/// <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);
}
public bool Equals(OptimizationDb other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime));
}
/// <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 OptimizationLibrary Initialize(SrmDocument document, IProgressMonitor loadMonitor)
{
if (_database != null || IsNone)
{
return(this);
}
var database = OptimizationDb.GetOptimizationDb(DatabasePath, loadMonitor, document);
// Check for the case where an exception was handled by the progress monitor
if (database == null)
{
return(null);
}
return(ChangeDatabase(database));
}
public OptimizationLibrary ChangeDatabase(OptimizationDb database)
{
return(ChangeProp(ImClone(this), im => im._database = database));
}
public bool Equals(OptimizationDb other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime);
}
public static OptimizationDb ConvertFromOldFormat(string path, IProgressMonitor loadMonitor, ProgressStatus status, SrmDocument document)
{
// Try to open assuming old format (Id, PeptideModSeq, Charge, Mz, Value, Type)
var precursors = new Dictionary <Target, HashSet <int> >(); // PeptideModSeq -> charges
var optimizations = new List <Tuple <DbOptimization, double> >(); // DbOptimization, product m/z
int maxCharge = 1;
using (SQLiteConnection connection = new SQLiteConnection(@"Data Source = " + path))
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = @"SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary";
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader[@"Type"];
var modifiedSequence = new Target(reader[@"PeptideModSeq"].ToString());
var charge = (int)reader[@"Charge"];
var productMz = (double)reader[@"Mz"];
var value = (double)reader[@"Value"];
optimizations.Add(new Tuple <DbOptimization, double>(new DbOptimization(type, modifiedSequence, Adduct.FromChargeProtonated(charge), string.Empty, Adduct.EMPTY, value), productMz));
if (!precursors.ContainsKey(modifiedSequence))
{
precursors[modifiedSequence] = new HashSet <int>();
}
precursors[modifiedSequence].Add(charge);
if (charge > maxCharge)
{
maxCharge = charge;
}
}
}
}
var peptideList = (from precursor in precursors
from charge in precursor.Value
select string.Format(@"{0}{1}", precursor.Key, Transition.GetChargeIndicator(Adduct.FromChargeProtonated(charge)))
).ToList();
var newDoc = new SrmDocument(document != null ? document.Settings : SrmSettingsList.GetDefault());
newDoc = newDoc.ChangeSettings(newDoc.Settings
.ChangePeptideLibraries(libs => libs.ChangePick(PeptidePick.filter))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName(@"ion 1")
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideProductCharges(Enumerable.Range(1, maxCharge).Select(Adduct.FromChargeProtonated).ToList()) // TODO(bspratt) negative charge peptides
.ChangePeptideIonTypes(new [] { IonType.y, IonType.b })) // TODO(bspratt) generalize to molecules?
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher();
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
// ReSharper disable LocalizableElement
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList));
// ReSharper restore LocalizableElement
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
foreach (var nodeGroup in nodePep.TransitionGroups)
{
var charge = nodeGroup.PrecursorAdduct;
var libKeyToMatch = newDoc.Settings.GetSourceTarget(nodePep).GetLibKey(charge).LibraryKey;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductAdduct.IsEmpty &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
var optLibKey = optimization.Item1.Target.GetLibKey(optimization.Item1.Adduct).LibraryKey;
if (!LibKeyIndex.KeysMatch(optLibKey, libKeyToMatch))
{
continue;
}
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductAdduct = nodeTran.Transition.Adduct;
++optimizationsUpdated;
}
}
}
}
if (optimizations.Count > optimizationsUpdated)
{
throw new OptimizationsOpeningException(string.Format(Resources.OptimizationDb_ConvertFromOldFormat_Failed_to_convert__0__optimizations_to_new_format_,
optimizations.Count - optimizationsUpdated));
}
using (var fs = new FileSaver(path))
{
OptimizationDb db = CreateOptimizationDb(fs.SafeName);
db.UpdateOptimizations(optimizations.Select(opt => opt.Item1).ToArray(), new DbOptimization[0]);
fs.Commit();
if (loadMonitor != null)
{
loadMonitor.UpdateProgress(status.ChangePercentComplete(100));
}
return(GetOptimizationDb(fs.RealName, null, null));
}
}
public OptimizationLibrary ChangeDatabase(OptimizationDb database)
{
return ChangeProp(ImClone(this), im => im._database = database);
}
