeMsec"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitDriftTimeHighEnergyOffsetMsec"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitCompensationVoltage"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitDeclusteringPotential"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitSLens"));
columnsToRemove.Add(PropertyPath.Root.Property("ExplicitConeVoltage"));
addRoot = true;
}
else if (columnDescriptor.PropertyType == typeof(Entities.Transition))
{
columnsToRemove.Add(PropertyPath.Root.Property("FragmentIonType"));
columnsToRemove.Add(PropertyPath.Root.Property("FragmentIonOrdinal"));
columnsToRemove.Add(PropertyPath.Root.Property("CleavageAa"));
columnsToRemove.Add(PropertyPath.Root.Property("LossNeutralMass"));
columnsToRemove.Add(PropertyPath.Root.Property("IsDecoy"));
columnsToRemove.Add(PropertyPath.Root.Property("ProductDecoyMzShift"));
columnsToRemove.Add(PropertyPath.Root.Property("IsotopeDistIndex"));
if (docHasOnlyCustomIons)
{
columnsToRemove.Add(PropertyPath.Root.Property("FragmentIon")); // Not interesting - only one product per precursor for small molecules
columnsToRemove.Add(PropertyPath.Root.Property("Losses")); // Doesn't mean anything for non-peptides
}
if (!docHasCustomIons)
{
// Stuff that only applies to small molecules
columnsToRemove.Add(PropertyPath.Root.Property("ProductIonFormula"));
}
addRoot = true;
}
else if (columnDescriptor.PropertyType == typeof(Replicate))
{
columnsToRemove.Add(PropertyPath.Root.Property("Name"));
addRoot = true;
}
viewSpec = viewSpec.SetSublistId(GetReplicateSublist(columnDescriptor.PropertyType));
if (addRoot)
{
viewSpec = viewSpec.SetColumns(new[] { new ColumnSpec(PropertyPath.Root) }.Concat(viewSpec.Columns));
}
viewSpec = viewSpec.SetColumns(viewSpec.Columns
.Where(columnSpec => !columnsToRemove.Contains(columnSpec.PropertyPath)));
}
if (addAnnotations)
{
var skylineDataSchema = (SkylineDataSchema)columnDescriptor.DataSchema;
viewSpec = viewSpec.SetColumns(viewSpec.Columns.Concat(
skylineDataSchema.GetAnnotations(columnDescriptor.PropertyType)
.Select(pd => new ColumnSpec(PropertyPath.Root.Property(pd.Name)))));
}
return(new ViewInfo(columnDescriptor, viewSpec).ChangeViewGroup(ViewGroup.BUILT_IN));
}