source: trunk/doc/3rd-party-components.txt @ 3452

Last change on this file since 3452 was 3452, checked in by Nicklas Nordborg, 15 years ago

Fixes #558 and #568

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 7.6 KB
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1==================================================================
2$Id: 3rd-party-components.txt 3452 2007-06-05 11:58:36Z nicklas $
3
4  Copyright (C) Authors contributing to this file.
5
6  This file is part of BASE - BioArray Software Environment.
7  Available at http://base.thep.lu.se/
8
9BASE is free software; you can redistribute it and/or
10modify it under the terms of the GNU General Public License
11as published by the Free Software Foundation; either version 2
12of the License, or (at your option) any later version.
13
14BASE is distributed in the hope that it will be useful,
15but WITHOUT ANY WARRANTY; without even the implied warranty of
16MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17GNU General Public License for more details.
18
19You should have received a copy of the GNU General Public License
20along with this program; if not, write to the Free Software
21Foundation, Inc., 59 Temple Place - Suite 330,
22Boston, MA  02111-1307, USA.
23==================================================================
24
25=================================
263rd-party components used by BASE
27=================================
28
29Here is list of 3rd-party components used by BASE. All the jar files
30needed are included in the <base>/lib directory or in
31<base>/www/plugins sub-directories for plug-ins based on others
32work. The URLs given here can be used if you need more information or
33need to update some component.
34
35
36Hibernate 3
37-----------
38An object/relational persistence and query service for Java. Shields
39us from most SQL and gives us database independece.
40
41More info : http://www.hibernate.org/
42Version   : 3.2.4.SP1
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate3.jar, antlr-2.7.6.jar, asm.jar, asm-attrs.jar,
45            cglib-2.1.3.jar, commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
46            dom4j-1.6.1.jar, ehcache-1.2.3.jar, jta.jar, c3p0-0.9.1.jar
47
48Note: Most of the jar files above are other 3rd-party components used by Hibernate.
49Base doesn't use these components directly.
50
51Log4j
52-----
53A loggins system that makes it easy to turn on or off debugging just by
54editing a configuration file. This component is also used by Hibernate
55and we are using the same version that ships with Hibernate.
56
57More info : http://logging.apache.org/log4j/docs/
58Version   : 1.2.14
59License   : Apache License 2.0 (apache.license-2.0.txt)
60Jar files : log4j-1.2.14.jar
61
62JDOM
63----
64A library for parsing and generating XML files.
65
66More info : http://www.jdom.org/
67Version   : 1.0
68License   : Apache-style open source license (jdom.license.txt)
69Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar
70
71
72Java Advanced Imaging (JAI)
73---------------------------
74An image toolkit from SUN. The package consists of a few jar files and
75libraries for native code for different operating systems. At the moment
76we are only using the jar files but we must also distribute the native
77code libraries in order to follow the license.
78
79More info : http://java.sun.com/products/java-media/jai/index.jsp
80Version   : 1.1.2
81License   : Sun Microsystems Binary Code License (jai.license.txt)
82Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar
83Other     : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll
84
85
86Java Servlet API
87----------------
88Required for creating servlets and tag libraries. From SUN. This
89library is only required for compiling and are not included in the
90distribution. The web server/servlet container should already have
91these API installed (that's what makes it a servlet container).
92
93More info : http://java.sun.com/products/servlet/index.jsp
94Version   : 2.4
95License   : N/A
96Jar files : jsp-api.jar, servlet-api.jar
97
98
99Xerces
100------
101A toolkit for handling XML documents. From the Apache Software
102Foundation. These libraries are also needed by JDOM.
103
104More info : http://xml.apache.org/xerces2-j/index.html
105Version   : 2.9.0
106License   : Apache Software License (xerces.license.txt)
107Jar files : xerces-2.9.0.jar, xml-apis.jar
108
109
110MySQL Connector/J
111-----------------
112A JDBC driver for the MySQL database from MySQL. This library is only
113needed if you are using MySQL as your database.
114
115More info : http://www.mysql.com/products/connector/j/
116Version   : 5.0.6
117License   : GPL (gpl.license.txt)
118Jar files : mysql-connector-java-5.0.6-bin.jar
119
120
121PostgreSQL JDBC driver
122----------------------
123A JDBC driver for the PostgreSQL database. This library is only
124needed if you are using PostgreSQL as your database.
125
126More info : http://jdbc.postgresql.org/
127Version   : 8.1.407
128License   : BSD License (postgres.license.txt)
129Jar files : postgresql-8.1-407.jdbc3.jar
130
131
132X-Doclet
133--------
134Used at compile-time only to generate the XML files needed by
135Hibernate for the database mapping. These libraries are not included in
136the distribution.
137
138More info : http://xdoclet.sourceforge.net/xdoclet/index.html
139Version   : 1.2
140License   : XDoclet License (xdoclet.license.txt)
141Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
142            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
143            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
144
145
146Java Math Expression Parser
147---------------------------
148Parses and evaluates mathematical expressions in string. Supports
149most operators and funcations as well as variables.
150
151More info : http://www.singularsys.com/jep/
152Version   : 2.4.0
153License   : GPL (gpl.license.txt)
154Jar files : jep-2.4.0.jar
155
156
157JFreeChart
158----------
159Plotting package for bar charts, line charts, pie charts and xy plots.
160
161More info : http://www.jfree.org/
162Version   : 1.0.3
163License   : LGPL (lgpl.txt)
164Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar
165
166
167MultiExperiment Viewer
168----------------------
169MeV is a versatile microarray data analysis tool, incorporating
170sophisticated algorithms for clustering, visualization,
171classification, statistical analysis and biological theme discovery.
172
173More info : http://www.tm4.org/
174Version   : Modified version based on official v4.0 release
175License   : The Artisic License (http://www.tm4.org/artistic_license.pdf)
176Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar
177
178Note: Most of the jar files above are other 3rd-party components used
179by MeV. BASE doesn't use these components directly. For access to the
180modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks
181
182
183Silk icon set
184-------------
185A very nice icon set containing 1000 icons. The entire icon set
186is available in the "misc" directory. We have converted the icons
187to GIF format (since we didn't want to scan through all web pages
188and replace .gif with .png). We have also created some new icons which
189are merely combinations of other icons, ie. taking an arrow on one icon
190an putting it on another.
191
192More info : http://www.famfamfam.com/lab/icons/silk/
193Version   : 1.3
194License   : Creative Commons Attribution 2.5 License
195            (http://creativecommons.org/licenses/by/2.5/)
196
197
198SvnAnt
199------
200An 'ant' task implementation for accessing subversion from the ant buildfile.
201
202More info : http://subclipse.tigris.org/svnant.html
203Version   : 1.1.0.RC2
204License   : Apache Software License 1.1 (apache.license.txt)
205Jar files : svnant.jar, javasvn.jar, svnClientAdapter.jar, svnjavahl.jar
206            ganymed.jar
207
208
209Docbook
210-------
211A set of DTD:s and stylesheets for creating documentation. We use
212the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
213
214More info: http://www.docbook.org/
215Version  : 4.5
216License  : docbook.license.txt
217Files    : Everything in lib/docbook/docbook
218
219
220Docbook styler guide
221--------------------
222An extension to docbook created by Dawid Weiss which simplifies
223file inclusion and building from ant.
224
225More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
226Version  : 2004_06_22-21_12
227License  : docbook.styler.guide.txt
228Files    : Everything in lib/docbook except the 'docbook' subdirectory
229
230
231
232
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