BioinfoFieldExtractor
Class LocalAlignment

java.lang.Object
  BioinfoFieldExtractor.LocalAlignment

public class LocalAlignment
extends java.lang.Object

Constructor Summary

LocalAlignment()

Method Summary

float[][]	alignLocally(java.util.ArrayList<java.lang.String> sequences)
float[][]	alignLocally(java.util.ArrayList<java.lang.String> sequences, float[][] similarityMtx) Performs Smith Waterman local alignment algorithm to calculate similarity between message sequences.
int	performSmithWatermanAlignment(int[] msg1, int[] msg2) Smith-Waterman algorithm to perform local alignment of two messages.

Methods inherited from class java.lang.Object

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

Constructor Detail

LocalAlignment

public LocalAlignment()

Method Detail

alignLocally

public float[][] alignLocally(java.util.ArrayList<java.lang.String> sequences)

alignLocally

public float[][] alignLocally(java.util.ArrayList<java.lang.String> sequences,
                              float[][] similarityMtx)

Performs Smith Waterman local alignment algorithm to calculate similarity between message sequences. Returns the distance matrix representing the "distance in similarity" between its members.

Parameters:

sequences - An array list of message sequences

similarityMtx - similarity matrix

Returns:

The distance matrix

performSmithWatermanAlignment

public int performSmithWatermanAlignment(int[] msg1,
                                         int[] msg2)

Smith-Waterman algorithm to perform local alignment of two messages. Returns the similarity score

Parameters:

msg1 - The first message in dec ascii representation

msg2 - The second message in dec ascii representation

sMatrix - The similarity matrix

Returns:

The similarity score between two messages