public PeptideSubIndex(IEnumerable <IndexItem> items)
{
_entries = new Dictionary <string, ImmutableList <PeptideEntry> >();
var singletonIndexes = new Dictionary <int, ImmutableList <int> >();
var indexes = new Dictionary <ImmutableList <int>, ImmutableList <int> >();
var modIndexComparer = Comparer <IList <int> > .Create(CompareModificationIndexes);
foreach (var group in items.Where(item => item.LibraryKey is PeptideLibraryKey)
.ToLookup(item => ((PeptideLibraryKey)item.LibraryKey).UnmodifiedSequence))
{
_entries.Add(group.Key, ImmutableList.ValueOf(group
.Select(item => PeptideEntry.NewInstance(singletonIndexes, indexes, item))
.OrderBy(entry => entry.ModificationIndexes, modIndexComparer)));
}
Count = _entries.Values.Sum(list => list.Count);
}
/// <summary>
/// Returns the set of entries with modifications on the same amino acids.
/// </summary>
private IEnumerable <PeptideEntry> ModificationIndexMatches(PeptideLibraryKey peptideLibraryKey,
[CanBeNull] out IList <KeyValuePair <int, string> > modifications)
{
modifications = null;
ImmutableList <PeptideEntry> entries;
if (!_entries.TryGetValue(peptideLibraryKey.UnmodifiedSequence, out entries))
{
return(ImmutableList <PeptideEntry> .EMPTY);
}
modifications = peptideLibraryKey.GetModifications();
var peptideEntry = new PeptideEntry(new IndexItem(peptideLibraryKey, -1), modifications);
var range = CollectionUtil.BinarySearch(entries, item => item.CompareModIndexes(peptideEntry));
return(Enumerable.Range(range.Start, range.Length)
.Select(index => entries[index]));
}
/// <summary>
/// Constructs a new PeptideEntry, and reuses ImmutableList values from the
/// passed in dictionaries to prevent redundant object creation.
/// </summary>
public static PeptideEntry NewInstance(IDictionary <int, ImmutableList <int> > singletonIndexCache,
IDictionary <ImmutableList <int>, ImmutableList <int> > indexCache, IndexItem indexItem)
{
var peptideEntry = new PeptideEntry(indexItem,
((PeptideLibraryKey)indexItem.LibraryKey).GetModifications());
if (peptideEntry.ModificationIndexes.Count == 0)
{
return(peptideEntry);
}
ImmutableList <int> newIndexes;
if (peptideEntry.ModificationIndexes.Count == 1)
{
if (singletonIndexCache.TryGetValue(peptideEntry.ModificationIndexes[0], out newIndexes))
{
peptideEntry.ModificationIndexes = newIndexes;
}
else
{
singletonIndexCache.Add(peptideEntry.ModificationIndexes[0], peptideEntry.ModificationIndexes);
}
}
else
{
if (indexCache.TryGetValue(peptideEntry.ModificationIndexes, out newIndexes))
{
peptideEntry.ModificationIndexes = newIndexes;
}
else
{
indexCache.Add(peptideEntry.ModificationIndexes, peptideEntry.ModificationIndexes);
}
}
return(peptideEntry);
}
public int CompareModIndexes(PeptideEntry that)
{
return(CompareModificationIndexes(ModificationIndexes, that.ModificationIndexes));
}
