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); }