hultig.align
Class SWaterman

java.lang.Object
  hultig.align.SWaterman

public final class SWaterman
extends Object

This class contains an implementation of the Smith Waterman algorithm for locally align sequence pairs. This algorithm have been used for DNA sequence alignment, in genetics, and is here adapted for the alignment of words, between sentence pairs. Another adaptation consists in the capability of output more than one sub-alignment.

University of Beira Interior (UBI)
Centre For Human Language Technology and Bioinformatics (HULTIG)

Constructor Summary

SWaterman(int[] vs1, int[] vs2)
JPC - Para vectores representando frases.

SWaterman(int[] vs1, int[] vs2, CorpusIndex dict)
JPC - Para vectores representando frases.

SWaterman(int[] vs1, int[] vs2, CorpusIndex dict, int[] vkeyws)

SWaterman(String str1, String str2)

Method Summary

Vector<int[][]>	getAlignementsOLD() Devolve um vector de sub-alinhamentos.
Vector<int[][]>	getAlignments() Devolve um vector de sub-alinhamentos.
double	getAlignmentScore() Get the alignment score between the two input strings.
int[][]	getAlignmentsVect(int i, int j, Vector<Integer> va1, Vector<Integer> va2) Returns the local alignments ending in the (i, j) cell.
List	getMatches() Return a set of Matches idenfied in Dynamic programming matrix.
Vector<String[]>	getParaAlignsHoriz() Introduced by JPC Modified: 2007/03/16.
Vector<SimpleChaining.Match>	getXBestMatches(List matches) Por JPC 20070317
static void	main(String[] args) M A I N
void	printAlignments() Output the local alignments with the maximum score.
void	printDPMatrix() print the dynmaic programming matrix
static void	printParaAligns(Text txt) INTRODUZIDO POR JPC OLD METHOD ==> vertical print.
static void	printParaAlignsHoriz(int[] v1, int[] v2, CorpusIndex dict) Introduced by JPC
static void	printParaAlignsHoriz(Text txt) Introduced by JPC
static boolean	processParaFile(String filename) INTRODUZIDO POR JPC
void	setDictionary(CorpusIndex dictionary)
static String	underscore(int n)
static void	x200607070830()
static void	x200607201745()

Methods inherited from class java.lang.Object

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

Constructor Detail

SWaterman

public SWaterman(String str1,
                 String str2)

SWaterman

public SWaterman(int[] vs1,
                 int[] vs2)

JPC - Para vectores representando frases.

SWaterman

public SWaterman(int[] vs1,
                 int[] vs2,
                 CorpusIndex dict)

JPC - Para vectores representando frases. Acrescenta a passagem do dicionário. 2007/03/14

SWaterman

public SWaterman(int[] vs1,
                 int[] vs2,
                 CorpusIndex dict,
                 int[] vkeyws)

Method Detail

setDictionary

public void setDictionary(CorpusIndex dictionary)

getAlignmentScore

public double getAlignmentScore()

Get the alignment score between the two input strings.

getAlignmentsVect

public int[][] getAlignmentsVect(int i,
                                 int j,
                                 Vector<Integer> va1,
                                 Vector<Integer> va2)

Returns the local alignments ending in the (i, j) cell. aligned1 and aligned2 are suffixes of final aligned strings found in backtracking before calling this function. Note: the strings are replicated at each recursive call. Use buffers or stacks to improve efficiency. adapted by JPC, 2006/07/07

getAlignementsOLD

public Vector<int[][]> getAlignementsOLD()

Devolve um vector de sub-alinhamentos.

Returns:

Vector

getAlignments

public Vector<int[][]> getAlignments()

Devolve um vector de sub-alinhamentos.

Returns:

Vector

underscore

public static String underscore(int n)

printAlignments

public void printAlignments()

Output the local alignments with the maximum score.

printDPMatrix

public void printDPMatrix()

print the dynmaic programming matrix

getMatches

public List getMatches()

Return a set of Matches idenfied in Dynamic programming matrix. A match is a pair of subsequences whose score is higher than the preset scoreThreshold

x200607070830

public static void x200607070830()

x200607201745

public static void x200607201745()

printParaAligns

public static void printParaAligns(Text txt)

INTRODUZIDO POR JPC OLD METHOD ==> vertical print.

printParaAlignsHoriz

public static void printParaAlignsHoriz(Text txt)

Introduced by JPC

getParaAlignsHoriz

public Vector<String[]> getParaAlignsHoriz()

Introduced by JPC Modified: 2007/03/16.

printParaAlignsHoriz

public static void printParaAlignsHoriz(int[] v1,
                                        int[] v2,
                                        CorpusIndex dict)

Introduced by JPC

processParaFile

public static boolean processParaFile(String filename)

INTRODUZIDO POR JPC

getXBestMatches

public Vector<SimpleChaining.Match> getXBestMatches(List matches)

Por JPC 20070317

Parameters:

matches - List

Returns:

Vector

main

public static void main(String[] args)

M A I N