private static ViewSpec MapViewSpec(IEnumerable <KeyValuePair <PropertyPath, PropertyPath> > mapping, ViewSpec viewSpec, Type newRowType)
{
viewSpec = viewSpec.SetColumns(viewSpec.Columns.Select(
col => col.SetPropertyPath(MapPropertyPath(mapping, col.PropertyPath))));
viewSpec = viewSpec.SetFilters(viewSpec.Filters.Select(
filter => filter.SetColumnId(MapPropertyPath(mapping, filter.ColumnId))));
//viewSpec = viewSpec.SetSublistId(MapPropertyPath(mapping, viewSpec.SublistId));
viewSpec = viewSpec.SetRowType(newRowType);
return(viewSpec);
}
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 static ViewSpec PivotIsotopeLabel(ViewSpec viewSpec, bool pivot)
{
PropertyPath pivotKey;
IList<PropertyPath> groupBy;
IList<PropertyPath> crossTabExclude;
IList<PropertyPath> crosstabValues;
if (viewSpec.RowSource == typeof (Precursor).FullName)
{
pivotKey = PropertyPath.Root.Property("IsotopeLabelType");
groupBy = new[]
{
PropertyPath.Root.Property("Peptide"),
PropertyPath.Root.Property("Charge"),
};
crosstabValues = PrecursorCrosstabValues;
crossTabExclude = new []{PropertyPath.Parse("Results!*.Value.PeptideResult")};
}
else if (viewSpec.RowSource == typeof (Transition).FullName)
{
pivotKey = PropertyPath.Root.Property("Precursor").Property("IsotopeLabelType");
groupBy = new[]
{
PropertyPath.Root.Property("ProductCharge"),
PropertyPath.Root.Property("FragmentIon"),
PropertyPath.Root.Property("Losses"),
PropertyPath.Root.Property("Precursor").Property("Peptide"),
PropertyPath.Root.Property("Precursor").Property("Charge"),
};
crosstabValues = new[]
{
PropertyPath.Root.Property("ProductNeutralMass"),
PropertyPath.Root.Property("ProductMz"),
PropertyPath.Root.Property("Note"),
PropertyPath.Root.Property("Results").LookupAllItems(),
PropertyPath.Root.Property("ResultSummary"),
}.Concat(PrecursorCrosstabValues.Select(
propertyPath => PropertyPath.Root.Property("Precursor").Concat(propertyPath)))
.ToArray();
crossTabExclude = new[] {PropertyPath.Parse("Results!*.Value.PrecursorResult.PeptideResult")};
}
else
{
return viewSpec;
}
var newColumns = new List<ColumnSpec>();
if (!pivot)
{
foreach (var column in viewSpec.Columns)
{
if (!column.Hidden)
{
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
}
}
else
{
bool pivotKeyHandled = false;
var missingGroupBy = new HashSet<PropertyPath>(groupBy);
foreach (var column in viewSpec.Columns)
{
if (pivotKey.Equals(column.PropertyPath))
{
pivotKeyHandled = true;
newColumns.Add(column.SetTotal(TotalOperation.PivotKey));
}
else if (crossTabExclude.Any(propertyPath => column.PropertyPath.StartsWith(propertyPath)))
{
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
else if (crosstabValues.Any(propertyPath => column.PropertyPath.StartsWith(propertyPath)))
{
newColumns.Add(column.SetTotal(TotalOperation.PivotValue));
}
else
{
missingGroupBy.Remove(column.PropertyPath);
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
}
if (!pivotKeyHandled)
{
newColumns.Add(new ColumnSpec(pivotKey).SetTotal(TotalOperation.PivotKey).SetHidden(true));
}
if (missingGroupBy.Count > 0)
{
foreach (var propertyPath in groupBy)
{
if (!missingGroupBy.Contains(propertyPath))
{
continue;
}
newColumns.Add(new ColumnSpec(propertyPath).SetTotal(TotalOperation.GroupBy).SetHidden(true));
