source: trunk/doc/3rd-party-components.txt @ 3675

==================================================================
$Id: 3rd-party-components.txt 3675 2007-08-16 14:16:43Z jari $

  Copyright (C) 2005 Johan Enell, Nicklas Nordborg
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
  Copyright (C) 2007 Johan Enell, Jari Häkkinen, Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

BASE is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

BASE 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
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA  02111-1307, USA.
==================================================================

=================================
3rd-party components used by BASE
=================================

Here is list of 3rd-party components used by BASE. All the jar files
needed are included in the <base>/lib directory or in
<base>/www/plugins sub-directories for plug-ins based on others
work. The URLs given here can be used if you need more information or
need to update some component.


Hibernate 3
-----------
An object/relational persistence and query service for Java. Shields
us from most SQL and gives us database independece.

More info : http://www.hibernate.org/
Version   : 3.2.4.SP1
License   : LGPL (hibernate.license.txt)
Jar files : hibernate3.jar, antlr-2.7.6.jar, asm.jar, asm-attrs.jar, 
            cglib-2.1.3.jar, commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
            dom4j-1.6.1.jar, ehcache-1.2.3.jar, jta.jar, c3p0-0.9.1.jar

Note: Most of the jar files above are other 3rd-party components used by Hibernate.
Base doesn't use these components directly.

Log4j
-----
A loggins system that makes it easy to turn on or off debugging just by
editing a configuration file. This component is also used by Hibernate
and we are using the same version that ships with Hibernate.

More info : http://logging.apache.org/log4j/docs/
Version   : 1.2.14
License   : Apache License 2.0 (apache.license-2.0.txt)
Jar files : log4j-1.2.14.jar

JDOM
----
A library for parsing and generating XML files.

More info : http://www.jdom.org/
Version   : 1.0
License   : Apache-style open source license (jdom.license.txt)
Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar


Java Advanced Imaging (JAI)
---------------------------
An image toolkit from SUN. The package consists of a few jar files and
libraries for native code for different operating systems. At the moment
we are only using the jar files but we must also distribute the native
code libraries in order to follow the license.

More info : http://java.sun.com/products/java-media/jai/index.jsp
Version   : 1.1.2
License   : Sun Microsystems Binary Code License (jai.license.txt)
Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar
Other     : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll


Java Servlet API
----------------
Required for creating servlets and tag libraries. From SUN. This
library is only required for compiling and are not included in the
distribution. The web server/servlet container should already have 
these API installed (that's what makes it a servlet container).

More info : http://java.sun.com/products/servlet/index.jsp
Version   : 2.4
License   : N/A
Jar files : jsp-api.jar, servlet-api.jar


Xerces
------
A toolkit for handling XML documents. From the Apache Software
Foundation. These libraries are also needed by JDOM.

More info : http://xml.apache.org/xerces2-j/index.html
Version   : 2.9.0
License   : Apache Software License (xerces.license.txt)
Jar files : xerces-2.9.0.jar, xml-apis.jar


MySQL Connector/J
-----------------
A JDBC driver for the MySQL database from MySQL. This library is only
needed if you are using MySQL as your database.

More info : http://www.mysql.com/products/connector/j/
Version   : 5.0.6
License   : GPL (gpl.license.txt)
Jar files : mysql-connector-java-5.0.6-bin.jar


PostgreSQL JDBC driver
----------------------
A JDBC driver for the PostgreSQL database. This library is only
needed if you are using PostgreSQL as your database.

More info : http://jdbc.postgresql.org/
Version   : 8.1.407
License   : BSD License (postgres.license.txt)
Jar files : postgresql-8.1-407.jdbc3.jar


X-Doclet
--------
Used at compile-time only to generate the XML files needed by
Hibernate for the database mapping. These libraries are not included in
the distribution.

More info : http://xdoclet.sourceforge.net/xdoclet/index.html
Version   : 1.2
License   : XDoclet License (xdoclet.license.txt)
Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar, 
            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar, 
            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar


Java Math Expression Parser
---------------------------
Parses and evaluates mathematical expressions in string. Supports
most operators and funcations as well as variables. 

More info : http://www.singularsys.com/jep/
Version   : 2.4.0
License   : GPL (gpl.license.txt)
Jar files : jep-2.4.0.jar


JFreeChart
----------
Plotting package for bar charts, line charts, pie charts and xy plots.

More info : http://www.jfree.org/
Version   : 1.0.3
License   : LGPL (lgpl.txt)
Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar


MultiExperiment Viewer
----------------------
MeV is a versatile microarray data analysis tool, incorporating
sophisticated algorithms for clustering, visualization,
classification, statistical analysis and biological theme discovery.

More info : http://www.tm4.org/
Version   : Modified version based on official v4.0 release
License   : The Artisic License (http://www.tm4.org/artistic_license.pdf)
Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar

Note: Most of the jar files above are other 3rd-party components used
by MeV. BASE doesn't use these components directly. For access to the
modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks


Silk icon set
-------------
A very nice icon set containing 1000 icons. The entire icon set
is available in the "misc" directory. We have converted the icons 
to GIF format (since we didn't want to scan through all web pages
and replace .gif with .png). We have also created some new icons which
are merely combinations of other icons, ie. taking an arrow on one icon
an putting it on another.

More info : http://www.famfamfam.com/lab/icons/silk/
Version   : 1.3
License   : Creative Commons Attribution 2.5 License 
            (http://creativecommons.org/licenses/by/2.5/)


SvnAnt
------
An 'ant' task implementation for accessing subversion from the ant buildfile.

More info : http://subclipse.tigris.org/svnant.html
Version   : 1.1.0.RC2
License   : Apache Software License 1.1 (apache.license.txt)
Jar files : svnant.jar, javasvn.jar, svnClientAdapter.jar, svnjavahl.jar
            ganymed.jar


Docbook
-------
A set of DTD:s and stylesheets for creating documentation. We use 
the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.

More info: http://www.docbook.org/ 
Version  : 4.5
License  : docbook.license.txt
Files    : Everything in lib/docbook/docbook


Docbook styler guide
--------------------
An extension to docbook created by Dawid Weiss which simplifies 
file inclusion and building from ant.

More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
Version  : 2004_06_22-21_12
License  : docbook.styler.guide.txt
Files    : Everything in lib/docbook except the 'docbook' subdirectory


Affymetrix Fusion SDK
---------------------
Package for reading various Affymetrix file formats.

More info: http://www.affymetrix.com/support/developer/fusion/index.affx
Version  : 1.09
License  : LGPL (lgpl.txt)
Files    : AffxFusion.jar

TAR file support
----------------
Package for reading and writing TAR files.

More info: http://www.trustice.com/java/tar/
Version  : 2.5
License  : tar.license.txt
Files    : tar.jar

BZIP file support
-----------------
Package for reading and writing BZIP files.

More info: http://www.kohsuke.org/bzip2/
Version  : unknown
License  : Apache software license (apache.license.txt)
Files    : bzip2.jar