public DbOptimization GetOptimization(OptimizationType type, string seq, int charge, string fragment, int productCharge)
{
RequireUsable();
var key = new OptimizationKey(type, seq, charge, fragment, productCharge);
double value;
return((_database.DictLibrary.TryGetValue(new OptimizationKey(type, seq, charge, fragment, productCharge), out value))
? new DbOptimization(key, value)
: null);
}
/// <summary>
/// Saves the database to a new directory with only the optimizations used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which peptides are to be kept</param>
/// <returns>The full path to the file saved</returns>
public string PersistMinimized(string pathDestDir, SrmDocument document)
{
RequireUsable();
string persistPath = Path.Combine(pathDestDir, Path.GetFileName(PersistencePath) ?? string.Empty); // ReSharper
using (var fs = new FileSaver(persistPath))
{
var optDbMinimal = OptimizationDb.CreateOptimizationDb(fs.SafeName);
// Calculate the minimal set of optimizations needed for this document
var persistOptimizations = new List <DbOptimization>();
var dictOptimizations = new OptimizationDictionary(_database.GetOptimizations());
var persistedKeys = new HashSet <OptimizationKey>();
foreach (PeptideGroupDocNode seq in document.MoleculeGroups)
{
// Skip peptide groups with no transitions
if (seq.TransitionCount == 0)
{
continue;
}
foreach (PeptideDocNode peptide in seq.Children)
{
foreach (TransitionGroupDocNode group in peptide.Children)
{
var modSeq = document.Settings.GetSourceTarget(peptide);
var charge = group.PrecursorAdduct;
foreach (TransitionDocNode transition in group.Children)
{
foreach (var optType in Enum.GetValues(typeof(OptimizationType)).Cast <OptimizationType>())
{
var optimizationKey = new OptimizationKey(optType, modSeq, charge, transition.FragmentIonName, transition.Transition.Adduct);
foreach (var dbOptimization in dictOptimizations.EntriesMatching(optimizationKey))
{
if (persistedKeys.Add(dbOptimization.Key))
{
persistOptimizations.Add(dbOptimization);
}
break;
}
}
}
}
}
}
optDbMinimal.UpdateOptimizations(persistOptimizations, new DbOptimization[0]);
fs.Commit();
}
return(persistPath);
}
/// <summary>
/// Saves the database to a new directory with only the optimizations used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which peptides are to be kept</param>
/// <returns>The full path to the file saved</returns>
public string PersistMinimized(string pathDestDir, SrmDocument document)
{
RequireUsable();
string persistPath = Path.Combine(pathDestDir, Path.GetFileName(PersistencePath) ?? string.Empty); // ReSharper
using (var fs = new FileSaver(persistPath))
{
var optDbMinimal = OptimizationDb.CreateOptimizationDb(fs.SafeName);
// Calculate the minimal set of optimizations needed for this document
var persistOptimizations = new List <DbOptimization>();
var dictOptimizations = _database.GetOptimizations().ToDictionary(opt => opt.Key);
foreach (PeptideGroupDocNode seq in document.MoleculeGroups)
{
// Skip peptide groups with no transitions
if (seq.TransitionCount == 0)
{
continue;
}
foreach (PeptideDocNode peptide in seq.Children)
{
foreach (TransitionGroupDocNode group in peptide.Children)
{
string modSeq = document.Settings.GetSourceTextId(peptide);
int charge = group.PrecursorCharge;
foreach (TransitionDocNode transition in group.Children)
{
foreach (var optType in Enum.GetValues(typeof(OptimizationType)).Cast <OptimizationType>())
{
var optimizationKey = new OptimizationKey(optType, modSeq, charge, transition.FragmentIonName, transition.Transition.Charge);
DbOptimization dbOptimization;
if (dictOptimizations.TryGetValue(optimizationKey, out dbOptimization))
{
persistOptimizations.Add(new DbOptimization(dbOptimization.Key, dbOptimization.Value));
// Only add once
dictOptimizations.Remove(optimizationKey);
