Package edu.uchsc.ccp.nlp.ei.mutation

Class MutationExtractor

  • Direct Known Subclasses:
    MutationFinder
    public abstract class MutationExtractor
extends Object
    A base class for extracting Mutations from text
    Version:
    1.0
    Author:
    William A. Baumgartner, Jr.
    william.baumgartner@uchsc.edu

    • Constructor Detail

      • MutationExtractor

        public MutationExtractor()

    • Method Detail

      • populateAminoAcidThreeToOneLookupMap

        protected static Map<String,​String> populateAminoAcidThreeToOneLookupMap()
        This method simple fills the two mappings between amino acid one letter code and the amino acid three letter code
        Returns:
        a mapping from three-letter code to one-letter code

      • populateAminoAcidNameToOneLookupMap

        protected static Map<String,​String> populateAminoAcidNameToOneLookupMap()
        This method simple fills the two mappings between amino acid name and the amino acid one-letter code
        Returns:
        a mapping from amino acid full name to one-letter code

      • extractMutations

        public abstract Map<Mutation,​Set<int[]>> extractMutations​(String rawText)
                                                         throws MutationException
        Extract point mutations mentions from raw_text and return them in a map. The result of this method is a mapping of PointMutation objects to a set of spans (int arrays of size 2) where they were identified. Spans are presented in the form of character-offsets in text. Example result:
        raw_text: 'We constructed A42G and L22G, and crystalized A42G.'
        result = {PointMutation(42,'A','G'):[(15,19),(46,50)],
        PointMutation(22,'L','G'):[(24,28)]}
        Note that the spans won't necessarily be in increasing order, due to the order of processing regular expressions.
        Parameters:
        rawText - the text to be processed
        Returns:
        Throws:
        MutationException

      • warn

        protected void warn​(String message)

      • error

        protected void error​(String message)