private void InitNames()
{
if (_alternativeNames != null)
{
return;
}
_alternativeNames = new List <ProteinMetadata>();
using (var proteomeDb = OpenProteomeDb())
using (var session = proteomeDb.OpenSession())
{
var protein = GetEntity(session);
foreach (var name in protein.Names)
{
if (name.Name == Name)
{
continue;
}
if (Name == null && name.IsPrimary)
{
_proteinMetadata = name.GetProteinMetadata();
}
else
{
_alternativeNames.Add(name.GetProteinMetadata());
}
}
}
}
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());
}
}
}
}
}
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 ProteinMetadata _proteinMetadata; // name, description, accession, gene etc
internal Protein(ProteomeDbPath proteomeDb, DbProtein protein)
: this(proteomeDb, protein, (DbProteinName)null)
{
_proteinMetadata = ProteinMetadata.EMPTY;
}
private static bool Matches(ProteinMetadata proteinMetadata, ProteinMatchType matchType, string ltext)
{
return(ContainsLowerCase(proteinMetadata.TextForMatchTypes(ProteinMatchTypes.Singleton(matchType)), ltext));
}