Class GoUtils


  • public final class GoUtils
    extends java.lang.Object
    • Method Detail

      • countCategories

        public static java.util.LinkedHashMap<GoId,​java.lang.Integer> countCategories​(java.util.List<GoTerm> categories,
                                                                                            java.util.List<GoTerm> experiment_set,
                                                                                            java.util.Map<GoId,​GoTerm> all_go_terms)
        This is for counting the how many times each GO term in 'categories' is a (direct or indirect) super term of the GO terms in 'experiment_set'.
        Parameters:
        categories - the set of super terms to be counted
        experiment_set - the list of GO terms to be analyzed
        all_go_terms - all terms in the ontology
        Returns:
      • countCategoriesId

        public static java.util.LinkedHashMap<GoId,​java.lang.Integer> countCategoriesId​(java.util.List<GoId> categories,
                                                                                              java.util.List<GoId> experiment_set,
                                                                                              java.util.Map<GoId,​GoTerm> all_go_terms)
      • createGoIdToGoTermMap

        public static java.util.Map<GoId,​GoTerm> createGoIdToGoTermMap​(java.util.List<GoTerm> go_terms)
      • getAllSuperGoIds

        public static java.util.SortedSet<GoId> getAllSuperGoIds​(GoId go_id,
                                                                 java.util.Map<GoId,​GoTerm> goid_to_term_map)
      • getAllSuperGoTerms

        public static java.util.SortedSet<GoTerm> getAllSuperGoTerms​(GoId go_id,
                                                                     java.util.List<GoTerm> go_terms)
      • getAllSuperGoTerms

        public static java.util.SortedSet<GoTerm> getAllSuperGoTerms​(GoId go_id,
                                                                     java.util.Map<GoId,​GoTerm> goid_to_term_map)
      • getAllSuperGoTerms

        public static java.util.SortedSet<GoTerm> getAllSuperGoTerms​(GoTerm go_term,
                                                                     java.util.Map<GoId,​GoTerm> goid_to_term_map)
      • getPenultimateGoTerm

        public static GoTerm getPenultimateGoTerm​(GoTerm go_term,
                                                  java.util.Map<GoId,​GoTerm> map)
      • getUltimateGoTerm

        public static GoTerm getUltimateGoTerm​(GoTerm go_term,
                                               java.util.Map<GoId,​GoTerm> map)
      • parseGoIds

        public static java.util.SortedMap<java.lang.String,​java.util.List<GoId>> parseGoIds​(java.lang.Object source,
                                                                                                  java.lang.String start_of_comment_line,
                                                                                                  java.lang.String start_of_label_line)
                                                                                           throws java.io.IOException
        Throws:
        java.io.IOException