// Copyright (C) 2014 Jost Waldmann
//
// This file is part of the FastaValidator Java Library. This library is free
// software; you can redistribute it and/or modify it under the
// terms of the GNU Lesser General Public License in version 3 (LGPL3) as 
// published by the Free Software Foundation.

// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// Lesser General Public License for more details.

// You should have received a copy of the Lesser General Public License along
// with this library; see the file COPYING.  If not, write to the Free
// Software Foundation, 59 Temple Place - Suite 330, Boston, MA 02111-1307,
// USA.

// If you have any questions, send an email to megx@mpi-bremen.de.


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FastaValidator 1.0
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Contact:

    Dipl.-Inf. Jost Waldmann

    Max Planck Institute for Marine Microbiology
    Dept. of Molecular Ecology
    Microbial Genomics and Bioinformatics Research Group
    Celsiusstrasse 1
    28359 Bremen
    Germany 

    e-mail: megx@mpi-bremen.de
    web:    http://www.microbial-genomics.de

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[PURPOSE]
FastaValidator is an open-source Java library to parse and validate FASTA formatted sequences in their applications.

For a ready-to-use application, which does not require any programing skills, have a look at the FastaValidatorUI seciton below.


[BUILDING REQUIREMENTS]
Java >=1.5
JFlex >=1.4.3
Ant >=1.8.1

Note:
All requirements must be added to the PATH environment variable.


[BUILD]
Type "ant" to build FastaValidator.

After you successfully built the software a jar-package 
FastaValidator-x.y.jar (version might change) can be found in the dist directory.
There are no further dependencies to other libraries excepting 
to the package itself (see demo).


[DEMO]
An example how to use the library, a short program can be found in build/demo/FVTester.java.
Type "java -classpath 'dist/FastaValidator-1.0.jar:build/demo' FVTester misc/testfiles/test01.fas" to test the parser.
If the input is valid it will be printed to STDOUT - otherwise an error message is shown.
There are also other test files available at 'misc/testfiles/' (some are in invalid FASTA format).

Have also a look at the sources of the FastaValidatorUi application in misc/FastaValidatorUi.


[FastaValidatorUi]
The FastaValidatorUI is an application for scientists, who simply want to validate their FASTA files.
It does not require any programming skills.

To build the FastaValidatorUi please type "ant fvui". This executes the file 
'build.xml' in the base directory of the FastaValidatorUi application 
(misc/FastaValidatorUi/) using ant.

To execute the FastaValidatorUi from top-level simply type 'java -jar misc/FastaValidatorUi/dist/FastaValidatorUi-1.0.jar'.
This launches the grpahical user interface of FastaValidatorUi.

For detailed documentation please refer to its README located at misc/FastaValidatorUi/README.