public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out List <PeptideGroupDocNode> peptideGroupsNew)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
peptideGroupsNew = importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)).ToList();
document = document.AddPeptideGroups(peptideGroupsNew, false, to, out firstAdded, out nextAdd);
}
return(document);
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out int emptyProteinCount)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
document = document.AddPeptideGroups(importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)),
false, null, out firstAdded, out nextAdd);
}
emptyProteinCount = importer.EmptyPeptideGroupCount;
return(document);
}
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<string, 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)) // Not L10N
using (SQLiteCommand command = new SQLiteCommand(connection))
{
connection.Open();
command.CommandText = "SELECT PeptideModSeq, Charge, Mz, Value, Type FROM OptimizationLibrary"; // Not L10N
using (SQLiteDataReader reader = command.ExecuteReader())
{
while (reader.Read())
{
var type = (OptimizationType)reader["Type"]; // Not L10N
var modifiedSequence = reader["PeptideModSeq"].ToString(); // Not L10N
var charge = (int)reader["Charge"]; // Not L10N
var productMz = (double)reader["Mz"]; // Not L10N
var value = (double)reader["Value"]; // Not L10N
optimizations.Add(new Tuple<DbOptimization, double>(new DbOptimization(type, modifiedSequence, charge, string.Empty, -1, 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(charge)) // Not L10N
).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") // Not L10N
.ChangeFragmentRangeLastName("last ion") // Not L10N
.ChangeProductCharges(Enumerable.Range(1, maxCharge).ToList())
.ChangeIonTypes(new []{ IonType.y, IonType.b }))
.ChangeTransitionLibraries(libs => libs.ChangePick(TransitionLibraryPick.none))
);
var matcher = new ModificationMatcher { FormatProvider = NumberFormatInfo.InvariantInfo };
matcher.CreateMatches(newDoc.Settings, peptideList, Settings.Default.StaticModList, Settings.Default.HeavyModList);
FastaImporter importer = new FastaImporter(newDoc, matcher);
string text = string.Format(">>{0}\r\n{1}", newDoc.GetPeptideGroupId(true), TextUtil.LineSeparate(peptideList)); // Not L10N
PeptideGroupDocNode imported = importer.Import(new StringReader(text), null, Helpers.CountLinesInString(text)).First();
int optimizationsUpdated = 0;
foreach (PeptideDocNode nodePep in imported.Children)
{
string sequence = newDoc.Settings.GetSourceTextId(nodePep);
foreach (var nodeGroup in nodePep.TransitionGroups)
{
int charge = nodeGroup.PrecursorCharge;
foreach (var nodeTran in nodeGroup.Transitions)
{
double productMz = nodeTran.Mz;
foreach (var optimization in optimizations.Where(opt =>
string.IsNullOrEmpty(opt.Item1.FragmentIon) &&
opt.Item1.ProductCharge == -1 &&
opt.Item1.PeptideModSeq == sequence &&
opt.Item1.Charge == charge &&
Math.Abs(opt.Item2 - productMz) < 0.00001))
{
optimization.Item1.FragmentIon = nodeTran.FragmentIonName;
optimization.Item1.ProductCharge = nodeTran.Transition.Charge;
++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 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));
}
}
