source: trunk/doc/3rd-party-components.txt @ 5676

Last change on this file since 5676 was 5676, checked in by Nicklas Nordborg, 11 years ago

References #1590: Documentation cleanup

  • Fixed link to syntax highlighter
  • Changed color of left border used on code examples and <hr> tags
  • Changed date format to "yyyy-MM-dd" for last modified footer
  • Added last modified information to title page
  • Decreased vertical white space around some headers
  • Added more links/title information to navigation header and footer
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 10.8 KB
Line 
1==================================================================
2$Id: 3rd-party-components.txt 5676 2011-06-29 07:40:33Z nicklas $
3
4  Copyright (C) 2005 Johan Enell, Nicklas Nordborg
5  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2007 Johan Enell, Jari Häkkinen, 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 3
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 BASE. If not, see <http://www.gnu.org/licenses/>.
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   : 3.6
43License   : LGPL (hibernate.license.txt)
44Jar files : hibernate3.jar, hibernate-jpa-2.0-api-1.0.0.Final.jar,
45            antlr-2.7.6.jar, c3p0-0.9.1.jar, commons-collections-3.1.jar,
46            dom4j-1.6.1.jar, ehcache-1.5.0.jar, javassist-3.12.0.GA.jar,
47            jta-1.1.jar, slf4j-api.1.5.8.jar, slf4j-log4j12-1.5.8.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 logging 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/1.2/index.html
59Version   : 1.2.16
60License   : Apache License 2.0 (apache.license-2.0.txt)
61Jar files : log4j-1.2.16.jar
62
63JDOM
64----
65A library for parsing and generating XML files.
66
67More info : http://www.jdom.org/
68Version   : 1.1.1
69License   : Apache-style open source license (jdom.license.txt)
70Jar files : jdom.jar, jaxen-1.1.1.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 : https://jai.dev.java.net/
81Version   : 1.1.3
82License   : Sun Microsystems Binary Code License (jai.license.txt)
83Jar files : jai_core.jar, jai_codec.jar
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   : 2.5
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   : 2.10.0
106License   : Apache Software License (xerces.license.txt)
107Jar files : xerces-2.10.0.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/
116Version   : 5.1.13
117License   : GPLv2 (gpl-2.license.txt)
118Jar files : mysql-connector-java-5.1.13-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   : 9.0.801
128License   : BSD License (postgres.license.txt)
129Jar files : postgresql-9.0-801.jdbc4.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   : GPLv2 (gpl-2.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/jfreechart/
162Version   : 1.0.13
163License   : LGPL (lgpl.txt)
164Jar files : jfreechart-1.0.13.jar jcommon-1.0.16.jar
165
166
167Apache HttpComponents
168---------------------
169Package for doing work with HTTP (eg. downloading files).
170
171More info : http://hc.apache.org/
172Version   : 4.0.3/4.0.1
173License   : Apache License 2.0 (apache.license-2.0.txt)
174Jar files : httpclient-4.0.3.jar, httpcore-4.0.1.jar, commons-codec-1.3.jar,
175            commons-logging-1.1.1.jar
176
177Apache Commons Email
178---------------------
179Package for sending email. Depends on JavaMail 1.4.
180
181More info : http://commons.apache.org/email/
182Version   : 1.2
183License   : Apache License 2.0 (apache.license-2.0.txt)
184Jar files : commons-email-1.2.jar
185
186
187JavaMail
188---------
189Low-level package for sending email. Used by Apache commons email.
190
191More info : http://www.oracle.com/technetwork/java/index-jsp-139225.html
192Version   : 1.4.3
193License   : Sun (mail-LICENSE.txt)
194Jar files : mail-1.4.3.jar
195
196
197JSON.simple
198-----------
199JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text.
200
201More info : http://code.google.com/p/json-simple/
202Version   : 1.1
203License   : Apache License 2.0 (apache.license-2.0.txt)
204Jar files : json-simple-1.1.jar
205
206
207JSON-js
208-------
209JSON parser/encoder for Javascript. Only needed for those browsers that
210doesn't have native support for JSON.
211
212More info : https://github.com/douglascrockford/JSON-js
213Version   : 2011-01-18
214License   : Public Domain
215Files     : www/include/scipts/json2.js
216
217
218Silk icon set
219-------------
