edu.uchsc.ccp.nlp.ei.mutation

Class Mutation

java.lang.Object

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

Direct Known Subclasses:

PointMutation

public class Mutation
extends Object

Mutation is a base class for different types of mutations. Currently the only Mutation type defined is a PointMutation, but in the future Insertion and Deletion objects may also be defined.

Version:

1.0

Author:

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

Constructor Summary

Constructors

Constructor and Description
Mutation(int position)
Mutation(String position)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj) To be overridden by subclasses
protected void	error(String message)
int	getId() Retrieves the pattern id
String	getPosition() Retrieves the mutation sequence position
int	hashCode() To be overridden by subclasses
void	setId(int id)
String	toString() To be overridden by subclasses
protected void	updateMapping(Map<String,String> inputMap, Map<String,String> additionalMappings)
protected void	warn(String message)

Methods inherited from class java.lang.Object

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

Constructor Detail

Mutation

public Mutation(int position)
         throws MutationException

Parameters:

position - -- the sequence position or start position of the mutation

Throws:

MutationException

Mutation

public Mutation(String position)

Parameters:

position - -- the sequence position or start position of the mutation

Method Detail

getPosition

public String getPosition()

Retrieves the mutation sequence position

Returns:

an int representing the position or start position of the mutation

getId

public int getId()

Retrieves the pattern id

Returns:

an int representing the patternId

setId

public void setId(int id)

updateMapping

protected void updateMapping(Map<String,String> inputMap,
                             Map<String,String> additionalMappings)

warn

protected void warn(String message)

error

protected void error(String message)

equals

public boolean equals(Object obj)

To be overridden by subclasses

Overrides:

equals in class Object

hashCode

public int hashCode()

To be overridden by subclasses

Overrides:

hashCode in class Object

toString

public String toString()

To be overridden by subclasses

Overrides:

toString in class Object