}
}
}
return viewSpec.SetColumns(newColumns);
}
// 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));
}
public static ViewSpec PivotIsotopeLabel(ViewSpec viewSpec, bool pivot)
{
PropertyPath pivotKey;
IList <PropertyPath> groupBy;
IList <PropertyPath> crossTabExclude;
IList <PropertyPath> crosstabValueStartsWith;
IList <PropertyPath> crosstabValueExact;
if (viewSpec.RowSource == typeof(Precursor).FullName)
{
pivotKey = PropertyPath.Root.Property("IsotopeLabelType");
groupBy = new[]
{
PropertyPath.Root.Property("Peptide"),
PropertyPath.Root.Property("Charge"),
};
crosstabValueStartsWith = PrecursorCrosstabValueStartsWith;
crosstabValueExact = PrecursorCrosstabValueExact;
crossTabExclude = new [] { PropertyPath.Parse("Results!*.Value.PeptideResult") };
}
else if (viewSpec.RowSource == typeof(Transition).FullName)
{
pivotKey = PropertyPath.Root.Property("Precursor").Property("IsotopeLabelType");
groupBy = new[]
{
PropertyPath.Root.Property("ProductCharge"),
PropertyPath.Root.Property("FragmentIon"),
PropertyPath.Root.Property("Losses"),
PropertyPath.Root.Property("Precursor").Property("Peptide"),
PropertyPath.Root.Property("Precursor").Property("Charge"),
};
crosstabValueStartsWith = new[]
{
PropertyPath.Root.Property("ProductNeutralMass"),
PropertyPath.Root.Property("ProductMz"),
PropertyPath.Root.Property("Note"),
PropertyPath.Root.Property("Results").LookupAllItems(),
PropertyPath.Root.Property("ResultSummary"),
}.Concat(PrecursorCrosstabValueStartsWith.Select(
propertyPath => PropertyPath.Root.Property("Precursor").Concat(propertyPath)))
.ToArray();
crosstabValueExact = PrecursorCrosstabValueExact.Select(
propertyPath => PropertyPath.Root.Property("Precursor").Concat(propertyPath))
.ToArray();
crossTabExclude = new[] { PropertyPath.Parse("Results!*.Value.PrecursorResult.PeptideResult") };
}
else
{
return(viewSpec);
}
var newColumns = new List <ColumnSpec>();
if (!pivot)
{
foreach (var column in viewSpec.Columns)
{
if (!column.Hidden)
{
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
}
}
else
{
bool pivotKeyHandled = false;
var missingGroupBy = new HashSet <PropertyPath>(groupBy);
foreach (var column in viewSpec.Columns)
{
if (pivotKey.Equals(column.PropertyPath))
{
pivotKeyHandled = true;
newColumns.Add(column.SetTotal(TotalOperation.PivotKey));
}
else if (crossTabExclude.Any(propertyPath => column.PropertyPath.StartsWith(propertyPath)))
{
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
else if (crosstabValueStartsWith.Any(propertyPath => column.PropertyPath.StartsWith(propertyPath)) ||
crosstabValueExact.Any(propertyPath => column.PropertyPath.Equals(propertyPath)))
{
newColumns.Add(column.SetTotal(TotalOperation.PivotValue));
}
else
{
missingGroupBy.Remove(column.PropertyPath);
newColumns.Add(column.SetTotal(TotalOperation.GroupBy));
}
}
if (!pivotKeyHandled)
{
newColumns.Add(new ColumnSpec(pivotKey).SetTotal(TotalOperation.PivotKey).SetHidden(true));
}
if (missingGroupBy.Count > 0)
{
foreach (var propertyPath in groupBy)
{
if (!missingGroupBy.Contains(propertyPath))
{
continue;
}
newColumns.Add(new ColumnSpec(propertyPath).SetTotal(TotalOperation.GroupBy).SetHidden(true));
}
}
}
return(viewSpec.SetColumns(newColumns));
}