220A very nice icon set containing 1000 icons. The entire icon set
221is available in the "misc" directory. We have converted the icons
222to GIF format (since we didn't want to scan through all web pages
223and replace .gif with .png). We have also created some new icons which
224are merely combinations of other icons, ie. taking an arrow on one icon
225an putting it on another.
226
227More info : http://www.famfamfam.com/lab/icons/silk/
228Version   : 1.3
229License   : Creative Commons Attribution 2.5 License
230            (http://creativecommons.org/licenses/by/2.5/)
231
232
233SvnAnt
234------
235An 'ant' task implementation for accessing subversion from the ant buildfile.
236
237More info : http://subclipse.tigris.org/svnant.html
238Version   : 1.3.0
239License   : Apache Software License 1.1 (apache.license.txt)
240Jar files : svnant.jar, svnkit.jar, svnClientAdapter.jar, svnjavahl.jar
241            ganymed.jar
242
243
244Docbook
245-------
246A set of DTD:s and stylesheets for creating documentation. We use
247the DocBook styler suite (see below) but has upgraded it to Docbook 4.5.
248
249More info: http://www.docbook.org/
250Version  : 4.5
251License  : docbook.license.txt
252Files    : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar
253
254
255Docbook styler guide
256--------------------
257An extension to docbook created by Dawid Weiss which simplifies
258file inclusion and building from ant.
259
260More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en
261Version  : 2004_06_22-21_12
262License  : docbook.styler.guide.txt
263Files    : Everything in lib/docbook except the 'docbook' subdirectory
264
265Example code syntax highlighter
266-------------------------------
267A javascript library that can be used to dynamically highlight
268the syntax in program examples. We have made minor changes to
269make it support the HTML produced by Docbook (ie. find the language
270from the 'language' attribute instead of the 'class' attribute).
271
272More info: http://alexgorbatchev.com/SyntaxHighlighter/
273Version  : 1.5.1
274License  : LGPL (lgpl.txt)
275Files    : Everything in the /doc/src/docbook/script and
276           /doc/src/docbook/css directories
277
278Affymetrix Fusion SDK
279---------------------
280Package for reading various Affymetrix file formats. We use a modified
281version that for some file formats can read from an InputStream instead
282of from a File object. This avoids a lot of copying and decompressing.
283
284More info: http://www.affymetrix.com/support/developer/fusion/index.affx
285         : (original version)
286         : http://dev.thep.lu.se/basehacks/wiki/AffxFusion
287         : (modified version)
288Version  : 1.09
289License  : LGPL (lgpl.txt)
290Files    : AffxFusion.jar
291
292TAR file support
293----------------
294Package for reading and writing TAR files.
295
296More info: http://www.trustice.com/java/tar/
297Version  : 2.5
298License  : tar.license.txt
299Files    : tar.jar
300
301BZIP file support
302-----------------
303Package for reading and writing BZIP files.
304
305More info: http://www.kohsuke.org/bzip2/
306Version  : unknown
307License  : Apache software license (apache.license.txt)
308Files    : bzip2.jar
309
310Axis2
311-----
312A core engine for webservices from Apache.
313
314More info : http://ws.apache.org/axis2/
315Version   : 1.3
316License   : Apache License 2.0 (apache.license-2.0.txt)
317Files     : Everything in the /lib/webservices directory
318
319SecondString
320------------
321A package with some fuzzy string matching algorithms developed
322by researchers at Carnegie Mellon University.
323
324More info : http://secondstring.sourceforge.net/
325Version   : CVS trunk checkout (2008-08-25)
326License   : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt)
327Files     : secondstring.jar
328
329
330jsDraw2D
331--------
332A vector graphics package for JavaScript.
333
334More info : http://jsdraw2d.jsfiction.com/
335Version   : 1.1.0
336License   : LGPL v3
337Files     : www/include/scripts/js-draw.js
338
339JavaSysMon
340----------
341A library for accessing CPU and memory information on some selected
342operating systems (including Linux, Windows and Mac OSX). It uses
343native libraries targeted for each platform
344
345More info : http://github.com/jezhumble/javasysmon
346Version   : 0.3.1
347License   : javasysmon-LICENSE.txt
348Files     : javasysmon-0.3.1.jar
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