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

java.lang.Object
  extended by 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