/// <summary>
/// Generate all possible combinations of glycans and peptides within the constraints of number of glycosylations
/// on a given peptide. Represent each combination as a GlycopeptideComposition.
/// </summary>
public void BuildCompositionHypothesis()
{
int peptideIter = 0;
foreach (MSDigestPeptide peptide in Peptides)
{
peptideIter++;
//Console.WriteLine("Working on Peptide {0}, {1}", peptideIter, peptide);
//Creates the unglycosylated peptide composition row.
GlycopeptideComposition rawPeptideComposition = new GlycopeptideComposition(peptide);
int numGlycosylations = rawPeptideComposition.GlycosylationCount;
rawPeptideComposition.GlycosylationCount = 0;
//If there were no glycosylations on this peptide to begin with, this step is done!
if (numGlycosylations == 0)
{
if (KeepUnglycosylatedPeptides)
{
GlycopeptideComposition.Compositions.Add(rawPeptideComposition);
}
continue;
}
//This is a combinations with replacement problem, meaning that the number of choices with each iteration does not shrink and order does not matter.
//Since convergent glycan compositions cannot be distinguished, we may be able to reduce the total number generated.
//Console.WriteLine("[{4}] This peptide has {0} (K) glycosylation sites, and there are {1} (N) glycans to choose from. Combinations = {2} new objects without convergent compositions. Current Memory Size: {3} ", numGlycosylations, GlycanCompositions.Compositions.Count, Numerics.Combinations(GlycanCompositions.Compositions.Count, numGlycosylations), GC.GetTotalMemory(false), peptideIter++);
//Represent the iterative increase in glycosylation as a set of queues. Each possible glycoform
//is generated incrementally from previously generated set of compositions. We only need the set of
//compositions we created from the last iteration to build the next iteration.
//I use a Queue here because C#'s List API doesn't have a notion of get-and-remove, and removing
Queue<GlycopeptideComposition> previousCompositions = new Queue<GlycopeptideComposition>();
Queue<GlycopeptideComposition> nextCompositions = new Queue<GlycopeptideComposition>();
previousCompositions.Enqueue(rawPeptideComposition);
for (int depthIter = 0; depthIter < numGlycosylations; depthIter++)
{
Dictionary<string, bool> glycanCompositionCache = new Dictionary<string, bool>();
int lengthOfPrevious = previousCompositions.Count;
while (previousCompositions.Count > 0)
{
GlycopeptideComposition template = previousCompositions.Dequeue();
GlycopeptideComposition.Compositions.Add(template);
foreach (GlycanComposition glycan in this.GlycanCompositions.Compositions)
{
GlycopeptideComposition instance = new GlycopeptideComposition(template);
instance.AttachGlycan(glycan);
string glycanTuple = instance.GlycanCompositionTuple(GlycopeptideComposition.MoleculeNames);
if (glycanCompositionCache.ContainsKey(glycanTuple))
{
continue;
}
else
{
glycanCompositionCache.Add(glycanTuple, true);
}
nextCompositions.Enqueue(instance);
}
}
int lengthOfNext = nextCompositions.Count;
Console.WriteLine("Length of run: {0:N}", lengthOfNext);
previousCompositions = nextCompositions;
nextCompositions = new Queue<GlycopeptideComposition>();
//Console.WriteLine("[{5}]{0} * {1} = {2}. Generated {3}. Saved {6}%\nMemory Size: {4}", lengthOfPrevious, GlycanCompositions.Compositions.Count, lengthOfPrevious * GlycanCompositions.Compositions.Count, lengthOfNext, GC.GetTotalMemory(false), depthIter, (1 - (lengthOfNext / (double)(lengthOfPrevious * GlycanCompositions.Compositions.Count))) * 100);
}
//After the last pass through the loop, previousComposition still holds all of the most recently generated values,
//so we need to add them to the total list.
GlycopeptideComposition.Compositions.AddRange(previousCompositions);
}
Console.WriteLine("Build complete.");
}
/// <summary>
/// Copy Constructor
/// </summary>
/// <param name="other"></param>
public GlycopeptideComposition(GlycopeptideComposition other)
: base(other as GlycanComposition)
{
this.MissedCleavages = other.MissedCleavages;
this.GlycosylationCount = other.GlycosylationCount;
this.StartAA = other.StartAA;
this.EndAA = other.EndAA;
this.PeptideSequence = other.PeptideSequence;
this.PeptideModification = other.PeptideModification;
this.ProteinID = other.ProteinID;
}