source: trunk/doc/3rd-party-components.txt @ 3849

Last change on this file since 3849 was 3849, checked in by Martin Svensson, 14 years ago

References #492 Updating license information and 3rd party components

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1==================================================================
2$Id: 3rd-party-components.txt 3849 2007-10-17 06:29:09Z martin $
3
4  Copyright (C) 2005 Johan Enell, Nicklas Nordborg
5  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2007 Johan Enell, Jari Hakkinen, Nicklas Nordborg
7
8  This file is part of BASE - BioArray Software Environment.
9  Available at http://base.thep.lu.se/
10
11BASE is free software; you can redistribute it and/or
12modify it under the terms of the GNU General Public License
13as published by the Free Software Foundation; either version 2
14of the License, or (at your option) any later version.
15
16BASE is distributed in the hope that it will be useful,
17but WITHOUT ANY WARRANTY; without even the implied warranty of
18MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19GNU General Public License for more details.
20
21You should have received a copy of the GNU General Public License
22along with this program; if not, write to the Free Software
23Foundation, Inc., 59 Temple Place - Suite 330,
24Boston, MA  02111-1307, USA.
25==================================================================
26
27=================================
283rd-party components used by BASE
29=================================
30
31Here is list of 3rd-party components used by BASE. All the jar files
32needed are included in the <base>/lib directory or in
33<base>/www/plugins sub-directories for plug-ins based on others
34work. The URLs given here can be used if you need more information or
35need to update some component.
36
37
38Hibernate 3
39-----------
40An object/relational persistence and query service for Java. Shields
41us from most SQL and gives us database independece.
42
43More info : http://www.hibernate.org/
44Version   : 3.2.4.SP1
45License   : LGPL (hibernate.license.txt)
46Jar files : hibernate3.jar, antlr-2.7.6.jar, asm.jar, asm-attrs.jar,
47            cglib-2.1.3.jar, commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
48            dom4j-1.6.1.jar, ehcache-1.2.3.jar, jta.jar, c3p0-0.9.1.jar
49
50Note: Most of the jar files above are other 3rd-party components used by Hibernate.
51Base doesn't use these components directly.
52
53Log4j
54-----
55A loggins system that makes it easy to turn on or off debugging just by
56editing a configuration file. This component is also used by Hibernate
57and we are using the same version that ships with Hibernate.
58
59More info : http://logging.apache.org/log4j/docs/
60Version   : 1.2.14
61License   : Apache License 2.0 (apache.license-2.0.txt)
62Jar files : log4j-1.2.14.jar
63
64JDOM
65----
66A library for parsing and generating XML files.
67
68More info : http://www.jdom.org/
69Version   : 1.0
70License   : Apache-style open source license (jdom.license.txt)
71Jar files : jdom.jar, jaxen-1.1-beta-7.jar, saxpath.jar
72
73
74Java Advanced Imaging (JAI)
75---------------------------
76An image toolkit from SUN. The package consists of a few jar files and
77libraries for native code for different operating systems. At the moment
78we are only using the jar files but we must also distribute the native
79code libraries in order to follow the license.
80
81More info : http://java.sun.com/products/java-media/jai/index.jsp
82Version   : 1.1.2
83License   : Sun Microsystems Binary Code License (jai.license.txt)
84Jar files : jai_core.jar, jai_codec.jar, mlibwrapper_jai.jar
85Other     : lbmlib_jai.so, checkmmx.exe, mlib_jai.dll, mlib_jai_mmx.dll
86
87
88Java Servlet API
89----------------
90Required for creating servlets and tag libraries. From SUN. This
91library is only required for compiling and are not included in the
92distribution. The web server/servlet container should already have
93these API installed (that's what makes it a servlet container).
94
95More info : http://java.sun.com/products/servlet/index.jsp
96Version   : 2.4
97License   : N/A
98Jar files : jsp-api.jar, servlet-api.jar
99
100
101Xerces
102------
103A toolkit for handling XML documents. From the Apache Software
104Foundation. These libraries are also needed by JDOM.
105
106More info : http://xml.apache.org/xerces2-j/index.html
107Version   : 2.9.0
108License   : Apache Software License (xerces.license.txt)
109Jar files : xerces-2.9.0.jar, xml-apis.jar
110
111
112MySQL Connector/J
113-----------------
114A JDBC driver for the MySQL database from MySQL. This library is only
115needed if you are using MySQL as your database.
116
117More info : http://www.mysql.com/products/connector/j/
118Version   : 5.0.6
119License   : GPL (gpl.license.txt)
120Jar files : mysql-connector-java-5.0.6-bin.jar
121
122
123PostgreSQL JDBC driver
124----------------------
125A JDBC driver for the PostgreSQL database. This library is only
126needed if you are using PostgreSQL as your database.
127
128More info : http://jdbc.postgresql.org/
129Version   : 8.1.407
130License   : BSD License (postgres.license.txt)
131Jar files : postgresql-8.1-407.jdbc3.jar
132
133
134X-Doclet
135--------
136Used at compile-time only to generate the XML files needed by
