org.forester.go
Class GoUtils

java.lang.Object
  org.forester.go.GoUtils

public final class GoUtils
extends java.lang.Object

Method Summary

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'.
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)
static java.util.Map<GoId,GoTerm>	createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoId>	getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>	getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
static java.util.SortedSet<GoTerm>	getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
static java.util.SortedSet<GoTerm>	getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
static GoTerm	getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
static GoTerm	getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
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)

Methods inherited from class java.lang.Object

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

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