}
}
}
}
}
}
optDbMinimal.UpdateOptimizations(persistOptimizations, new DbOptimization[0]);
fs.Commit();
}
return(persistPath);
}
/// <summary>
/// Saves the database to a new directory with only the optimizations used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which peptides are to be kept</param>
/// <returns>The full path to the file saved</returns>
public string PersistMinimized(string pathDestDir, SrmDocument document)
{
RequireUsable();
string persistPath = Path.Combine(pathDestDir, Path.GetFileName(PersistencePath) ?? string.Empty); // ReSharper
using (var fs = new FileSaver(persistPath))
{
var optDbMinimal = OptimizationDb.CreateOptimizationDb(fs.SafeName);
// Calculate the minimal set of optimizations needed for this document
var persistOptimizations = new List<DbOptimization>();
var dictOptimizations = _database.GetOptimizations().ToDictionary(opt => opt.Key);
foreach (PeptideGroupDocNode seq in document.MoleculeGroups)
{
// Skip peptide groups with no transitions
if (seq.TransitionCount == 0)
continue;
foreach (PeptideDocNode peptide in seq.Children)
{
foreach (TransitionGroupDocNode group in peptide.Children)
{
string modSeq = document.Settings.GetSourceTextId(peptide);
int charge = group.PrecursorCharge;
foreach (TransitionDocNode transition in group.Children)
{
foreach (var optType in Enum.GetValues(typeof(OptimizationType)).Cast<OptimizationType>())
{
var optimizationKey = new OptimizationKey(optType, modSeq, charge, transition.FragmentIonName, transition.Transition.Charge);
DbOptimization dbOptimization;
if (dictOptimizations.TryGetValue(optimizationKey, out dbOptimization))
{
persistOptimizations.Add(new DbOptimization(dbOptimization.Key, dbOptimization.Value));
// Only add once
dictOptimizations.Remove(optimizationKey);
}
}
}
}
}
}
optDbMinimal.UpdateOptimizations(persistOptimizations, new DbOptimization[0]);
fs.Commit();
}
return persistPath;
}
public DbOptimization GetOptimization(OptimizationType type, string seq, int charge, string fragment, int productCharge)
{
RequireUsable();
var key = new OptimizationKey(type, seq, charge, fragment, productCharge);
double value;
return (_database.DictLibrary.TryGetValue(new OptimizationKey(type, seq, charge, fragment, productCharge), out value))
? new DbOptimization(key, value)
: null;
}
public OptimizationKey(OptimizationKey other)
: this(other.OptType, other.PeptideModSeq, other.PrecursorAdduct, other.FragmentIon, other.ProductAdduct)
{
}
public DbOptimization(OptimizationType type, Target seq, Adduct charge, string fragmentIon, Adduct productCharge, double value)
{
Key = new OptimizationKey(type, seq, charge, fragmentIon, productCharge);
Value = value;
}
public DbOptimization(OptimizationKey key, double value)
: this(key.OptType, key.PeptideModSeq, key.PrecursorAdduct, key.FragmentIon, key.ProductAdduct, value)
{
}
protected DbOptimization()
{
Key = new OptimizationKey();
}
public OptimizationKey(OptimizationKey other)
: this(other.OptType, other.PeptideModSeq, other.Charge, other.FragmentIon, other.ProductCharge)
{
}
public DbOptimization(OptimizationKey key, double value)
: this(key.OptType, key.PeptideModSeq, key.Charge, key.FragmentIon, key.ProductCharge, value)
{
}
protected DbOptimization()
{
Key = new OptimizationKey();
}
public DbOptimization(OptimizationType type, string seq, int charge, string fragmentIon, int productCharge, double value)
{
Key = new OptimizationKey(type, seq, charge, fragmentIon, productCharge);
Value = value;
}
public DbOptimization(OptimizationKey key, double value)
: this(key.OptType, key.PeptideModSeq, key.Charge, key.FragmentIon, key.ProductCharge, value)
{
}
public OptimizationKey(OptimizationKey other)
: this(other.OptType, other.PeptideModSeq, other.Charge, other.FragmentIon, other.ProductCharge)
{
}
