Package org.forester.go
Class GoUtils
- java.lang.Object
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- org.forester.go.GoUtils
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public final class GoUtils extends java.lang.Object
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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)
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Method Detail
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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 countedexperiment_set
- the list of GO terms to be analyzedall_go_terms
- all terms in the ontology- Returns:
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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)
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createGoIdToGoTermMap
public static java.util.Map<GoId,GoTerm> createGoIdToGoTermMap(java.util.List<GoTerm> go_terms)
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getAllSuperGoIds
public static java.util.SortedSet<GoId> getAllSuperGoIds(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
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getAllSuperGoTerms
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, java.util.List<GoTerm> go_terms)
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getAllSuperGoTerms
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoId go_id, java.util.Map<GoId,GoTerm> goid_to_term_map)
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getAllSuperGoTerms
public static java.util.SortedSet<GoTerm> getAllSuperGoTerms(GoTerm go_term, java.util.Map<GoId,GoTerm> goid_to_term_map)
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getPenultimateGoTerm
public static GoTerm getPenultimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
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getUltimateGoTerm
public static GoTerm getUltimateGoTerm(GoTerm go_term, java.util.Map<GoId,GoTerm> map)
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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
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