| 1 | ================================================================== |
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| 2 | $Id: 3rd-party-components.txt 7152 2016-05-20 06:30:09Z nicklas $ |
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| 3 | |
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| 4 | Copyright (C) 2005 Johan Enell, Nicklas Nordborg |
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| 5 | Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic |
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| 6 | Copyright (C) 2007 Johan Enell, Jari Häkkinen, Nicklas Nordborg |
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| 7 | |
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| 8 | This file is part of BASE - BioArray Software Environment. |
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| 9 | Available at http://base.thep.lu.se/ |
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| 10 | |
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| 11 | BASE is free software; you can redistribute it and/or |
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| 12 | modify it under the terms of the GNU General Public License |
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| 13 | as published by the Free Software Foundation; either version 3 |
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| 14 | of the License, or (at your option) any later version. |
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| 15 | |
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| 16 | BASE is distributed in the hope that it will be useful, |
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| 17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 19 | GNU General Public License for more details. |
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| 20 | |
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| 21 | You should have received a copy of the GNU General Public License |
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| 22 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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| 23 | ================================================================== |
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| 24 | |
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| 25 | ================================= |
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| 26 | 3rd-party components used by BASE |
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| 27 | ================================= |
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| 28 | |
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| 29 | Here is list of 3rd-party components used by BASE. All the jar files |
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| 30 | needed are included in the <base>/lib directory or in |
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| 31 | <base>/www/plugins sub-directories for plug-ins based on others |
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| 32 | work. The URLs given here can be used if you need more information or |
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| 33 | need to update some component. |
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| 34 | |
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| 35 | |
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| 36 | Hibernate |
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| 37 | --------- |
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| 38 | An object/relational persistence and query service for Java. Shields |
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| 39 | us from most SQL and gives us database independece. |
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| 40 | |
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| 41 | More info : http://www.hibernate.org/ |
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| 42 | Version : 5.0.7 |
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| 43 | License : LGPL (hibernate.license.txt) |
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| 44 | Jar files : hibernate-core-5.0.7.Final.jar, hibernate-commons-annotations-5.0.1.Final.jar, |
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| 45 | hibernate-jpa-2.1-api-1.0.0.Final.jar, |
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| 46 | antlr-2.7.7.jar, dom4j-1.6.1.jar, jandex-2.0.0.Final.jar, |
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| 47 | javassist-3.18.1-GA.jar, jboss-logging-3.3.0.Final.jar, |
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| 48 | c3p0-0.9.5-pre8.jar, hibernate-c3p0-5.0.7.Final.jar, mchange-commons-java-0.2.7.jar, |
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| 49 | hibernate-ehcache-5.0.7.Final.jar, slf4j-api.1.6.4.jar, slf4j-log4j12-1.6.4.jar, |
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| 50 | geronimo-jta_1.1_spec-1.1.1.jar |
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| 51 | |
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| 52 | Note: Most of the jar files above are other 3rd-party components used by Hibernate. |
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| 53 | BASE doesn't use these components directly. |
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| 54 | |
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| 55 | Ehcahce |
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| 56 | ------- |
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| 57 | Used by Hibernate for caching entities and query results. Is no |
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| 58 | longer part of the main Hibernate distribution. |
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| 59 | |
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| 60 | More info : http://ehcache.org/ |
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| 61 | Version : 2.6.3 |
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| 62 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 63 | Jar files : ehcache-core-2.6.3.jar |
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| 64 | |
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| 65 | |
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| 66 | Log4j |
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| 67 | ----- |
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| 68 | A logging system that makes it easy to turn on or off debugging just by |
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| 69 | editing a configuration file. |
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| 70 | |
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| 71 | More info : http://logging.apache.org/log4j/1.2/index.html |
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| 72 | Version : 1.2.17 |
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| 73 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 74 | Jar files : log4j-1.2.17.jar |
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| 75 | |
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| 76 | JDOM |
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| 77 | ---- |
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| 78 | A library for parsing and generating XML files. |
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| 79 | |
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| 80 | More info : http://www.jdom.org/ |
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| 81 | Version : 2.0.6 |
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| 82 | License : Apache-style open source license (jdom.license.txt) |
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| 83 | Jar files : jdom-2.0.6.jar, jaxen-1.1.6.jar |
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| 84 | |
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| 85 | |
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| 86 | Xerces |
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| 87 | ------ |
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| 88 | A toolkit for handling XML documents. From the Apache Software |
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| 89 | Foundation. These libraries are also needed by JDOM. |
