Class SnpEffPredictorFactoryFeatures

  • Direct Known Subclasses:
    SnpEffPredictorFactoryEmbl, SnpEffPredictorFactoryGenBank

    public abstract class SnpEffPredictorFactoryFeatures
    extends SnpEffPredictorFactory
    This class creates a SnpEffectPredictor from a 'features' file. This includes derived formats as GenBank and Embl. References: http://www.ebi.ac.uk/embl/Documentation/User_manual/printable.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
    Author:
    pcingola
    • Constructor Detail

      • SnpEffPredictorFactoryFeatures

        public SnpEffPredictorFactoryFeatures​(Config config)
    • Method Detail

      • addFeatures

        protected void addFeatures​(Features features)
        Add all features
      • geneId

        protected java.lang.String geneId​(Feature f,
                                          int start,
                                          int end)
        Try to get geneIDs
      • geneName

        protected java.lang.String geneName​(Feature f,
                                            int start,
                                            int end)
        Get gene name from feature