org.forester.go

Class GoUtils

java.lang.Object

org.forester.go.GoUtils

public final class GoUtils
extends Object

Method Summary

Modifier and Type	Method and Description
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'.
static LinkedHashMap<GoId,Integer>	countCategoriesId(List<GoId> categories, List<GoId> experiment_set, Map<GoId,GoTerm> all_go_terms)
static Map<GoId,GoTerm>	createGoIdToGoTermMap(List<GoTerm> go_terms)
static SortedSet<GoId>	getAllSuperGoIds(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
static SortedSet<GoTerm>	getAllSuperGoTerms(GoId go_id, List<GoTerm> go_terms)
static SortedSet<GoTerm>	getAllSuperGoTerms(GoId go_id, Map<GoId,GoTerm> goid_to_term_map)
static SortedSet<GoTerm>	getAllSuperGoTerms(GoTerm go_term, Map<GoId,GoTerm> goid_to_term_map)
static GoTerm	getPenultimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)
static GoTerm	getUltimateGoTerm(GoTerm go_term, Map<GoId,GoTerm> map)
static SortedMap<String,List<GoId>>	parseGoIds(Object source, String start_of_comment_line, String start_of_label_line)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

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