| 1 | ================================================================== |
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| 2 | $Id: 3rd-party-components.txt 5868 2011-11-11 08:55:02Z 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 3 |
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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 : 3.6 |
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| 43 | License : LGPL (hibernate.license.txt) |
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| 44 | Jar files : hibernate3.jar, hibernate-jpa-2.0-api-1.0.0.Final.jar, |
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| 45 | antlr-2.7.6.jar, c3p0-0.9.1.jar, commons-collections-3.1.jar, |
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| 46 | dom4j-1.6.1.jar, ehcache-1.5.0.jar, javassist-3.12.0.GA.jar, |
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| 47 | jta-1.1.jar, slf4j-api.1.5.8.jar, slf4j-log4j12-1.5.8.jar |
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| 48 | |
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| 49 | Note: Most of the jar files above are other 3rd-party components used by Hibernate. |
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| 50 | BASE doesn't use these components directly. |
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| 51 | |
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| 52 | Log4j |
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| 53 | ----- |
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| 54 | A logging system that makes it easy to turn on or off debugging just by |
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| 55 | editing a configuration file. This component is also used by Hibernate |
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| 56 | and we are using the same version that ships with Hibernate. |
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| 57 | |
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| 58 | More info : http://logging.apache.org/log4j/1.2/index.html |
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| 59 | Version : 1.2.16 |
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| 60 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 61 | Jar files : log4j-1.2.16.jar |
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| 62 | |
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| 63 | JDOM |
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| 64 | ---- |
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| 65 | A library for parsing and generating XML files. |
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| 66 | |
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| 67 | More info : http://www.jdom.org/ |
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| 68 | Version : 1.1.2 |
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| 69 | License : Apache-style open source license (jdom.license.txt) |
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| 70 | Jar files : jdom-1.1.2.jar, jaxen-1.1.1.jar |
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| 71 | |
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| 72 | |
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| 73 | Xerces |
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| 74 | ------ |
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| 75 | A toolkit for handling XML documents. From the Apache Software |
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| 76 | Foundation. These libraries are also needed by JDOM. |
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| 77 | |
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| 78 | More info : http://xml.apache.org/xerces2-j/index.html |
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| 79 | Version : 2.11.0 |
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| 80 | License : Apache Software License (xerces.license.txt) |
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| 81 | Jar files : xerces-2.11.0.jar, xml-apis.jar |
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| 82 | |
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| 83 | |
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| 84 | Java Advanced Imaging (JAI) |
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| 85 | --------------------------- |
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| 86 | An image toolkit from SUN. The package consists of a few jar files and |
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| 87 | libraries for native code for different operating systems. At the moment |
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| 88 | we are only using the jar files but we must also distribute the native |
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| 89 | code libraries in order to follow the license. |
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| 90 | |
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| 91 | More info : https://jai.dev.java.net/ |
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| 92 | Version : 1.1.3 |
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| 93 | License : Sun Microsystems Binary Code License (jai.license.txt) |
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| 94 | Jar files : jai_core.jar, jai_codec.jar |
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| 95 | |
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| 96 | |
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| 97 | Java Servlet API |
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| 98 | ---------------- |
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| 99 | Required for creating servlets and tag libraries. From SUN. This |
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| 100 | library is only required for compiling and are not included in the |
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| 101 | distribution. The web server/servlet container should already have |
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| 102 | these API installed (that's what makes it a servlet container). |
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| 103 | |
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| 104 | More info : http://java.sun.com/products/servlet/index.jsp |
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| 105 | Version : 2.5 |
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| 106 | License : N/A |
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| 107 | Jar files : jsp-api.jar, servlet-api.jar |
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| 108 | |
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| 109 | |
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| 110 | MySQL Connector/J |
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| 111 | ----------------- |
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| 112 | A JDBC driver for the MySQL database from MySQL. This library is only |
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| 113 | needed if you are using MySQL as your database. |
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| 114 | |
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| 115 | More info : http://www.mysql.com/products/connector/ |
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| 116 | Version : 5.1.13 |
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| 117 | License : GPLv2 (gpl-2.license.txt) |
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| 118 | Jar files : mysql-connector-java-5.1.13-bin.jar |
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| 119 | |
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| 120 | |
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| 121 | PostgreSQL JDBC driver |
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| 122 | ---------------------- |
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| 123 | A JDBC driver for the PostgreSQL database. This library is only |
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| 124 | needed if you are using PostgreSQL as your database. |
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| 125 | |
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| 126 | More info : http://jdbc.postgresql.org/ |
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| 127 | Version : 9.0.801 |
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| 128 | License : BSD License (postgres.license.txt) |
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| 129 | Jar files : postgresql-9.0-801.jdbc4.jar |
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| 130 | |
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| 131 | |
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| 132 | X-Doclet |
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| 133 | -------- |
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| 134 | Used at compile-time only to generate the XML files needed by |
