Class GoUtils

Method Details

• countCategories

  public static LinkedHashMap<GoId,Integer> countCategories(List<GoTerm> categories, List<GoTerm> experiment_set, 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 LinkedHashMap<GoId,Integer> countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId,GoTerm> all_go_terms)

• createGoIdToGoTermMap

  public static Map<GoId,GoTerm> createGoIdToGoTermMap(List<GoTerm> go_terms)

• getAllSuperGoIds

  public static SortedSet<GoId> getAllSuperGoIds(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)

• getAllSuperGoTerms

  public static SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, List<GoTerm> go_terms)

• getAllSuperGoTerms

  public static SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)

• getAllSuperGoTerms

  public static SortedSet<GoTerm> getAllSuperGoTerms(GoTerm go_term, Map<GoId,GoTerm> goid_to_term_map)

• getPenultimateGoTerm

  public static GoTerm getPenultimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)

• getUltimateGoTerm

  public static GoTerm getUltimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)

• parseGoIds

  public static SortedMap<String,List<GoId>> parseGoIds(Object source, String start_of_comment_line, String start_of_label_line) throws IOException

  Throws:

  IOException