public static int DescendingSummedMorpheusScoreProteinGroupComparison(ProteinGroup left, ProteinGroup right)
{
int comparison = -(left.SummedMorpheusScore.CompareTo(right.SummedMorpheusScore));
if (comparison != 0)
{
return(comparison);
}
else
{
return(left.Target.CompareTo(right.Target));
}
}
public static List <ProteinGroup> ApplyProteinParsimony(IEnumerable <PeptideSpectrumMatch> peptideSpectrumMatches, double morpheusScoreThreshold, FileStream proteinFastaDatabase, bool onTheFlyDecoys, IDictionary <string, Modification> knownVariableModifications, Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior, int maximumThreads)
{
// make a list of the all the distinct base leucine peptide sequences
Dictionary <string, List <Protein> > peptide_proteins = new Dictionary <string, List <Protein> >();
foreach (PeptideSpectrumMatch psm in peptideSpectrumMatches)
{
if (psm.MorpheusScore >= morpheusScoreThreshold)
{
if (!peptide_proteins.ContainsKey(psm.Peptide.BaseLeucineSequence))
{
peptide_proteins.Add(psm.Peptide.BaseLeucineSequence, new List <Protein>());
}
}
}
// record all proteins that could have been the source of each peptide
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Parallel.ForEach(ProteomeDatabaseReader.ReadProteins(proteinFastaDatabase, onTheFlyDecoys, REQUIRE_MATCHING_KNOWN_MODIFICATIONS_IN_PROTEIN_PARSIMONY ? knownVariableModifications : null), parallel_options, protein =>
{
foreach (Peptide peptide in protein.Digest(protease, maximumMissedCleavages, initiatorMethionineBehavior, null, null))
{
lock (peptide_proteins)
{
List <Protein> proteins;
if (peptide_proteins.TryGetValue(peptide.BaseLeucineSequence, out proteins))
{
List <Peptide> peptides;
if (!protein.IdentifiedPeptides.TryGetValue(peptide.BaseLeucineSequence, out peptides))
{
peptides = new List <Peptide>();
peptides.Add(peptide);
protein.IdentifiedPeptides.Add(peptide.BaseLeucineSequence, peptides);
}
else
{
peptides.Add(peptide);
}
proteins.Add(protein);
}
}
}
}
);
// create protein groups (initially with just one protein each) and assign PSMs to them
Dictionary <string, ProteinGroup> proteins_by_description = new Dictionary <string, ProteinGroup>();
foreach (PeptideSpectrumMatch psm in peptideSpectrumMatches)
{
if (psm.MorpheusScore >= morpheusScoreThreshold)
{
foreach (Protein protein in peptide_proteins[psm.Peptide.BaseLeucineSequence])
{
if (REQUIRE_MATCHING_KNOWN_MODIFICATIONS_IN_PROTEIN_PARSIMONY)
{
// check to make sure this protein's known modifications match the PSM's
bool known_modification_match = true;
if (psm.Peptide.VariableModifications != null && psm.Peptide.VariableModifications.Count > 0)
{
foreach (KeyValuePair <int, Modification> kvp in psm.Peptide.VariableModifications)
{
if (kvp.Value.Known)
{
List <Modification> protein_modifications = null;
if (protein.KnownModifications == null ||
!protein.KnownModifications.TryGetValue(psm.Peptide.StartResidueNumber - 1 + kvp.Key, out protein_modifications) ||
!protein_modifications.Contains(kvp.Value))
{
known_modification_match = false;
break;
}
}
}
if (!known_modification_match)
{
continue;
}
}
}
ProteinGroup protein_group;
if (!proteins_by_description.TryGetValue(protein.Description, out protein_group))
{
protein_group = new ProteinGroup();
protein_group.Add(protein);
protein_group.PeptideSpectrumMatches.Add(psm);
proteins_by_description.Add(protein.Description, protein_group);
}
else
{
protein_group.PeptideSpectrumMatches.Add(psm);
}
}
}
}
List <ProteinGroup> protein_groups = new List <ProteinGroup>(proteins_by_description.Values);
protein_groups.Sort(ProteinGroup.DescendingSummedMorpheusScoreProteinGroupComparison);
// todo: remove shared peptides from lower-scoring protein group?
// merge indistinguishable proteins (technically protein groups but they only contain a single protein thus far)
for (int i = 0; i < protein_groups.Count - 1; i++)
{
ProteinGroup protein_group = protein_groups[i];
int j = i + 1;
while (j < protein_groups.Count)
{
ProteinGroup lower_protein_group = protein_groups[j];
if (lower_protein_group.SummedMorpheusScore < protein_group.SummedMorpheusScore)
{
break;
}
if (lower_protein_group.BaseLeucinePeptideSequences.SetEquals(protein_group.BaseLeucinePeptideSequences))
{
protein_group.UnionWith(lower_protein_group); // should only ever be one protein in the group to add
protein_groups.RemoveAt(j);
}
else
{
j++;
}
}
}
// remove subset and subsumable protein groups
int k = protein_groups.Count - 1;
while (k >= 1)
{
ProteinGroup protein_group = protein_groups[k];
HashSet <string> protein_group_peptides = new HashSet <string>(protein_group.BaseLeucinePeptideSequences);
for (int l = 0; l < k; l++)
{
ProteinGroup higher_protein_group = protein_groups[l];
protein_group_peptides.ExceptWith(higher_protein_group.BaseLeucinePeptideSequences);
if (protein_group_peptides.Count == 0)
{
break;
}
}
if (protein_group_peptides.Count == 0)
{
protein_groups.RemoveAt(k);
}
k--;
}
return(protein_groups);
}
