public DatabaseSearcherThreadLocalStorage(bool minimize_memory_usage, int psms_length)
{
this.num_target_peptides = 0;
this.num_decoy_peptides = 0;
this.proteins = 0;
if (!minimize_memory_usage)
this.peptides_observed = new Dictionary<FastSubstring, bool>(new LeucineSequenceEqualityComparer());
else
this.peptides_observed = null;
digested_peptides_buf = new FastListOfBoxes<Peptide>(1000);
modified_peptides_buf = new FastListOfBoxes<Peptide>(1000);
fixed_modifications_buf = new Dictionary<int, List<Modification>>(1000);
possible_modifications_buf = new Dictionary<int, List<Modification>>(1000);
mass_spectra_indices_buf = new List<int>(1000);
product_masses_buf = new double[1000];
fast_q_sorter = new FastQSorter();
psm = new PeptideSpectrumMatch();
psms = new PeptideSpectrumMatch[psms_length];
}
// This method figures out the variable modifications of the current
// peptide and stores them in the argument out_peptides. (The
// out_peptides list is cleared before the new variably modified
// peptides are added to it.)
//
// The variable out_possible_modifications is used for temporary,
// intermediate storage. We pass in this dictionary instead of
// allocating a new one inside the method because profiling showed that
// a large number of dictionaries were allocated by this method.
// (However, since each dictionary entry is itself a list of
// modifications, and these are still newly allocated by this method,
// it isn't clear how much is really saved, in practice, by reusing
// only the dictionary. Further optimization might be beneficial here.)
// This dictionary is not useful outside this method, only internally.
//
// To be clear: The arguments out_peptides and
// out_possible_modifications are modified by this method.
public void GetVariablyModifiedPeptides(IEnumerable<Modification> variableModifications, int maximumVariableModificationIsoforms,
FastListOfBoxes<Peptide> out_peptides,
Dictionary<int, List<Modification>> out_possible_modifications)
{
out_peptides.Clear();
out_possible_modifications.Clear();
foreach(Modification variable_modification in variableModifications)
{
if(variable_modification.Type == ModificationType.ProteinNTerminus && (StartResidueNumber == 1 || (StartResidueNumber == 2 && Parent[0] == 'M'))
&& (variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List<Modification> prot_n_term_variable_mods;
if(!out_possible_modifications.TryGetValue(0, out prot_n_term_variable_mods))
{
prot_n_term_variable_mods = new List<Modification>();
prot_n_term_variable_mods.Add(variable_modification);
out_possible_modifications.Add(0, prot_n_term_variable_mods);
}
else
{
prot_n_term_variable_mods.Add(variable_modification);
}
}
if(variable_modification.Type == ModificationType.PeptideNTerminus && (variable_modification.AminoAcid == char.MinValue || this[0] == variable_modification.AminoAcid))
{
List<Modification> pep_n_term_variable_mods;
if(!out_possible_modifications.TryGetValue(1, out pep_n_term_variable_mods))
{
pep_n_term_variable_mods = new List<Modification>();
pep_n_term_variable_mods.Add(variable_modification);
out_possible_modifications.Add(1, pep_n_term_variable_mods);
}
else
{
pep_n_term_variable_mods.Add(variable_modification);
}
}
for(int r = 0; r < Length; r++)
{
if(variable_modification.Type == ModificationType.AminoAcidResidue && this[r] == variable_modification.AminoAcid)
{
List<Modification> residue_variable_mods;
if(!out_possible_modifications.TryGetValue(r + 2, out residue_variable_mods))
{
residue_variable_mods = new List<Modification>();
residue_variable_mods.Add(variable_modification);
out_possible_modifications.Add(r + 2, residue_variable_mods);
}
else
{
residue_variable_mods.Add(variable_modification);
}
}
}
if(variable_modification.Type == ModificationType.PeptideCTerminus && (variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List<Modification> pep_c_term_variable_mods;
if(!out_possible_modifications.TryGetValue(Length + 2, out pep_c_term_variable_mods))
{
pep_c_term_variable_mods = new List<Modification>();
pep_c_term_variable_mods.Add(variable_modification);
out_possible_modifications.Add(Length + 2, pep_c_term_variable_mods);
}
else
{
pep_c_term_variable_mods.Add(variable_modification);
}
}
if(variable_modification.Type == ModificationType.ProteinCTerminus && (EndResidueNumber == Parent.Length - 1)
&& (variable_modification.AminoAcid == char.MinValue || this[Length - 1] == variable_modification.AminoAcid))
{
List<Modification> prot_c_term_variable_mods;
if(!out_possible_modifications.TryGetValue(Length + 3, out prot_c_term_variable_mods))
{
prot_c_term_variable_mods = new List<Modification>();
prot_c_term_variable_mods.Add(variable_modification);
out_possible_modifications.Add(Length + 3, prot_c_term_variable_mods);
}
else
{
prot_c_term_variable_mods.Add(variable_modification);
}
}
}
int variable_modification_isoforms = 0;
foreach(Dictionary<int, Modification> kvp in GetVariableModificationPatterns(out_possible_modifications))
{
Peptide added_peptide = out_peptides.Add();
added_peptide.CopyFrom(this);
added_peptide.FixedModifications = FixedModifications;
added_peptide.VariableModifications = kvp;
variable_modification_isoforms++;
if(variable_modification_isoforms == maximumVariableModificationIsoforms)
{
break;
}
}
}
