edu.uchsc.ccp.nlp.ei.mutation

Class PointMutation

java.lang.Object

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

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

public class PointMutation
extends Mutation

A class for storing information about protein point mutations

Version:

1.0

Author:

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

Constructor Summary

Constructors

Constructor and Description
PointMutation(String position, String wtResidue, String mutResidue)

Method Summary

Modifier and Type	Method and Description
static PointMutation	createPointMutationFrom_wNm(String wNm) Create PointMutation from wNm-format, single-letter abbreviated mention.
boolean	equals(Object obj) Two PointMutation objects are equal if their Position, WtResidue, and MutResidue values are all equal.
char	getMutResidue() Return the mutant residue for this point mutation.
char	getWtResidue() Return the wild-type residue for this point mutation.
int	hashCode() To be overridden by subclasses
boolean	isMatchesLongForm() Return if the originally matched wildtype or mutated allele matched a long form (e.g., Lysine -> true, L -> false)
boolean	isValid() Only Nucleotide Sequence Mutations (NSM) are allowed to have a positional offset of < 0 This method checks if the position of a mutation is valid;
char	normalizeResidueIdentity(String residue) Normalize three-letter and full residue names to their one-letter abbreviations.
protected Map<String,String>	populateAminoAcidOneToOneLookupMap()
String	toString() Override toString(), returns mutation as a string in wNm format

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

error, getId, getPosition, setId, updateMapping, warn

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PointMutation

public PointMutation(String position,
                     String wtResidue,
                     String mutResidue)
              throws MutationException

Throws:

MutationException

Method Detail

isValid

public boolean isValid()

Only Nucleotide Sequence Mutations (NSM) are allowed to have a positional offset of < 0 This method checks if the position of a mutation is valid;

Returns:

normalizeResidueIdentity

public char normalizeResidueIdentity(String residue)
                              throws MutationException

Normalize three-letter and full residue names to their one-letter abbreviations. If a residue identity is passed in which does not fall into the set of canonical amino acids a MutationError is raised.

Parameters:

residue -

Returns:

Throws:

MutationException

populateAminoAcidOneToOneLookupMap

protected Map<String,String> populateAminoAcidOneToOneLookupMap()

getMutResidue

public char getMutResidue()

Return the mutant residue for this point mutation.

Returns:

getWtResidue

public char getWtResidue()

Return the wild-type residue for this point mutation.

Returns:

isMatchesLongForm

public boolean isMatchesLongForm()

Return if the originally matched wildtype or mutated allele matched a long form (e.g., Lysine -> true, L -> false)

Returns:

equals

public boolean equals(Object obj)

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

Overrides:

equals in class Mutation

Returns:

hashCode

public int hashCode()

Description copied from class: Mutation

To be overridden by subclasses

Overrides:

hashCode in class Mutation

toString

public String toString()

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

Overrides:

toString in class Mutation

Returns:

createPointMutationFrom_wNm

public static PointMutation createPointMutationFrom_wNm(String wNm)
                                                 throws MutationException

Create PointMutation from wNm-format, single-letter abbreviated mention. This wrapper function creates a PointMutation object from a mutation mention formatted in wNm-format, where w and m are the wild-type and mutant amino acids in their SINGLE-LETTER abbreviations, and N is an integer representing the sequence position.

Parameters:

wNm - a 3-character String representing a mutation mention in the wNm format

Returns:

Throws:

MutationException