temprunner.java

/*
 * 
Copyright (c) 2010 The Regents of the University of California.
All rights reserved.
Permission is hereby granted, without written agreement and without
license or royalty fees, to use, copy, modify, and distribute this
software and its documentation for any purpose, provided that the above
copyright notice and the following two paragraphs appear in all copies
of this software.

IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.

THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
ENHANCEMENTS, OR MODIFICATIONS..
 */

package sequencing;

import java.io.File;
import java.io.IOException;

/**
 *
 * @author jcanderson_Home
 */
public class temprunner {

 public static void main(String[] args){
        ABITrace abi1=null, abi2=null, abi3=null, abi4=null, abi5=null;

    /**
     * Put in the String of the sequence you want to compare
     */
        //GAATTCATGAGATCTCAGCTGAAGTGACCGGATTAGCAACGCAGTAACCCGAAATCCTCTTTGACAAAGACAAAGCGTGTCAGGCTGATTCTGATGCGCTTTTTTTTGAAATGTCACAAAAATTCCATGCGGGAGATGAGAGCTAAAATCCCCGTGCAGAACTTTCCACCCAGGGCGAGAAAACTTGTCATTTTGACCTGTTCGCCCTTCGGAACAGTCGAAATCGATCGCGCATCGCTTTCGTGCATAGTTATGCAGCCCTCTAAAAACGATTCTGGCGCGTTTTTCTGGTTTGGCCTGGTGTTTTCTTGTCTTTTTGCGTTTTTTGCGCCAGAAAGCGACTGAGGGCGTTTTAAGGGGTACGTACAACGGGAGTTATGGTAAATGGATCGGGTTTTCGGGAAGGTTCGACAGGATTTGCCGTTGGGTGTAGTGTAAGCGACTGAAAAACAAACGCCCCTGAAATCATGTCCAGATCCGGCAAGATTCAACATGAAATACAGAGGGCGTGTAGGTCGCATAACCCGGAGTGAATCGTAACACATGAGCGCCGCGCTTCAATACTTCGACGAAAATTTACCCCATCGTCCCTATCACACGGATGATCTCGCTTTTGGTCTTCGCATCTCCGGAAAAGGGGGTGCGCTTCTTGGGCGGTACCTACAGCACAACCAGCCTCATGCGCAGTTCTGGGTGGTTTTTGATGTTGACCGGGGGGGGGCGGCGATTGGGAGGAGCGACAAGAACCCCCCCCCGACCAACACCATAAAAAAAACCGCCAACGATCACCCCCACCTGCTGTACTCACTCAATATCGCCGTGAGAACCGCGCCTGCTGCTTCGGTTAAGGCGCTGAAATACGCCGCCGCGATTGAACGTGCGTTGTGTGAAAAAAAGGGCGCAGATGTAAACTACAGCGGCCTGATTTGCAAAAATCCGTTCCATCTGGAATGGCAGGTGATGGAGTGGCGTGAGGAAGCCTATACCCTCGATGAACTGGCTGATTATCTTGATTTGAGCACTTCAGCGCGCCGTAGCATCGATAAACATTACGGGATGGGGCGAAACTGCCATCTGTTCGAAATGACGCGCAAATGGGCTTACAGGGCGATTCGTCAGGGCTGGCCAGCATTCTCACAGTGGCTTGATGCCGTGATTCAGCGTGTCGAAATGTACAACGCATCGCTTCCCGTTCCGCTTTCACCTCCTGAATGTCGGGCTATTGGCAAGAGTATTGCGAAATACACGCACAGGAACTTCACGGCGGAAACTTTCGCACAGTATGTGGCTGATACGCACACGCCAGAAATACAGGCCAAGAGAGGCAGGAAAGGTGGCATCGCTAAAGGCGAAGCCTACGATGACAAGCGTTTCATGGCGCTATGTATGCTGGAGAATGGATATTCTCAGAAAGCTATTGCGGCGATGTTGGAGGTTTCTACTCGAACCATTCGAAACTGGAAAAGCGGAAAATAGGGATCC
        String BG4_seq="GAATTCATGAGATCTCAGCTGAAGTGACCGGATTAGCAACGCAGTAACCCGAAATCCTCTTTGACAAAGACAAAGCGTGTCAGGCTGATTCTGATGCGCTTTTTTTTGAAATGTCACAAAAATTCCATGCGGGAGcTGAGAGCTAAAATCCCCGTGCAGAACTTTCCACCCAGGGCGAGAAAACTTGTCATTTTGACCTGTTCGCCCTTCGGAACAGTCGAAATCGATCGCGCATCGCTTTCGTGCTAGTTATGCAGCCCTCTAAAAACGATTCTGGCGCGTTTTTCTGGTTTGGCCTGGTGTTTTCTTGTCTTTTTGCGTTTTTTGCGCCAGAAAGCGACTGAGGGCGTTTTAAGGGGTACGTACAACGGGAGTTATGGCTAAATGGATCGGGTTTTCGGGAAGGTTCGACAGGATTTGCCGTTGGGTGTAGTGTAAGCGACTGAAAAACAAACGCCCCTGAAATCATGTCCAGATCCGGCAAGATTCAACATGAAATACAGAGGGCGTGTAGGTCGCATAACCCGGAGTGAATCGTAACACATGAGCGCCGCGCTTCAATACTTCGACGAAAATTTACCCCATCGTCCCTATCACACGGATGATCTCGCTTTTGGTCTTCGCATCTCCGGAAAAGGGGGTGCGCTTCTTGGGCGGTACCTACAGCACAACCAGCCTCATGCGCAGTTCTGGGTGGTTTTTGATGTTGACCGGGGGGGGGCGGCGATTGGGAGGAGCGACAAGAACCCCCCCCCGACCAACACCATAAAAAAAACCGCCAACGATCACCCCCACCTGCTGTACTCACTCAATATCGCCGTGAGAACCGCGCCTGCTGCTTCGGTTAAGGCGCTGAAATACGCCGCCGCGATTGAACGTGCGTTGTGTGAAAAAAAGGGCGCAGATGTAAACTACAGCGGCCTGATTTGCAAAAATCCGTTCCATCTGGAATGGCAGGTGATGGAGTGGCGTGAGGAAGCCTATACCCTCGATGAACTGGCTGATTATCTTGATTTGAGCACTTCAGCGCGCCGTAGCATCGATAAACATTACGGGATGGGGCGAAACTGCCATCTGTTCGAAATGACGCGCAAATGGGCTTACAGGGCGATTCGTCAGGGCTGGCCAGCATTCTCACAGTGGCTTGATGCCGTGATTCAGCGTGTCGAAATGTACAACGCATCGCTTCCCGTTCCGCTTTCACCTCCTGAATGTCGGGCTATTGGCAAGAGTATTGCGAAATACACGCACAGGAACTTCACGGCGGAAACTTTCGCACAGTATGTGGCTGATACGCACACGCCAGAAATACAGGCCAAGAGAGGCAGGAAAGGTGGCATCGCTAAAGGCGAAGCCTACGATGACAAGCGTTTCATGGCGCTATGTATGCTGGAGAATGGATATTCTCAGAAAGCTATTGCGGCGATGTTGGAGGTTTCTACTCGAACCATTCGAAACTGGAAAAGCGGAAAATAGGGATCC";
        String CF8_seq="GAATTCATGAGATCTTGTTCGGAGCCGCTTTAACCCACTCTGTGGAAGTGCTGGATCC";
        String CC4_seq="GAATTCATGAGATCTAGAACCGCAACTCCCAATAAACGCAAACCCAAAACTCCAACGGATAATCGCTGATGGCTGCTAGACCCCGATCTCACAAAATCTCTATACCCAATTTATATTGCAAATTAGATAAGCGAACCGGAAAGGTATATTGGCAATACAAACATCCACTATCCGGTCGTTTTCATAGCTTAGGAACTGATGAGAATGAAGCAAAACAAGTTGCTACTGAAGCAAATACCATTATTGCTGAACAACGTACCAGACAAATATTAAGCGTCAATGAGCGTCTGGAAAGAATGAAAGGCAGGCGCTCAGACATTACGGTGACAGAATGGCTTGATAAATATATTTCTATCCAGGAGGACAGGCTGCAACATAATGAACTAAGACCCAACTCCTATCGGCAAAAAGGCAAACCCATTCGTCTTTTCCGTGAGCATTGTGGAATGCAACACCTCAAGGATATTACCGCACTTGATATTGCCGAAATAATTGATGCTGTAAAGGCTGAAGGTCATAACAGGATGGCGCAAGTCGTGAGAATGGTGTTGATCGACGTCTTCAAAGAAGCACAACACGCAGGACATGTTCCGCCAGGATTTAACCCAGCGCAGGCAACAAAACAACCGCGAAATCGAGTAAACCGCCAAAGATTGTCACTGCTCGAATGGCAGGCAATATTTGAAAGCGTAAGCAGACGGCAGCCCTATTTAAAATGCGGCATGCTACTTGCTCTTGTTACTGGACAACGTTTAGGCGATATCTGCAATTTGAAATTCTCTGATATATGGGACGACATGTTGCACATTACTCAGGAAAAAACCGGTTCAAAACTTGCTATTCCGCTTAACCTGAAATGCGATGCTCTGAATATTACCCTTCGTGAAGTTATATCTCAGTGCAGGGATGCTGTTGTTAGTAAATATCTGGTCCATTACCGTCACACTACCTCTCAAGCAAACAGAGGAGACCAGGTTTCTGCAAATACTCTGACAACGGCTTTTAAAAAGGCCAAGGAAAAATGTGGCATAAAATGGGAGCAAGGAACTGCGCCCACATTTCATGAACAGCGATCTCTGTCAGAACGATTATATCGGGAACAGGGTCTGGATACGCAAAAGTTGTTAGGCCATAAATCCAGAAAAATGACCGACCGATACAATGATGATCGTGGTAAAGACTGGATTATCGTAGATATCAAAACAGCATAGGGATCC";

    /**
     * Load the .abi file(s) that should match that sequence
     */
        try{
            //Corresponds to BG4_seq
            abi1=new ABITrace(new File("BG4_ca998_2010-03-20_B03_029.ab1"));

        }
        catch(IOException e){
            System.out.println("The ABI files need to be put in the class path of the project");
        }
    }


    ///////////////////////////////////////////////////////////////////
    ////                      private variables                    ////
}