public ReplicateGroup(string groupName, ReplicateIndexSet replicateIndexes, ChromFileInfo fileInfo = null, bool isAllGroup = false)
{
GroupName = groupName;
FileInfo = fileInfo;
ReplicateIndexes = replicateIndexes;
IsAllGroup = isAllGroup;
}
private void AddReplicateGroup(ICollection <ReplicateGroup> replicateGroups, DocNode docNode, int replicateIndex)
{
var nodeGroup = docNode as TransitionGroupDocNode;
if (nodeGroup != null)
{
var chromSet = _document.MeasuredResults.Chromatograms[replicateIndex];
foreach (var c in nodeGroup.ChromInfos)
{
var info = chromSet.GetFileInfo(c.FileId);
if (info != null)
{
replicateGroups.Add(new ReplicateGroup(chromSet.Name, ReplicateIndexSet.Singleton(replicateIndex), info));
}
}
return;
}
var nodePep = docNode as PeptideDocNode;
if (nodePep != null)
{
nodePep.TransitionGroups.ForEach(n => AddReplicateGroup(replicateGroups, n, replicateIndex));
}
}
private void InsertAllGroupsAndPointPairLists(string[] uniqueGroupNames, int docNodeCount)
{
var uniqueGroups = uniqueGroupNames.Select(n => new ReplicateGroup(n,
ReplicateIndexSet.OfValues(ReplicateGroups.Where(r => r.GroupName == n).SelectMany(r => r.ReplicateIndexes)),
null, true));
var newGroups = ReplicateGroups.ToList();
foreach (var group in uniqueGroups)
{
var group1 = group;
var firstIndex = newGroups.IndexOf(r => r.GroupName == group1.GroupName);
newGroups.Insert(firstIndex, group);
for (var node = 0; node < docNodeCount; ++node)
{
for (var step = 0; step < PointPairLists[node].Count; ++step)
{
if (PointPairLists[node][step].Any())
{
PointPairLists[node][step].Insert(firstIndex, new PointPair(firstIndex, double.NaN));
}
}
}
}
ReplicateGroups = newGroups;
}
private IEnumerable <ReplicateGroup> GetReplicateGroups(IEnumerable <int> replicateIndexes)
{
var chromatograms = _document.Settings.MeasuredResults.Chromatograms;
if (ReplicateGroupOp.GroupByAnnotation == null)
{
return
(replicateIndexes.Select(replicateIndex
=> new ReplicateGroup(chromatograms[replicateIndex].Name,
ReplicateIndexSet.Singleton(replicateIndex))));
}
var lookup = replicateIndexes.ToLookup(replicateIndex => chromatograms[replicateIndex].Annotations.GetAnnotation(ReplicateGroupOp.GroupByAnnotation));
var keys = lookup.Select(grouping => grouping.Key).ToList();
if (keys.Count > 2)
{
// If there are more than 2 groups then exclude replicates with blank annotation values.
keys.Remove(null);
}
keys.Sort();
// ReSharper disable AssignNullToNotNullAttribute
return(keys.Select(key => new ReplicateGroup((key ?? string.Empty).ToString(), ReplicateIndexSet.OfValues(lookup[key]))));
// ReSharper restore AssignNullToNotNullAttribute
}
protected virtual IEnumerable <ReplicateGroup> GetReplicateGroups(IEnumerable <int> replicateIndexes)
{
if (_document.Settings.MeasuredResults == null)
{
return(new ReplicateGroup[0]); // Likely user removed all results while Mass Errors window was open
}
var annotationCalculator = new AnnotationCalculator(_document);
var chromatograms = _document.Settings.MeasuredResults.Chromatograms;
var result = new List <ReplicateGroup>();
if (ReplicateGroupOp.GroupByValue == null)
{
foreach (var index in replicateIndexes)
{
var chromatogram = _document.MeasuredResults.Chromatograms[index];
result.AddRange(chromatogram.MSDataFileInfos.Select(fileInfo => new ReplicateGroup(chromatogram.Name, ReplicateIndexSet.Singleton(index), fileInfo)));
}
var query = result.OrderBy(g => 0);
if (!string.IsNullOrEmpty(OrderByReplicateAnnotation))
{
var orderByReplicateValue = ReplicateValue.FromPersistedString(_document.Settings, OrderByReplicateAnnotation);
if (orderByReplicateValue != null)
{
query = result.OrderBy(
g => orderByReplicateValue.GetValue(annotationCalculator,
chromatograms[g.ReplicateIndexes.First()]), CollectionUtil.ColumnValueComparer);
}
}
if (ReplicateOrder == SummaryReplicateOrder.document)
{
result = new List <ReplicateGroup>(query.ThenBy(g => g.ReplicateIndexes.ToArray(),
Comparer <int[]> .Create((a, b) =>
{
for (var i = 0; i < Math.Min(a.Length, b.Length); ++i)
{
if (a[i] != b[i])
{
return(a[i].CompareTo(b[i]));
}
}
return(a.Length.CompareTo(b.Length));
})).ThenBy(g => g.FileInfo.FileIndex));
}
else if (ReplicateOrder == SummaryReplicateOrder.time)
{
result = new List <ReplicateGroup>(query
.ThenBy(g => g.FileInfo.RunStartTime,
Comparer <DateTime?> .Create(
(a, b) => (a ?? DateTime.MaxValue).CompareTo(
b ?? DateTime.MaxValue))).ThenBy(g => g.FileInfo.FileIndex).ToList());
}
}
else
{
var lookup = replicateIndexes.ToLookup(replicateIndex =>
ReplicateGroupOp.GroupByValue.GetValue(annotationCalculator, chromatograms[replicateIndex]));
var keys = lookup.Select(grouping => grouping.Key).ToList();
if (keys.Count > 2)
{
// If there are more than 2 groups then exclude replicates with blank annotation values.
keys.Remove(null);
}
keys.Sort(CollectionUtil.ColumnValueComparer);
// ReSharper disable AssignNullToNotNullAttribute
foreach (var key in keys)
{
result.Add(new ReplicateGroup(key?.ToString() ?? string.Empty, ReplicateIndexSet.OfValues(lookup[key])));
}
// ReSharper restore AssignNullToNotNullAttribute
}
return(result.Distinct());
}
public ReplicateGroup(string groupName, ReplicateIndexSet replicateIndexes)
{
GroupName = groupName;
ReplicateIndexes = replicateIndexes;
}