/** * Constructor. * * @param extraSynonyms a set of lists of unofficial names or common typos * @param ontologyManager the object that gives access to some of controlled vocabularies/ontologies (OBO) */ public XrefHelper(Set<List<String>> extraSynonyms, BiopaxOntologyManager ontologyManager) { // all database names and ID patterns go here this.dataPatterns = new ConcurrentHashMap<String, Pattern>(); // copy/normalize provided extra synonyms this.extraGroups = new CompositeCollection<String>(); if(extraSynonyms != null) { for(List<String> group : extraSynonyms) { Collection<String> newG = new ArrayList<String>(); for(String s : group) newG.add(dbName(s)); //trim, uppercase, add this.extraGroups.addComposited(newG); } } this.ontologyManager = ontologyManager; }
/** * Constructor. * * @param extraSynonyms a set of lists of unofficial names or common typos * @param ontologyManager the object that gives access to some of controlled vocabularies/ontologies (OBO) */ public XrefHelper(Set<List<String>> extraSynonyms, BiopaxOntologyManager ontologyManager) { // all database names and ID patterns go here this.dataPatterns = new ConcurrentHashMap<String, Pattern>(); // copy/normalize provided extra synonyms this.extraGroups = new CompositeCollection<String>(); if(extraSynonyms != null) { for(List<String> group : extraSynonyms) { Collection<String> newG = new ArrayList<String>(); for(String s : group) newG.add(dbName(s)); //trim, uppercase, add this.extraGroups.addComposited(newG); } } this.ontologyManager = ontologyManager; }
allSynonyms.addComposited(synonyms); synonyms.add(s); allSynonyms.addComposited(synonyms); allSynonyms.addComposited((Collection<? extends String>[]) extraGroups.getCollections().toArray()); merged.add(0, primary); this.allSynonyms.addComposited(merged); } else { assert !groupsToMerge.isEmpty(); //one! this.allSynonyms.addComposited(groupsToMerge.iterator().next());
allSynonyms.addComposited(synonyms); synonyms.add(s); allSynonyms.addComposited(synonyms); allSynonyms.addComposited((Collection<? extends String>[]) extraGroups.getCollections().toArray()); merged.add(0, primary); this.allSynonyms.addComposited(merged); } else { assert !groupsToMerge.isEmpty(); //one! this.allSynonyms.addComposited(groupsToMerge.iterator().next());