public ViewSpec()
{
Columns = ImmutableList.Empty <ColumnSpec>();
Filters = ImmutableList.Empty <FilterSpec>();
}
private IList <RunAbundance> SummarizeDataRowsWithMedianPolish(IList <DataRowDetails> dataRows)
{
IList <IGrouping <IdentityPath, DataRowDetails> > dataRowsByFeature =
SumMs1Transitions(dataRows).ToLookup(row => row.IdentityPath)
.Where(IncludeFeatureForMedianPolish)
.ToArray();
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
if (false)
{
// For debugging purposes, we might want to order these features in the same order as MSstats R code
Array.Sort((IGrouping <IdentityPath, DataRowDetails>[])dataRowsByFeature, (group1, group2) =>
{
String s1 = GetFeatureKey(SrmDocument, group1.Key);
String s2 = GetFeatureKey(SrmDocument, group2.Key);
return(String.Compare(s1.ToLowerInvariant(), s2.ToLowerInvariant(), StringComparison.Ordinal));
});
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
var featureCount = dataRowsByFeature.Count;
if (featureCount == 0)
{
return(ImmutableList.Empty <RunAbundance>());
}
var rows = new List <double?[]>();
IDictionary <int, int> replicateRowIndexes = new Dictionary <int, int>();
for (int iFeature = 0; iFeature < dataRowsByFeature.Count; iFeature++)
{
foreach (DataRowDetails dataRowDetails in dataRowsByFeature[iFeature])
{
int rowIndex;
if (!replicateRowIndexes.TryGetValue(dataRowDetails.ReplicateIndex, out rowIndex))
{
rowIndex = rows.Count;
rows.Add(new double?[featureCount]);
replicateRowIndexes.Add(dataRowDetails.ReplicateIndex, rowIndex);
}
var row = rows[rowIndex];
row[iFeature] = dataRowDetails.GetLog2Abundance();
}
}
var matrix = new double?[rows.Count, featureCount];
for (int iRow = 0; iRow < rows.Count; iRow++)
{
for (int iCol = 0; iCol < featureCount; iCol++)
{
matrix[iRow, iCol] = rows[iRow][iCol];
}
}
var medianPolish = MedianPolish.GetMedianPolish(matrix);
List <RunAbundance> runAbundances = new List <RunAbundance>();
foreach (var replicateIndexDetails in _replicateIndexes)
{
int rowIndex;
if (!replicateRowIndexes.TryGetValue(replicateIndexDetails.Key, out rowIndex))
{
continue;
}
double value = medianPolish.OverallConstant + medianPolish.RowEffects[rowIndex];
runAbundances.Add(new RunAbundance()
{
ReplicateIndex = replicateIndexDetails.Key,
BioReplicate = replicateIndexDetails.Value.BioReplicate,
Control = replicateIndexDetails.Value.IsControl,
Log2Abundance = value
});
}
return(runAbundances);
}
public PivotedProperties(ItemProperties itemProperties) : this(itemProperties, ImmutableList.Empty <SeriesGroup>())
{
}
private RowFilter()
{
Text = null;
CaseSensitive = true;
ColumnFilters = ImmutableList.Empty <ColumnFilter>();
}
/// <summary>
/// Ensure that the document peptide settings contain all of the necessary heavy label types (i.e. "heavy1", "heavy2", ...)
/// to accomodate the specified number of possible permutations.
/// </summary>
public SrmDocument EnsureLabelTypes(IProgressMonitor progressMonitor, SrmDocument document, int maxPermutationCount, List <IsotopeLabelType> partialLabelTypes)
{
if (partialLabelTypes.Count == 0)
{
partialLabelTypes.Add(IsotopeLabelType.light);
}
var labelTypesByName = document.Settings.PeptideSettings.Modifications.GetHeavyModificationTypes()
.ToDictionary(label => label.Name);
int maxSortValue = 0;
if (labelTypesByName.Any())
{
maxSortValue = labelTypesByName.Values.Max(label => label.SortOrder);
}
var labelTypesToAdd = new List <IsotopeLabelType>();
for (int i = partialLabelTypes.Count; i < maxPermutationCount - 1; i++)
{
if (progressMonitor.IsCanceled)
{
throw new OperationCanceledException();
}
var name = FullyHeavyLabelType.Name + i;
IsotopeLabelType labelType;
if (!labelTypesByName.TryGetValue(name, out labelType))
{
labelType = new IsotopeLabelType(name, ++maxSortValue);
labelTypesToAdd.Add(labelType);
}
partialLabelTypes.Add(labelType);
}
if (!labelTypesByName.ContainsKey(FullyHeavyLabelType.Name))
{
labelTypesToAdd.Add(FullyHeavyLabelType);
}
if (labelTypesToAdd.Any())
{
var settings = document.Settings;
var heavyModifications = settings.PeptideSettings.Modifications.HeavyModifications.ToList();
heavyModifications.AddRange(labelTypesToAdd.Select(labelType => new TypedModifications(labelType, ImmutableList.Empty <StaticMod>())));
var peptideModifications = settings.PeptideSettings.Modifications;
peptideModifications = new PeptideModifications(peptideModifications.StaticModifications, peptideModifications.MaxVariableMods, peptideModifications.MaxNeutralLosses,
heavyModifications, peptideModifications.InternalStandardTypes);
settings = settings.ChangePeptideSettings(settings.PeptideSettings.ChangeModifications(peptideModifications));
document = document.ChangeSettings(settings);
}
return(document);
}
private ProcessingQueue()
: this(ImmutableList.Empty <IProcessingStep>())
{
}
public static RowItemValues Empty(Type propertyType)
{
return(new RowItemValues(propertyType, ImmutableList.Empty <ColumnDescriptor>(),
ImmutableList.Empty <PivotKey>(), ImmutableList.Empty <DataPropertyDescriptor>()));
}
public ViewSpec()
{
Columns = ImmutableList.Empty <ColumnSpec>();
Filters = ImmutableList.Empty <FilterSpec>();
UiMode = string.Empty;
}
