edu.uchsc.ccp.nlp.ei.mutation

Class MutationExtractor

java.lang.Object

edu.uchsc.ccp.nlp.ei.mutation.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

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,String>	populateAminoAcidNameToOneLookupMap This method simple fills the two mappings between amino acid name and the amino acid one-letter code
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

Constructor Summary

Constructors

Constructor and Description
MutationExtractor()

Method Summary

Modifier and Type	Method and Description
protected void	error(String message)
abstract Map<Mutation,Set<int[]>>	extractMutations(String rawText) Extract point mutations mentions from raw_text and return them in a map.
protected void	warn(String message)

Methods inherited from class java.lang.Object

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

Field Detail

populateAminoAcidThreeToOneLookupMap

public 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

populateAminoAcidNameToOneLookupMap

public static Map<String,String> populateAminoAcidNameToOneLookupMap

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

Constructor Detail

MutationExtractor

public MutationExtractor()

Method Detail

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)