BioinfoFieldExtractor
Class GlobalAlignment

java.lang.Object
  BioinfoFieldExtractor.GlobalAlignment

public class GlobalAlignment
extends java.lang.Object

This class provides functionality for global alignment for 2 messages sequences based on the NeedlemanWunsch algorithm.

Author:

Serge Gorbunov

Constructor Summary

GlobalAlignment()

Method Summary

NeedlemanWunschHolder	alignGlobally(java.util.ArrayList<java.lang.Integer> msg1, java.util.ArrayList<java.lang.Integer> msg2)
NeedlemanWunschHolder	alignGlobally(java.util.ArrayList<java.lang.Integer> msg1, java.util.ArrayList<java.lang.Integer> msg2, float[][] similarityMatrix) Converts the strings into a byte array and calls the main alignGlobaly method.
NeedlemanWunschHolder	alignGlobally(int[] msg1, int[] msg2, float[][] similarityMtx) Performs NeedlemanWunsch global alignment algorithm to calculate similarity between message sequences.
int[]	convertToDec(java.lang.String msg) Converts string to an array of dec representations of the chars

Methods inherited from class java.lang.Object

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

Constructor Detail

GlobalAlignment

public GlobalAlignment()

Method Detail

alignGlobally

public NeedlemanWunschHolder alignGlobally(java.util.ArrayList<java.lang.Integer> msg1,
                                           java.util.ArrayList<java.lang.Integer> msg2)

alignGlobally

public NeedlemanWunschHolder alignGlobally(java.util.ArrayList<java.lang.Integer> msg1,
                                           java.util.ArrayList<java.lang.Integer> msg2,
                                           float[][] similarityMatrix)

Converts the strings into a byte array and calls the main alignGlobaly method.

alignGlobally

public NeedlemanWunschHolder alignGlobally(int[] msg1,
                                           int[] msg2,
                                           float[][] similarityMtx)

Performs NeedlemanWunsch global alignment algorithm to calculate similarity between message sequences. TODO: implement the use of the similarity matrix

Parameters:

msg1 - The first message

msg2 - The second message

similarityMtx - similarity matrix

Returns:

The needlemanWunch Holder object with the alignment info

convertToDec

public int[] convertToDec(java.lang.String msg)

Converts string to an array of dec representations of the chars