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| 90 | |
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| 91 | More info : http://xml.apache.org/xerces2-j/index.html |
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| 92 | Version : 2.11.0 |
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| 93 | License : Apache Software License (xerces.license.txt) |
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| 94 | Jar files : xerces-2.11.0.jar, xml-apis.jar |
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| 95 | |
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| 96 | |
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| 97 | Java Advanced Imaging (JAI) |
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| 98 | --------------------------- |
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| 99 | An image toolkit from SUN. The package consists of a few jar files and |
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| 100 | libraries for native code for different operating systems. At the moment |
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| 101 | we are only using the jar files but we must also distribute the native |
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| 102 | code libraries in order to follow the license. |
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| 103 | |
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| 104 | More info : http://www.oracle.com/technetwork/java/current-142188.html |
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| 105 | Version : 1.1.3 |
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| 106 | License : Sun Microsystems Binary Code License (jai.license.txt) |
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| 107 | Jar files : jai_core.jar, jai_codec.jar |
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| 108 | |
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| 109 | |
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| 110 | Java Servlet API |
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| 111 | ---------------- |
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| 112 | Required for creating servlets and tag libraries. This |
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| 113 | library is only required for compiling and are not included in the |
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| 114 | distribution. The web server/servlet container should already have |
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| 115 | these API installed. We use files from the Tomcat 8 distribution. |
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| 116 | |
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| 117 | More info : http://tomcat.apache.org/whichversion.html |
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| 118 | Version : 3.1 |
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| 119 | License : N/A |
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| 120 | Jar files : jsp-api.jar, servlet-api.jar |
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| 121 | |
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| 122 | |
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| 123 | MySQL Connector/J |
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| 124 | ----------------- |
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| 125 | A JDBC driver for the MySQL database from MySQL. This library is only |
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| 126 | needed if you are using MySQL as your database. |
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| 127 | |
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| 128 | More info : http://www.mysql.com/products/connector/ |
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| 129 | Version : 5.1.35 |
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| 130 | License : GPLv2 (gpl-2.license.txt) |
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| 131 | Jar files : mysql-connector-java-5.1.35-bin.jar |
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| 132 | |
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| 133 | |
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| 134 | PostgreSQL JDBC driver |
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| 135 | ---------------------- |
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| 136 | A JDBC driver for the PostgreSQL database. This library is only |
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| 137 | needed if you are using PostgreSQL as your database. |
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| 138 | |
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| 139 | More info : http://jdbc.postgresql.org/ |
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| 140 | Version : 9.4.1201 |
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| 141 | License : BSD License (postgres.license.txt) |
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| 142 | Jar files : postgresql-9.4-1201.jdbc41.jar |
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| 143 | |
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| 144 | |
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| 145 | X-Doclet |
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| 146 | -------- |
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| 147 | Used at compile-time only to generate the XML files needed by |
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| 148 | Hibernate for the database mapping. These libraries are not included in |
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| 149 | the distribution. |
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| 150 | |
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| 151 | More info : http://xdoclet.sourceforge.net/xdoclet/index.html |
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| 152 | Version : 1.2 |
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| 153 | License : XDoclet License (xdoclet.license.txt) |
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| 154 | Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar, |
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| 155 | xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar, |
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| 156 | commons-collections-2.1.1.jar, commons-logging-1.0.4.jar |
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| 157 | |
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| 158 | |
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| 159 | Java Math Expression Parser |
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| 160 | --------------------------- |
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| 161 | Parses and evaluates mathematical expressions in string. Supports |
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| 162 | most operators and funcations as well as variables. |
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| 163 | |
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| 164 | More info : http://www.singularsys.com/jep/ |
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| 165 | Version : 2.4.0 |
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| 166 | License : GPLv2 (gpl-2.license.txt) |
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| 167 | Jar files : jep-2.4.0.jar |
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| 168 | |
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| 169 | |
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| 170 | JFreeChart |
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| 171 | ---------- |
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| 172 | Plotting package for bar charts, line charts, pie charts and xy plots. |
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| 173 | |
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| 174 | More info : http://www.jfree.org/jfreechart/ |
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| 175 | Version : 1.0.19 |
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| 176 | License : LGPL (lgpl.txt) |
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| 177 | Jar files : jfreechart-1.0.19.jar jcommon-1.0.23.jar |
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| 178 | |