137Hibernate for the database mapping. These libraries are not included in
138the distribution.
139
140More info : http://xdoclet.sourceforge.net/xdoclet/index.html
141Version   : 1.2
142License   : XDoclet License (xdoclet.license.txt)
143Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar,
144            xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar,
145            commons-collections-2.1.1.jar, commons-logging-1.0.4.jar
146
147
148Java Math Expression Parser
149---------------------------
150Parses and evaluates mathematical expressions in string. Supports
151most operators and funcations as well as variables.
152
153More info : http://www.singularsys.com/jep/
154Version   : 2.4.0
155License   : GPL (gpl.license.txt)
156Jar files : jep-2.4.0.jar
157
158
159JFreeChart
160----------
161Plotting package for bar charts, line charts, pie charts and xy plots.
162
163More info : http://www.jfree.org/
164Version   : 1.0.3
165License   : LGPL (lgpl.txt)
166Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar
167
168
169MultiExperiment Viewer
170----------------------
171MeV is a versatile microarray data analysis tool, incorporating
172sophisticated algorithms for clustering, visualization,
173classification, statistical analysis and biological theme discovery.
174
175More info : http://www.tm4.org/
176Version   : Modified version based on official v4.0 release
177License   : The Artisic License (http://www.tm4.org/artistic_license.pdf)
178Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar
179
180Note: Most of the jar files above are other 3rd-party components used
181by MeV. BASE doesn't use these components directly. For access to the
182modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks
183
184
185Silk icon set
186-------------
187A very nice icon set containing 1000 icons. The entire icon set
188is available in the "misc" directory. We have converted the icons
189to GIF format (since we didn't want to scan through all web pages
190and replace .gif with .png). We have also created some new icons which
191are merely combinations of other icons, ie. taking an arrow on one icon
192an putting it on another.
193
194More info : http://www.famfamfam.com/lab/icons/silk/
195Version   : 1.3
196License   : Creative Commons Attribution 2.5 License
197            (http://creativecommons.org/licenses/by/2.5/)
198
199
200SvnAnt
201------
202An 'ant' task implementation for accessing subversion from the ant buildfile.
203
204More info : http://subclipse.tigris.org/svnant.html
205Version   : 1.1.0.RC2
206License   : Apache Software License 1.1 (apache.license.txt)
207Jar files : svnant.jar, javasvn.jar, svnClientAdapter.jar, svnjavahl.jar
208            ganymed.jar
209
210
211Docbook
212-------
213A set of DTD:s and stylesheets for creating documentation. We use
214the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
215
216More info: http://www.docbook.org/
217Version  : 4.5
218License  : docbook.license.txt
219Files    : Everything in lib/docbook/docbook
220
221
222Docbook styler guide
223--------------------
224An extension to docbook created by Dawid Weiss which simplifies
225file inclusion and building from ant.
226
227More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
228Version  : 2004_06_22-21_12
229License  : docbook.styler.guide.txt
230Files    : Everything in lib/docbook except the 'docbook' subdirectory
231
232Example code syntax highlighter
233-------------------------------
234A javascript library that can be used to dynamically highlight
235the syntax in program examples. We have made minor changes to
236make it support the HTML produced by Docbook (ie. find the language
237from the 'language' attribute instead of the 'class' attribute).
238
239More info: http://www.dreamprojections.com/syntaxhighlighter
240Version  : 1.5.1
241License  : LGPL (lgpl.txt)
242Files    : Everything in the /doc/src/docbook/script and
243           /doc/src/docbook/css directories
244
245Affymetrix Fusion SDK
246---------------------
247Package for reading various Affymetrix file formats. We use a modified
248version that for some file formats can read from an InputStream instead
249of from a File object. This avoids a lot of copying and decompressing.
250
251More info: http://www.affymetrix.com/support/developer/fusion/index.affx
252         : (original version)
253         : http://trac.thep.lu.se/trac/basehacks/wiki/AffxFusion
254         : (modified version)
255Version  : 1.09
256License  : LGPL (lgpl.txt)
257Files    : AffxFusion.jar
258
259TAR file support
260----------------
261Package for reading and writing TAR files.
262
263More info: http://www.trustice.com/java/tar/
264Version  : 2.5
265License  : tar.license.txt
266Files    : tar.jar
267
268BZIP file support
269-----------------
270Package for reading and writing BZIP files.
271
272More info: http://www.kohsuke.org/bzip2/
273Version  : unknown
274License  : Apache software license (apache.license.txt)
275Files    : bzip2.jar
276
277Axis2
278-----
279A core engine for webservices from Apache.
280
281More info : http://ws.apache.org/axis2/
282Version   : 1.3
283License   : Apache License 2.0 (apache.license-2.0.txt)
284Files     : Everything in the /lib/webservices directory
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