org.forester.go
Class GoUtils
java.lang.Object
org.forester.go.GoUtils
public final class GoUtils
- extends Object
Method Summary |
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)
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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)
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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)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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 countedexperiment_set
- the list of GO terms to be analyzedall_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)
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)
getAllSuperGoIds
public static SortedSet<GoId> getAllSuperGoIds(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