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| 179 | |
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| 180 | Apache HttpComponents |
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| 181 | --------------------- |
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| 182 | Package for doing work with HTTP (eg. downloading files). |
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| 183 | |
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| 184 | More info : http://hc.apache.org/ |
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| 185 | Version : 4.4.1 |
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| 186 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 187 | Jar files : httpclient-4.4.1.jar, httpcore-4.4.1.jar, commons-codec-1.9.jar, |
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| 188 | commons-logging-1.2.jar |
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| 189 | |
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| 190 | Apache Commons Email |
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| 191 | --------------------- |
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| 192 | Package for sending email. Depends on JavaMail 1.5. |
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| 193 | |
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| 194 | More info : http://commons.apache.org/email/ |
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| 195 | Version : 1.3.3 |
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| 196 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 197 | Jar files : commons-email-1.3.3.jar |
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| 198 | |
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| 199 | |
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| 200 | JavaMail |
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| 201 | --------- |
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| 202 | Low-level package for sending email. Used by Apache commons email. |
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| 203 | |
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| 204 | More info : https://java.net/projects/javamail/pages/Home |
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| 205 | Version : 1.5.3 |
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| 206 | License : Common Development and Distribution License (CDDL) v1.1 and GNU General Public License (GPL) v2 with Classpath Exception (javax-mail-LICENSE.txt) |
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| 207 | Jar files : javax-mail-1.5.3.jar |
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| 208 | |
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| 209 | |
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| 210 | jBCrypt |
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| 211 | ------- |
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| 212 | Package for safe encryption of passwords using the 'bcrypt' algorithm. |
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| 213 | |
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| 214 | More info : http://www.mindrot.org/projects/jBCrypt/ |
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| 215 | Version : 0.4 |
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| 216 | License : ISC/BSD licence (jbcrypt-license.txt) |
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| 217 | Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java |
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| 218 | |
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| 219 | JSON.simple |
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| 220 | ----------- |
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| 221 | JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text. |
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| 222 | |
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| 223 | More info : http://code.google.com/p/json-simple/ |
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| 224 | Version : 1.1.1 |
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| 225 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 226 | Jar files : json-simple-1.1.1.jar |
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| 227 | |
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| 228 | |
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| 229 | Silk icon set |
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| 230 | ------------- |
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| 231 | A very nice icon set containing 1000 icons. The entire icon set |
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| 232 | is available in the "misc" directory. We have converted the icons |
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| 233 | to GIF format (since we didn't want to scan through all web pages |
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| 234 | and replace .gif with .png). We have also created some new icons which |
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| 235 | are merely combinations of other icons, ie. taking an arrow on one icon |
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| 236 | an putting it on another. |
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| 237 | |
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| 238 | More info : http://www.famfamfam.com/lab/icons/silk/ |
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| 239 | Version : 1.3 |
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| 240 | License : Creative Commons Attribution 2.5 License |
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| 241 | (http://creativecommons.org/licenses/by/2.5/) |
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| 242 | |
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| 243 | |
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| 244 | SvnAnt |
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| 245 | ------ |
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| 246 | An 'ant' task implementation for accessing subversion from the ant buildfile. |
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| 247 | |
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| 248 | More info : http://subclipse.tigris.org/svnant.html |
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| 249 | Version : 1.4-dev (http://subclipse.tigris.org/svn/subclipse/trunk/svnant@5584) |
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| 250 | License : Apache Software License 1.1 (apache.license.txt) |
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| 251 | Jar files : Everything in lib/svn/ |
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| 252 | |
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| 253 | |
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| 254 | Docbook |
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| 255 | ------- |
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| 256 | A set of DTD:s and stylesheets for creating documentation. We use |
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| 257 | the DocBook styler suite (see below) but has upgraded it to Docbook 4.5. |
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| 258 | |
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| 259 | More info: http://www.docbook.org/ |
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| 260 | Version : 4.5 |
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| 261 | License : docbook.license.txt |
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| 262 | Files : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar |
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| 263 | |
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| 264 | |
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| 265 | Docbook styler guide |
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| 266 | -------------------- |
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| 267 | An extension to docbook created by Dawid Weiss which simplifies |
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| 268 | file inclusion and building from ant. |
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| 269 | |
