Package de.julielab.jules.ae.genemapping.resources

Class DictionaryFamilyDomainFilter

  • public class DictionaryFamilyDomainFilter
extends java.lang.Object

    Removes gene synonyms from the given dictionary that look like gene families or gene domains or are otherwise unspecific.This is yet another dictionary cleaning algorithm besied DictionaryGeneralFilter and the DictCleaner.pl script in the update_resources_and_indices directory.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static boolean isFiltered​(de.julielab.jules.ae.genemapping.CandidateFilter cf, java.lang.String synonym)
      Checks the synonym for length and token number and if it looks as though it wouldn't designate a concrete gene but rather a family or domain.
      static void main​(java.lang.String[] args)  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • DictionaryFamilyDomainFilter

        public DictionaryFamilyDomainFilter()

    • Method Detail

      • main

        public static void main​(java.lang.String[] args)

      • isFiltered

        public static boolean isFiltered​(de.julielab.jules.ae.genemapping.CandidateFilter cf,
                                 java.lang.String synonym)
        Checks the synonym for length and token number and if it looks as though it wouldn't designate a concrete gene but rather a family or domain.
        Parameters:
        cf - A CandidateFilter instance.
        synonym - The synonym under scrutiny.
        Returns:
        true if the synonym should be removed from the dictionary, false otherwise.