public bool TryUpdateSymbol(TranscriptDataSource source, MutableGene gene, string geneId)
{
var dict = source == TranscriptDataSource.Ensembl ? _ensemblIdToSymbol : _entrezGeneIdToSymbol;
UniqueString newSymbol;
if (!dict.TryGetValue(geneId, out newSymbol)) return false;
if (newSymbol.HasConflict) return false;
gene.Symbol = newSymbol.Value;
return true;
}
public static MutableGene Clone(MutableGene gene)
{
return(new MutableGene
{
ReferenceIndex = gene.ReferenceIndex,
Start = gene.Start,
End = gene.End,
OnReverseStrand = gene.OnReverseStrand,
Symbol = gene.Symbol,
EntrezGeneId = gene.EntrezGeneId,
EnsemblId = gene.EnsemblId,
HgncId = gene.HgncId,
MimNumber = gene.MimNumber,
TranscriptDataSource = gene.TranscriptDataSource
});
}
private static bool TryUpdateHgncId(string geneId, Dictionary<string, UniqueInt> dict, MutableGene gene)
{
if (geneId == null) return false;
UniqueInt newHgncId;
if (!dict.TryGetValue(geneId, out newHgncId)) return false;
if (newHgncId.HasConflict) return false;
gene.HgncId = newHgncId.Value;
return true;
}
public bool TryUpdateHgncId(string ensemblId, string entrezGeneId, MutableGene gene)
{
if (TryUpdateHgncId(ensemblId, _ensemblIdToHgnc, gene)) return true;
if (TryUpdateHgncId(entrezGeneId, _entrezGeneIdToHgnc, gene)) return true;
return false;
}
