public final class GoUtils
extends java.lang.Object
Modifier and Type | Method | Description |
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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) |
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)
categories
- the set of super terms to be countedexperiment_set
- the list of GO terms to be analyzedall_go_terms
- all terms in the ontologypublic 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)
public static java.util.Map<GoId,GoTerm> createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
public static java.util.SortedSet<GoId> getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
public static GoTerm getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
public static GoTerm getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
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
java.io.IOException