VT Ensimag Biosecurity iGEM 2010 team
Author: Gaelle Letort

This document is a documentation about the User primer calculator software.
An example of the principle of the finding of User Primer is given in the team wiki page: http://2010.igem.org/Team:VT-ENSIMAG/User_primer.


********************************************
Primer Founder help
*********************************************


1/Use of Primer Founder
-----------------------
double click on user_primer.jar for interface use.

To use it on command-line command is 
java -jar user_primer.jar
arguments can be added:
	 - file of result and file in 
	 - file of result and file in and temperature
	 - file of result and 3 DNA sequences
	 - file of result and 3 DNA sequences and temperature
example: 
java -jar user_primer.jar result.txt input.txt 69.5
execute the software with DNA sequences from input.txt file, put results on
result.txt file, and melting temperature is 69.5


The input file has to have the following format:
line 1: name of input 1
line 2: DNA sequence
line 3:
line 4: name of input 2
line 5: DNA sequence
line 6:
line 7:name of input 3
line 8: DNA sequence


2/Results extraction
--------------------
After each run, a result file is created in the current folder, which
contained the results visible in the application. If you want to save them,
you just have to choose the name of the file and type it in the Result file
name case. By default, the results are saved in result.txt file. 

Caution: don't forget that if the following run is made with the same result file name, the previous results will be deleted!


3/Error message
---------------
If an error occured during the run, if it's an input error, a message should
appears in the Error case. Otherwise, the error is not handled at all, and you
must check your sequences and if they are ok, the program has a bugg, you must
change the code. The source code are given in the src folder.