uk.ac.sanger.cgp.standalonecsa.jabawat
Class Jabawat

java.lang.Object
  uk.ac.sanger.cgp.standalonecsa.jabawat.Jabawat

public class Jabawat
extends java.lang.Object

Originally part of CGP's internal geneutil package JaBaWAT basically stands for Java Basic Word Alignment Tool. It aligns a string with a larger string and finds the coordinates of the hit within the larger string.

Author:

kg1, $Author: kr2 $

Constructor Summary

Jabawat()
Creates a new instance of Jabawat

Method Summary

static JabawatResults

runJabawat(java.lang.String target, java.lang.String query, JabawatResults jr, int mismatches) Runs the core of the JaBaWAT alignment program using two strings representing the sequences.

Methods inherited from class java.lang.Object

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

Constructor Detail

Jabawat

public Jabawat()

Creates a new instance of Jabawat

Method Detail

runJabawat

public static JabawatResults runJabawat(java.lang.String target,
                                        java.lang.String query,
                                        JabawatResults jr,
                                        int mismatches)

Runs the core of the JaBaWAT alignment program using two strings representing the sequences.

Parameters:

target - Target sequence

query - Query sequence

jr - results object

mismatches - number of mismatches allowed

Returns:

jabawat results object