public static IAnnotator GetAnnotator(IAnnotationProvider taProvider, ISequenceProvider sequenceProvider,
IAnnotationProvider saProviders, IAnnotationProvider conservationProvider,
IGeneAnnotationProvider geneAnnotationProviders, IEnumerable <IPlugin> plugins = null)
{
return(new Annotator(taProvider, sequenceProvider, saProviders, conservationProvider,
geneAnnotationProviders, plugins));
}
public Annotator(IAnnotationProvider taProvider, ISequenceProvider sequenceProvider,
IAnnotationProvider saProviders, IAnnotationProvider conservationProvider,
IGeneAnnotationProvider geneAnnotationProvider, IEnumerable <IPlugin> plugins = null)
{
_saProviders = saProviders;
_taProvider = taProvider;
_sequenceProvider = sequenceProvider;
_conservationProvider = conservationProvider;
_geneAnnotationProvider = geneAnnotationProvider;
_affectedGenes = new HashSet <string>();
_plugins = plugins;
GenomeAssembly = GetGenomeAssembly();
}
public Annotator(IAnnotationProvider taProvider, ISequenceProvider sequenceProvider,
IAnnotationProvider saProvider, IAnnotationProvider conservationProvider,
IGeneAnnotationProvider geneAnnotationProvider, IRepeatExpansionProvider repeatExpansionProvider)
{
_saProvider = saProvider;
_taProvider = taProvider;
_sequenceProvider = sequenceProvider;
_conservationProvider = conservationProvider;
_geneAnnotationProvider = geneAnnotationProvider;
_repeatExpansionProvider = repeatExpansionProvider;
_affectedGenes = new HashSet <string>();
Assembly = GetAssembly();
}
public static List <IAnnotatedGene> Annotate(IEnumerable <string> geneNames, IGeneAnnotationProvider geneAnnotationProvider)
{
var annotatedGenes = new List <IAnnotatedGene>();
foreach (var geneName in geneNames)
{
var annotation = geneAnnotationProvider.Annotate(geneName);
if (annotation != null)
{
annotatedGenes.Add(annotation);
}
}
return(annotatedGenes);
}