edu.uchsc.ccp.nlp.ei.mutation

Class MutationFinder

java.lang.Object

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

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

public class MutationFinder
extends MutationExtractor

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

Version:

1.0

Author:

William A. Baumgartner, Jr.
william.baumgartner@uchsc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected static Set<String>	ambiguous
protected static String	MUT_RES
protected static String	POS
protected static String	WT_RES

Fields inherited from class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

populateAminoAcidNameToOneLookupMap, populateAminoAcidThreeToOneLookupMap

Constructor Summary

Constructors

Constructor and Description
MutationFinder() Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.
MutationFinder(File file) Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.
MutationFinder(Set<String> unprocessed_python_regexes) Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.
MutationFinder(String fileName) Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

Method Summary

Modifier and Type	Method and Description
static Map<String,Integer>	extractMappingsFromPythonRegex(String pythonRegex)
Map<Mutation,Set<int[]>>	extractMutations(String rawText) Extract point mutations mentions from raw_text and return them in a map.
static void	main(String[] args) The main method demonstrates the execution of MutationFinder.
static String	removeTagsFromPythonRegex(String regexStr)

Methods inherited from class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

error, warn

Methods inherited from class java.lang.Object

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

Field Detail

MUT_RES

protected static final String MUT_RES

See Also:

Constant Field Values

WT_RES

protected static final String WT_RES

See Also:

Constant Field Values

POS

protected static final String POS

See Also:

Constant Field Values

ambiguous

protected static final Set<String> ambiguous

Constructor Detail

MutationFinder

public MutationFinder()

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations. This constructor loads the regular expressions from the attached Java Archive at resources/mutations.txt.

MutationFinder

public MutationFinder(String fileName)

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations. This constructor loads the regular expressions from a file designated by the filename input parameter.

Parameters:

fileName - Since the original development of MutationFinder was conducted in Python, the input file contains regular expressions that are Python-specific (due to the fact that that Java does not handle explicitly named groups). These regular expressions must therefore be converted prior to use in the Java implementation. This conversion is handled by this constructor.

MutationFinder

public MutationFinder(File file)

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations. This constructor loads the regular expressions from a file designated by the Java File input parameter.

Parameters:

file - Since the original development of MutationFinder was conducted in Python, the input file contains regular expressions that are Python-specific (due to the fact that that Java does not handle explicitly named groups). These regular expressions must therefore be converted prior to use in the Java implementation. This conversion is handled by this constructor.

MutationFinder

public MutationFinder(Set<String> unprocessed_python_regexes)

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations. This constructor loads the regular expressions from a Set of Strings representing the regular expressions.

Parameters:

unprocessed_python_regexes - Since the original development of MutationFinder was conducted in Python, the set of regular expressions used is Python-specific in that Java does not handle explicitly named groups. These regular expressions must therefore be converted prior to use in the Java implementation. This conversion is handled by this constructor.

Method Detail

extractMappingsFromPythonRegex

public static Map<String,Integer> extractMappingsFromPythonRegex(String pythonRegex)

removeTagsFromPythonRegex

public static String removeTagsFromPythonRegex(String regexStr)

extractMutations

public 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.

Specified by:

extractMutations in class MutationExtractor

Parameters:

rawText - the text to be processed

Returns:

Throws:

MutationException

main

public static void main(String[] args)

The main method demonstrates the execution of MutationFinder. Three input arguments are required, the regular expression file used by MutationFinder, an input file to process, and output file to write the generated results.

The input file in this case contains one document per line, where each line takes the format:

documentIDdocumentText

The output file will contain the mutations found for each document (one document per line) where each line takes the format:

documentIDmutationmutationmutation...

Parameters:

args - args[0] - the regular expression file
args[1] - the input file containing text to process
args[2] - the output file