Beispiel #1
0
 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));
 }
Beispiel #2
0
 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();
 }
Beispiel #3
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 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();
 }
Beispiel #4
0
        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);
        }