internal IList <long> GetProteinIdsThatMightHaveSequence(IStatelessSession session, ICollection <string> sequencesToLookFor)
{
Func <ICollection <String>, IEnumerable <long> > functionToCall;
IList <String> uniqueStrings;
bool useSubsequenceTable;
if (UseSubsequenceTable.HasValue)
{
useSubsequenceTable = UseSubsequenceTable.Value;
}
else
{
useSubsequenceTable = ProteomeDb.HasSubsequencesTable(() => session.Connection) &&
!sequencesToLookFor.Any(s => s.Length < ProteomeDb.MIN_SEQUENCE_LENGTH);
}
if (useSubsequenceTable)
{
functionToCall = batchedArgs => QuerySubsequencesTableForSubstrings(session, batchedArgs);
uniqueStrings = RemoveSuperstrings(sequencesToLookFor
.Select(s => s.Substring(0, Math.Min(s.Length, ProteomeDb.MAX_SEQUENCE_LENGTH))));
}
else
{
functionToCall = batchedArgs => QueryProteinTableForSubstrings(session, batchedArgs);
uniqueStrings = RemoveSuperstrings(sequencesToLookFor);
}
return(ProteomeDb.BatchUpArgumentsForFunction(functionToCall, uniqueStrings, 500).Distinct().ToArray());
}
public Digestion(ProteomeDb proteomeDb, DbDigestion digestion) : base(proteomeDb, digestion)
{
Name = digestion.Name;
Description = digestion.Description;
MinSequenceLength = digestion.MinSequenceLength;
MaxSequenceLength = digestion.MaxSequenceLength;
}
public IDictionary <String, List <Protein> > GetProteinsWithSequences(IEnumerable <string> sequences)
{
using (var session = ProteomeDb.OpenStatelessSession(false))
{
return(GetProteinsWithSequences(session, sequences));
}
}
private void ExecuteBackground()
{
try
{
ProteinMatchTypes matchTypesRemaining = Settings.MatchTypes;
using (var proteomeDb = ProteomeDb.OpenProteomeDb(Settings.ProteomeDbPath.FilePath, CancellationToken))
using (var session = proteomeDb.OpenStatelessSession(false))
{
if (matchTypesRemaining.Contains(ProteinMatchType.sequence) && IsAminoAcidSequence(Settings.SearchText))
{
AddProteinMatches(session, () => proteomeDb.GetDigestion()
.GetProteinIdsThatMightHaveSequence(session, new[] { Settings.SearchText }));
}
matchTypesRemaining = matchTypesRemaining.Except(ProteinMatchType.sequence);
if (DoMatching)
{
string pattern = @"%" + Settings.SearchText + @"%";
if (Settings.SearchText.Length < MIN_FREE_SEARCH_LENGTH)
{
// That could cast a pretty wide net - only match to beginning of keywords, and not to description or species
pattern = Settings.SearchText + @"%";
matchTypesRemaining = matchTypesRemaining.Except(ProteinMatchType.description, ProteinMatchType.species);
}
var exprLike = new List <string>();
foreach (ProteinMatchType matchType in matchTypesRemaining)
{
exprLike.Add(String.Format(@"pn.{0} LIKE :expr", ProteinMatchTypeDbFieldName(matchType)));
}
String hql = @"SELECT distinct pn.Protein FROM " + typeof(DbProteinName) + @" pn "
// ReSharper disable LocalizableElement
+ String.Format("\nWHERE {0}", String.Join(" OR ", exprLike))
+ "\nORDER BY pn.IsPrimary DESC, pn.Name";
// ReSharper restore LocalizableElement
IQuery query = session.CreateQuery(hql).SetParameter(@"expr", pattern);
query.SetMaxResults(MaxResults);
AddProteinMatches(session, () =>
{
return(query.List <DbProtein>()
.Where(dbProtein => null != dbProtein)
.Select(dbProtein => dbProtein.Id.Value));
});
}
}
}
catch (Exception exception)
{
if (CancellationToken.IsCancellationRequested)
{
return;
}
Trace.TraceError(@"Unhandled exception: {0}", exception);
}
}
/// <summary>
/// Executes the query (which must be a query on the DbProtein table), and adds
/// all of the rows in that query to the ProteinMatches.
/// </summary>
private void AddProteinMatches(IStatelessSession session, Func <IEnumerable <long> > proteinIdQuery)
{
Dictionary <long, ProteinMatch> newMatches = new Dictionary <long, ProteinMatch>();
lock (this)
{
if (_matches != null)
{
foreach (var entry in _matches)
{
newMatches.Add(entry.Key, entry.Value);
}
}
}
var newProteinIds = new List <long>();
CancellationToken.ThrowIfCancellationRequested();
foreach (long id in proteinIdQuery())
{
CancellationToken.ThrowIfCancellationRequested();
if (newMatches.ContainsKey(id))
{
continue;
}
newProteinIds.Add(id);
}
if (newProteinIds.Count == 0)
{
return;
}
using (var proteomeDb = ProteomeDb.OpenProteomeDb(Settings.ProteomeDbPath.FilePath, CancellationToken))
{
// We fetched the protein ids. Now fetch all the protein rows themselves.
var proteins = proteomeDb.GetProteinsWithIds(session, newProteinIds);
foreach (var protein in proteins)
{
var proteinMatch = new ProteinMatch(Settings, protein);
newMatches.Add(protein.Id, proteinMatch);
}
SetProteinMatches(newMatches);
}
}
public EntityModel(ProteomeDb proteomeDb, T entity) : this(proteomeDb.ProteomeDbPath, entity)
{
}
public Digestion(ProteomeDb proteomeDb)
{
ProteomeDb = proteomeDb;
}
// ReSharper disable NonLocalizedString
private IList <Protein> GetProteinsWithIds(IStatelessSession session, IList <long> ids)
{
return(ProteomeDb.GetProteinsWithIds(session, ids));
}
private ProteinMatchSettings CreateProteinMatchSettings(SrmDocument srmDocument, ProteinMatchType matchTypes, String searchText)
{
var peptideSettings = srmDocument.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
if (backgroundProteome.IsNone)
{
return null;
}
try
{
if (_proteomeDb != null && _proteomeDb.Path != backgroundProteome.DatabasePath)
{
_proteomeDb.Dispose();
_proteomeDb = null;
}
if (_proteomeDb == null)
{
_proteomeDb = backgroundProteome.OpenProteomeDb();
}
return new ProteinMatchSettings(_proteomeDb.ProteomeDbPath,
new ProteaseImpl(peptideSettings.Enzyme),
matchTypes,
searchText);
}
catch (SQLiteException)
{
// CONSIDER: Silent failure could be confusing. Show a message box
// about failing to open the database.
return null;
}
}
public void Detach()
{
if (TextBox == null)
{
return;
}
HideStatementCompletionForm();
if (_proteinMatcher != null)
{
_proteinMatcher.Cancel();
_proteinMatcher = null;
}
if (null != _proteomeDb)
{
_proteomeDb.Dispose();
_proteomeDb = null;
}
TextBox.KeyDown -= TextBox_KeyDown;
TextBox.TextChanged -= TextBox_TextChanged;
TextBox.GotFocus -= TextBox_GotFocus;
TextBox.LostFocus -= TextBox_LostFocus;
TextBox.LocationChanged -= TextBox_LocationChanged;
TextBox = null;
}
public Digestion GetDigestion(ProteomeDb proteomeDb, PeptideSettings peptideSettings)
{
return proteomeDb.GetDigestion(peptideSettings.Enzyme.Name);
}