source: trunk/doc/3rd-party-components.txt @ 3190

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1==================================================================
2$Id: 3rd-party-components.txt 3190 2007-03-13 10:05:42Z enell $
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 3.1
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   : 3.2.2.GA
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.jar, jta.jar, log4j-1.2.11.jar,
47            c3p0-0.9.1.jar
48
49Note: Most of the jar files above are other 3rd-party components used by Hibernate.
50Base doesn't use these components directly.
51
52Log4j
53-----
54A loggins system that makes it easy to turn on or off debugging just by
55editing a configuration file. This component is also used by Hibernate
56and we are using the same version that ships with Hibernate.
57
58More info : http://logging.apache.org/log4j/docs/
59Version   : 1.2.14
60License   : Apache License 2.0 (apache.license-2.0.txt)
61Jar files : log4j-1.2.14.jar
62
63JDOM
64----
65A library for parsing and generating XML files.
66
67More info : http://www.jdom.org/
68Version   : 1.0
69License   : Apache-style open source license (jdom.license.txt)
70Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar
71
72
73Java Advanced Imaging (JAI)
74---------------------------
75An image toolkit from SUN. The package consists of a few jar files and
76libraries for native code for different operating systems. At the moment
77we are only using the jar files but we must also distribute the native
78code libraries in order to follow the license.
79
80More info : http://java.sun.com/products/java-media/jai/index.jsp
81Version   : 1.1.2
82License   : Sun Microsystems Binary Code License (jai.license.txt)
83Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar
84Other     : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll
85
86
87Java Servlet API
88----------------
89Required for creating servlets and tag libraries. From SUN. This
90library is only required for compiling and are not included in the
91distribution. The web server/servlet container should already have
92these API installed (that's what makes it a servlet container).
93
94More info : http://java.sun.com/products/servlet/index.jsp
95Version   : 2.4
96License   : N/A
97Jar files : jsp-api.jar, servlet-api.jar
98
99
100Xerces
101------
102A toolkit for handling XML documents. From the Apache Software
103Foundation. These libraries are also needed by JDOM.
104
105More info : http://xml.apache.org/xerces2-j/index.html
106Version   : 2.9.0
107License   : Apache Software License (xerces.license.txt)
108Jar files : xerces-2.9.0.jar, xml-apis.jar
109
110
111MySQL Connector/J
112-----------------
113A JDBC driver for the MySQL database from MySQL. This library is only
114needed if you are using MySQL as your database.
115
116More info : http://www.mysql.com/products/connector/j/
117Version   : 5.0.4
118License   : GPL (gpl.license.txt)
119Jar files : mysql-connector-java-5.0.4-bin.jar
120
121
122PostgreSQL JDBC driver
123----------------------
124A JDBC driver for the PostgreSQL database. This library is only
125needed if you are using PostgreSQL as your database.
126
127More info : http://jdbc.postgresql.org/
128Version   : 8.1.407
129License   : BSD License (postgres.license.txt)
130Jar files : postgresql-8.1-407.jdbc3.jar
131
132
133X-Doclet
134--------
135Used at compile-time only to generate the XML files needed by
136Hibernate for the database mapping. These libraries are not included in
137the distribution.
138
139More info : http://xdoclet.sourceforge.net/xdoclet/index.html
140Version   : 1.2
141License   : XDoclet License (xdoclet.license.txt)
142Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
143            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
144            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
145
146
147Java Math Expression Parser
148---------------------------
149Parses and evaluates mathematical expressions in string. Supports
150most operators and funcations as well as variables.
151
152More info : http://www.singularsys.com/jep/
153Version   : 2.4.0
154License   : GPL (gpl.license.txt)
155Jar files : jep-2.4.0.jar
156
157
158JFreeChart
159----------
160Plotting package for bar charts, line charts, pie charts and xy plots.
161
162More info : http://www.jfree.org/
163Version   : 1.0.3
164License   : LGPL (lgpl.txt)
165Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar
166
167
168MultiExperiment Viewer
169----------------------
170MeV is a versatile microarray data analysis tool, incorporating
171sophisticated algorithms for clustering, visualization,
172classification, statistical analysis and biological theme discovery.
173
174More info : http://www.tm4.org/
175Version   : Modified version based on official v4.0 release
176License   : The Artisic License (http://www.tm4.org/artistic_license.pdf)
177Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar
178
179Note: Most of the jar files above are other 3rd-party components used
180by MeV. BASE doesn't use these components directly. For access to the
181modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks
182
183
184Silk icon set
185-------------
186A very nice icon set containing 1000 icons. The entire icon set
187is available in the "misc" directory. We have converted the icons
188to GIF format (since we didn't want to scan through all web pages
189and replace .gif with .png). We have also created some new icons which
190are merely combinations of other icons, ie. taking an arrow on one icon
191an putting it on another.
192
193More info : http://www.famfamfam.com/lab/icons/silk/
194Version   : 1.3
195License   : Creative Commons Attribution 2.5 License
196            (http://creativecommons.org/licenses/by/2.5/)
197
198
199SvnAnt
200------
201An 'ant' task implementation for accessing subversion from the ant buildfile.
202
203More info : http://subclipse.tigris.org/svnant.html
204Version   : 1.1.0.RC2
205License   : Apache Software License 1.1 (apache.license.txt)
206Jar files : svnant.jar, javasvn.jar, svnClientAdapter.jar, svnjavahl.jar
207            ganymed.jar
208
209
210Docbook
211-------
212A set of DTD:s and stylesheets for creating documentation. We use
213the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
214
215More info: http://www.docbook.org/
216Version  : 4.5
217License  : docbook.license.txt
218Files    : Everything in lib/docbook/docbook
219
220
221Docbook styler guide
222--------------------
223An extension to docbook created by Dawid Weiss which simplifies
224file inclusion and building from ant.
225
226More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
227Version  : 2004_06_22-21_12
228License  : docbook.styler.guide.txt
229Files    : Everything in lib/docbook except the 'docbook' subdirectory
230
231
232
233
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