/// <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 static IList<ProteinMatch> RefineMatches(IEnumerable<ProteinMatch> matches, ProteinMatchSettings settings)
{
var newMatches = new List<ProteinMatch>();
foreach (var match in matches)
{
var newMatch = new ProteinMatch(settings, match.Protein);
if (newMatch.MatchType != 0)
{
newMatches.Add(newMatch);
}
}
return newMatches;
}
/// <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(IQuery query)
{
Dictionary <long, ProteinMatch> newMatches = new Dictionary <long, ProteinMatch>();
lock (this)
{
if (_matches != null)
{
foreach (var entry in _matches)
{
newMatches.Add(entry.Key, entry.Value);
}
}
}
query.SetMaxResults(MaxResults);
var newProteinIds = new List <long>();
ThrowIfCancelled();
foreach (DbProtein dbProtein in query.Enumerable())
{
ThrowIfCancelled();
if (!dbProtein.Id.HasValue || newMatches.ContainsKey(dbProtein.Id.Value))
{
continue;
}
newProteinIds.Add(dbProtein.Id.Value);
}
if (newProteinIds.Count == 0)
{
return;
}
// We fetched the protein ids. Now fetch all the protein rows themselves.
var newProteins = new List <DbProtein>();
_session.CreateCriteria(typeof(DbProtein))
.Add(Restrictions.In("Id", newProteinIds)) // Not L10N
.List(newProteins);
// Now fetch all of the protein name records at once
var criteria = _session.CreateCriteria(typeof(DbProteinName))
.Add(Restrictions.In("Protein", newProteins)); // Not L10N
var proteinNames = new Dictionary <DbProtein, List <DbProteinName> >();
foreach (DbProteinName proteinName in criteria.List())
{
List <DbProteinName> names;
if (!proteinNames.TryGetValue(proteinName.Protein, out names))
{
names = new List <DbProteinName>();
proteinNames.Add(proteinName.Protein, names);
}
names.Add(proteinName);
}
// Create a ProteinMatch for each Protein
foreach (var entry in proteinNames)
{
var proteinMatch = new ProteinMatch(Settings, new Protein(Settings.ProteomeDbPath, entry.Key, entry.Value));
if (entry.Key.Id.HasValue)
{
newMatches.Add(entry.Key.Id.Value, proteinMatch);
}
}
SetProteinMatches(newMatches);
}
/// <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(IQuery query)
{
Dictionary<long, ProteinMatch> newMatches = new Dictionary<long, ProteinMatch>();
lock (this)
{
if (_matches != null)
{
foreach (var entry in _matches)
{
newMatches.Add(entry.Key, entry.Value);
}
}
}
query.SetMaxResults(MaxResults);
var newProteinIds = new List<long>();
ThrowIfCancelled();
foreach (DbProtein dbProtein in query.Enumerable())
{
ThrowIfCancelled();
if (!dbProtein.Id.HasValue || newMatches.ContainsKey(dbProtein.Id.Value))
{
continue;
}
newProteinIds.Add(dbProtein.Id.Value);
}
if (newProteinIds.Count == 0)
{
return;
}
// We fetched the protein ids. Now fetch all the protein rows themselves.
var newProteins = new List<DbProtein>();
_session.CreateCriteria(typeof (DbProtein))
.Add(Restrictions.In("Id", newProteinIds)) // Not L10N
.List(newProteins);
// Now fetch all of the protein name records at once
var criteria = _session.CreateCriteria(typeof (DbProteinName))
.Add(Restrictions.In("Protein", newProteins)); // Not L10N
var proteinNames = new Dictionary<DbProtein, List<DbProteinName>>();
foreach (DbProteinName proteinName in criteria.List())
{
List<DbProteinName> names;
if (!proteinNames.TryGetValue(proteinName.Protein, out names))
{
names = new List<DbProteinName>();
proteinNames.Add(proteinName.Protein, names);
}
names.Add(proteinName);
}
// Create a ProteinMatch for each Protein
foreach (var entry in proteinNames)
{
var proteinMatch = new ProteinMatch(Settings, new Protein(Settings.ProteomeDbPath, entry.Key, entry.Value));
if (entry.Key.Id.HasValue)
newMatches.Add(entry.Key.Id.Value, proteinMatch);
}
SetProteinMatches(newMatches);
}
