org.specrunner.util.aligner.core
Class NeedlemanWunschAligner

java.lang.Object
  org.specrunner.util.aligner.core.NeedlemanWunschAligner

All Implemented Interfaces:

IStringAligner

public class NeedlemanWunschAligner
extends Object
implements IStringAligner

Default alignment implementation, a Needleman-Wunsch algorithm.

Author:

Thiago Santos

Field Summary

protected String	expected The expected value.
protected StringBuilder	expectedAligned The expected value aligned.
protected char	fillCharacter The character to be using on error report.
protected String	received The received string.
protected StringBuilder	receivedAligned The received value aligned.

Constructor Summary

NeedlemanWunschAligner(String expected, String received)
Creates an aligner with default fill character.

NeedlemanWunschAligner(String expected, String received, char fillCharacter)
Creates an aligner with both strings and fill character.

Method Summary

protected void	align() Perform alignment.
protected List<Character>	alphabet(String a, String b) Creates the local alphabet.
protected int[][]	calculate(String a, String b, List<Character> list, int[][] s, int d) Calculate the matrix of gaps.
String	getExpected() The expected string.
StringBuilder	getExpectedAligned() The base string aligned.
char	getFillCharacter() Fill character in alignment.
String	getReceived() The received string.
StringBuilder	getReceivedAligned() The received string aligned.
protected int	penalty(int size) Calculate penalty.
protected int[][]	scoring(int size) The scoring matrix.
protected String	toString(int[][] d) String representation of a matrix.
protected void	traceback(String a, String b, List<Character> list, int[][] s, int d, int[][] f) Fill the alignment result.

Methods inherited from class java.lang.Object

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

Field Detail

expected

protected String expected

The expected value.

expectedAligned

protected StringBuilder expectedAligned

The expected value aligned.

fillCharacter

protected char fillCharacter

The character to be using on error report.

received

protected String received

The received string.

receivedAligned

protected StringBuilder receivedAligned

The received value aligned.

Constructor Detail

NeedlemanWunschAligner

public NeedlemanWunschAligner(String expected,
                              String received)

Creates an aligner with default fill character.

Parameters:

expected - The expected string.

received - The received string.

NeedlemanWunschAligner

public NeedlemanWunschAligner(String expected,
                              String received,
                              char fillCharacter)

Creates an aligner with both strings and fill character.

Parameters:

expected - The expected string.

received - The received string.

fillCharacter - The fill character.

Method Detail

getExpected

public String getExpected()

Description copied from interface: IStringAligner

The expected string.

Specified by:

getExpected in interface IStringAligner

Returns:

Base string.

getExpectedAligned

public StringBuilder getExpectedAligned()

Description copied from interface: IStringAligner

The base string aligned.

Specified by:

getExpectedAligned in interface IStringAligner

Returns:

The string expected filled with 'fill character' where necessary.

getFillCharacter

public char getFillCharacter()

Description copied from interface: IStringAligner

Fill character in alignment.

Specified by:

getFillCharacter in interface IStringAligner

Returns:

The fill alignment.

getReceived

public String getReceived()

Description copied from interface: IStringAligner

The received string.

Specified by:

getReceived in interface IStringAligner

Returns:

Received string.

getReceivedAligned

public StringBuilder getReceivedAligned()

Description copied from interface: IStringAligner

The received string aligned.

Specified by:

getReceivedAligned in interface IStringAligner

Returns:

The string received filled with 'fill character' where necessary.

align

protected void align()

Perform alignment.

alphabet

protected List<Character> alphabet(String a,
                                   String b)

Creates the local alphabet.

Parameters:

a - Left string.

b - Right string.

Returns:

The list of characters.

calculate

protected int[][] calculate(String a,
                            String b,
                            List<Character> list,
                            int[][] s,
                            int d)

Calculate the matrix of gaps.

Parameters:

a - The left string.

b - The right string.

list - The alphabet.

s - The scoring matrix.

d - The penalty.

Returns:

The proximity matrix.

scoring

protected int[][] scoring(int size)

The scoring matrix.

Parameters:

size - The size.

Returns:

The scoring matrix.

penalty

protected int penalty(int size)

Calculate penalty.

Parameters:

size - The size of alphabet.

Returns:

The penalty.

traceback

protected void traceback(String a,
                         String b,
                         List<Character> list,
                         int[][] s,
                         int d,
                         int[][] f)

Fill the alignment result.

Parameters:

a - The left string.

b - The right string.

list - The alphabet.

s - The scoring matrix.

d - The penalty.

f - The current proximity matrix.

toString

protected String toString(int[][] d)

String representation of a matrix.

Parameters:

d - The matrix.

Returns:

The string for the matrix.