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);
}
}
public static string TextForMatchTypes(this ProteinMetadata p, ProteinMatchTypes types)
{
if (types.IsSingleton(ProteinMatchType.sequence))
{
return(null);
}
var results = new List <string>();
if (types.Contains(ProteinMatchType.name))
{
results.Add(p.Name ?? String.Empty);
}
if (types.Contains(ProteinMatchType.accession))
{
results.Add(p.Accession ?? String.Empty);
}
if (types.Contains(ProteinMatchType.preferredName))
{
results.Add(p.PreferredName ?? String.Empty);
}
if (types.Contains(ProteinMatchType.gene))
{
results.Add(p.Gene ?? String.Empty);
}
if (types.Contains(ProteinMatchType.species))
{
results.Add(p.Species ?? String.Empty);
}
if (types.Contains(ProteinMatchType.description)) // put this last, as it likely contains the others
{
results.Add(p.Description ?? String.Empty);
}
if (results.Count > 0)
{
return(String.Join(@" ", results));
}
return(null);
}
private static bool Matches(ProteinMetadata proteinMetadata, ProteinMatchType matchType, string ltext)
{
return(ContainsLowerCase(proteinMetadata.TextForMatchTypes(ProteinMatchTypes.Singleton(matchType)), ltext));
}
public ProteinMatchSettings(ProteomeDbPath proteomeDbPath, ProteinMatchTypes proteinMatchTypes, String searchText)
{
ProteomeDbPath = proteomeDbPath;
MatchTypes = proteinMatchTypes;
SearchText = searchText;
}