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| 270 | More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en |
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| 271 | Version : 2004_06_22-21_12 |
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| 272 | License : docbook.styler.guide.txt |
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| 273 | Files : Everything in lib/docbook except the 'docbook' subdirectory |
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| 274 | |
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| 275 | Example code syntax highlighter |
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| 276 | ------------------------------- |
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| 277 | A javascript library that can be used to dynamically highlight |
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| 278 | the syntax in program examples. We have made minor changes to |
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| 279 | make it support the HTML produced by Docbook (ie. find the language |
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| 280 | from the 'language' attribute instead of the 'class' attribute). |
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| 281 | |
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| 282 | More info: http://alexgorbatchev.com/SyntaxHighlighter/ |
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| 283 | Version : 1.5.1 |
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| 284 | License : LGPL (lgpl.txt) |
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| 285 | Files : Everything in the /doc/src/docbook/script and |
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| 286 | /doc/src/docbook/css directories |
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| 287 | |
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| 288 | Affymetrix Fusion SDK |
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| 289 | --------------------- |
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| 290 | Package for reading various Affymetrix file formats. We use a modified |
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| 291 | version that for some file formats can read from an InputStream instead |
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| 292 | of from a File object. This avoids a lot of copying and decompressing. |
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| 293 | |
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| 294 | More info: http://www.affymetrix.com/support/developer/fusion/index.affx |
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| 295 | : (original version) |
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| 296 | : http://dev.thep.lu.se/basehacks/wiki/AffxFusion |
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| 297 | : (modified version) |
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| 298 | Version : 1.09 |
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| 299 | License : LGPL (lgpl.txt) |
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| 300 | Files : AffxFusion.jar |
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| 301 | |
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| 302 | TAR file support |
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| 303 | ---------------- |
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| 304 | Package for reading and writing TAR files. |
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| 305 | |
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| 306 | More info: http://www.trustice.com/java/tar/ |
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| 307 | Version : 2.5 |
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| 308 | License : tar.license.txt |
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| 309 | Files : tar.jar |
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| 310 | |
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| 311 | BZIP file support |
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| 312 | ----------------- |
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| 313 | Package for reading and writing BZIP files. |
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| 314 | |
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| 315 | More info: http://www.kohsuke.org/bzip2/ |
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| 316 | Version : unknown |
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| 317 | License : Apache software license (apache.license.txt) |
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| 318 | Files : bzip2.jar |
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| 319 | |
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| 320 | Parallel GZIP compression |
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| 321 | ------------------------- |
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| 322 | Package for multi-threaded compression to GZIP format. |
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| 323 | |
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| 324 | More info: https://github.com/shevek/parallelgzip |
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| 325 | Version : 1.0.1 |
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| 326 | License : Apache software license (parallelgzip-LICENSE.txt) |
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| 327 | Files : parallelgzip-1.0.1.jar |
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| 328 | |
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| 329 | SecondString |
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| 330 | ------------ |
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| 331 | A package with some fuzzy string matching algorithms developed |
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| 332 | by researchers at Carnegie Mellon University. |
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| 333 | |
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| 334 | More info : http://secondstring.sourceforge.net/ |
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| 335 | Version : CVS trunk checkout (2008-08-25) |
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| 336 | License : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt) |
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| 337 | Files : secondstring.jar |
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| 338 | |
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| 339 | |
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| 340 | jsDraw2D |
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| 341 | -------- |
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| 342 | A vector graphics package for JavaScript. |
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| 343 | |
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| 344 | More info : http://jsdraw2d.jsfiction.com/ |
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| 345 | Version : 1.1.0 |
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| 346 | License : LGPL v3 |
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| 347 | Files : www/include/scripts/js-draw.js |
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| 348 | |
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| 349 | JavaSysMon |
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| 350 | ---------- |
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| 351 | A library for accessing CPU and memory information on some selected |
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| 352 | operating systems (including Linux, Windows and Mac OSX). It uses |
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| 353 | native libraries targeted for each platform |
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| 354 | |
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| 355 | More info : http://github.com/jezhumble/javasysmon |
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| 356 | Version : 0.3.5 |
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| 357 | License : javasysmon-LICENSE.txt |
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| 358 | Files : javasysmon-0.3.5.jar |
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