internal static IList <Protein> GetProteinWithIds(ProteomeDbPath proteomeDbPath, IStatelessSession session, ICollection <long> ids)
{
if (ids.Count == 0)
{
return(new Protein[0]);
}
// ReSharper disable LocalizableElement
var hql = "SELECT p, pn"
+ "\nFROM " + typeof(DbProtein) + " p, " + typeof(DbProteinName) + " pn"
+ "\nWHERE p.Id = pn.Protein.Id AND p.Id IN (:Ids)";
var query = session.CreateQuery(hql);
query.SetParameterList("Ids", ids);
// ReSharper restore LocalizableElement
var proteins = new List <Protein>();
var rowsByProteinId = query.List().Cast <object[]>().ToLookup(row => ((DbProtein)row[0]).Id.Value);
foreach (var grouping in rowsByProteinId)
{
var protein = (DbProtein)grouping.First()[0];
var names = grouping.Select(row => row[1]).Cast <DbProteinName>();
proteins.Add(new Protein(proteomeDbPath, protein, names));
}
return(proteins);
}
public ProteinMatchSettings(ProteomeDbPath proteomeDbPath, IProtease protease, ProteinMatchType proteinMatchTypes, String searchText)
{
ProteomeDbPath = proteomeDbPath;
Protease = protease;
if (protease != null)
{
using (var proteomeDb = proteomeDbPath.OpenProteomeDb())
{
Digestion = proteomeDb.GetDigestion(protease.Name);
}
}
MatchTypes = proteinMatchTypes;
SearchText = searchText;
}
internal Protein(ProteomeDbPath proteomeDbPath, DbProtein protein, IEnumerable <DbProteinName> proteinNames)
: this(proteomeDbPath, protein, (DbProteinName)null)
{
_proteinMetadata = ProteinMetadata.EMPTY;
_alternativeNames = new List <ProteinMetadata>();
foreach (DbProteinName proteinName in proteinNames)
{
if (proteinName.IsPrimary)
{
_proteinMetadata = proteinName.GetProteinMetadata();
}
else
{
_alternativeNames.Add(proteinName.GetProteinMetadata()); // copies the ProteinMetadata info
}
}
}
internal Protein(ProteomeDbPath proteomeDb, DbProtein protein, DbProteinName primaryName)
: base(proteomeDb, protein)
{
Sequence = protein.Sequence;
if (primaryName != null)
{
_proteinMetadata = primaryName.GetProteinMetadata();
if (primaryName.Protein != null)
{
// grab the alternative names now, rather than going back to the db later
_alternativeNames = new List <ProteinMetadata>();
foreach (var name in primaryName.Protein.Names)
{
if (!name.IsPrimary)
{
_alternativeNames.Add(name.GetProteinMetadata());
}
}
}
}
}
private ProteinMetadata _proteinMetadata; // name, description, accession, gene etc
internal Protein(ProteomeDbPath proteomeDb, DbProtein protein)
: this(proteomeDb, protein, (DbProteinName)null)
{
_proteinMetadata = ProteinMetadata.EMPTY;
}
public ProteinMatchSettings(ProteomeDbPath proteomeDbPath, ProteinMatchTypes proteinMatchTypes, String searchText)
{
ProteomeDbPath = proteomeDbPath;
MatchTypes = proteinMatchTypes;
SearchText = searchText;
}
protected EntityModel(ProteomeDbPath proteomeDb, T entity)
{
_entity = entity;
ProteomeDbPath = proteomeDb;
}
