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C

createPointMutationFrom_wNm(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Create PointMutation from wNm-format, single-letter abbreviated mention.

D

de.julielab.jcore.ae.mutationfinder - package de.julielab.jcore.ae.mutationfinder

E

edu.uchsc.ccp.nlp.ei.mutation - package edu.uchsc.ccp.nlp.ei.mutation

equals(Object) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

equals(Object) - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Two PointMutation objects are equal if their Position, WtResidue, and MutResidue values are all equal.

error(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

error(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

extractMappingsFromPythonRegex(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

extractMutations(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

Extract point mutations mentions from raw_text and return them in a map.

extractMutations(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Extract point mutations mentions from raw_text and return them in a map.

G

getMutResidue() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Return the mutant residue for this point mutation.

getPosition() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

Retrieves the mutation sequence position

getWtResidue() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Return the wild-type residue for this point mutation.

H

hashCode() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

hashCode() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

I

initialize(UimaContext) - Method in class de.julielab.jcore.ae.mutationfinder.MutationAnnotator

M

main(String[]) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

The main method demonstrates the execution of MutationFinder.

MUT_RES - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Mutation - Class in edu.uchsc.ccp.nlp.ei.mutation

Mutation is a base class for different types of mutations.

Mutation(int) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.Mutation

Mutation(String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.Mutation

MutationAnnotator - Class in de.julielab.jcore.ae.mutationfinder

MutationAnnotator() - Constructor for class de.julielab.jcore.ae.mutationfinder.MutationAnnotator

MutationException - Exception in edu.uchsc.ccp.nlp.ei.mutation

Exception thrown by MutationFinder

MutationException(String) - Constructor for exception edu.uchsc.ccp.nlp.ei.mutation.MutationException

MutationExtractor - Class in edu.uchsc.ccp.nlp.ei.mutation

A base class for extracting Mutations from text

MutationExtractor() - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

MutationFinder - Class in edu.uchsc.ccp.nlp.ei.mutation

This is the Java implementation of MutationFinder (original version in Python by J.

MutationFinder(File) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationFinder(InputStream) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

MutationFinder(String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationFinder(Set<String>) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

N

normalizeResidueIdentity(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Normalize three-letter and full residue names to their one-letter abbreviations.

P

PointMutation - Class in edu.uchsc.ccp.nlp.ei.mutation

A class for storing information about protein point mutations

PointMutation(int, String, String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Initialize the object and call the base class constructor.

PointMutation(String, String, String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

populateAminoAcidNameToOneLookupMap() - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

This method simple fills the two mappings between amino acid name and the amino acid one-letter code

populateAminoAcidOneToOneLookupMap() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

populateAminoAcidThreeToOneLookupMap() - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

This method simple fills the two mappings between amino acid one letter code and the amino acid three letter code

POS - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

process(JCas) - Method in class de.julielab.jcore.ae.mutationfinder.MutationAnnotator

R

removeTagsFromPythonRegex(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

T

toString() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

toString() - Method in exception edu.uchsc.ccp.nlp.ei.mutation.MutationException

toString() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Override toString(), returns mutation as a string in wNm format

U

updateMapping(Map<String, String>, Map<String, String>) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

W

warn(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

warn(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

WT_RES - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

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