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| 135 | Hibernate for the database mapping. These libraries are not included in |
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| 136 | the distribution. |
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| 137 | |
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| 138 | More info : http://xdoclet.sourceforge.net/xdoclet/index.html |
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| 139 | Version : 1.2 |
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| 140 | License : XDoclet License (xdoclet.license.txt) |
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| 141 | Jar files : xdoclet-1.2.2.jar, xdoclet-hibernate-module-1.2.2.jar, |
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| 142 | xdoclet-xdoclet-module-1.2.2.jar, xjavadoc-1.1-j5-v3.jar, |
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| 143 | commons-collections-2.1.1.jar, commons-logging-1.0.4.jar |
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| 144 | |
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| 145 | |
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| 146 | Java Math Expression Parser |
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| 147 | --------------------------- |
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| 148 | Parses and evaluates mathematical expressions in string. Supports |
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| 149 | most operators and funcations as well as variables. |
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| 150 | |
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| 151 | More info : http://www.singularsys.com/jep/ |
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| 152 | Version : 2.4.0 |
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| 153 | License : GPLv2 (gpl-2.license.txt) |
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| 154 | Jar files : jep-2.4.0.jar |
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| 155 | |
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| 156 | |
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| 157 | JFreeChart |
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| 158 | ---------- |
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| 159 | Plotting package for bar charts, line charts, pie charts and xy plots. |
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| 160 | |
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| 161 | More info : http://www.jfree.org/jfreechart/ |
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| 162 | Version : 1.0.13 |
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| 163 | License : LGPL (lgpl.txt) |
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| 164 | Jar files : jfreechart-1.0.13.jar jcommon-1.0.16.jar |
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| 165 | |
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| 166 | |
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| 167 | Apache HttpComponents |
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| 168 | --------------------- |
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| 169 | Package for doing work with HTTP (eg. downloading files). |
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| 170 | |
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| 171 | More info : http://hc.apache.org/ |
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| 172 | Version : 4.0.3/4.0.1 |
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| 173 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 174 | Jar files : httpclient-4.0.3.jar, httpcore-4.0.1.jar, commons-codec-1.3.jar, |
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| 175 | commons-logging-1.1.1.jar |
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| 176 | |
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| 177 | Apache Commons Email |
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| 178 | --------------------- |
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| 179 | Package for sending email. Depends on JavaMail 1.4. |
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| 180 | |
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| 181 | More info : http://commons.apache.org/email/ |
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| 182 | Version : 1.2 |
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| 183 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 184 | Jar files : commons-email-1.2.jar |
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| 185 | |
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| 186 | |
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| 187 | JavaMail |
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| 188 | --------- |
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| 189 | Low-level package for sending email. Used by Apache commons email. |
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| 190 | |
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| 191 | More info : http://www.oracle.com/technetwork/java/index-jsp-139225.html |
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| 192 | Version : 1.4.3 |
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| 193 | License : Sun (mail-LICENSE.txt) |
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| 194 | Jar files : mail-1.4.3.jar |
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| 195 | |
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| 196 | |
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| 197 | jBCrypt |
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| 198 | ------- |
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| 199 | Package for safe encryption of passwords using the 'bcrypt' algorithm. |
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| 200 | |
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| 201 | More info : http://www.mindrot.org/projects/jBCrypt/ |
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| 202 | Version : 0.3 |
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| 203 | License : ISC/BSD licence (jbcrypt-license.txt) |
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| 204 | Jar files : None. Distributed as source only. All code is in net/sf/basedb/util/bcrypt/BCrypt.java |
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| 205 | |
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| 206 | JSON.simple |
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| 207 | ----------- |
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| 208 | JSON.simple is a simple Java toolkit for JSON. You can use JSON.simple to encode or decode JSON text. |
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| 209 | |
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| 210 | More info : http://code.google.com/p/json-simple/ |
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| 211 | Version : 1.1 |
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| 212 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 213 | Jar files : json-simple-1.1.jar |
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| 214 | |
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| 215 | |
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| 216 | JSON-js |
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| 217 | ------- |
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| 218 | JSON parser/encoder for Javascript. Only needed for those browsers that |
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| 219 | doesn't have native support for JSON. |
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| 220 | |
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| 221 | More info : https://github.com/douglascrockford/JSON-js |
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| 222 | Version : 2011-01-18 |
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| 223 | License : Public Domain |
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| 224 | Files : www/include/scipts/json2.js |
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| 225 | |
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| 226 | |
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| 227 | Silk icon set |
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| 228 | ------------- |
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| 229 | A very nice icon set containing 1000 icons. The entire icon set |
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| 230 | is available in the "misc" directory. We have converted the icons |
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| 231 | to GIF format (since we didn't want to scan through all web pages |
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| 232 | and replace .gif with .png). We have also created some new icons which |
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| 233 | are merely combinations of other icons, ie. taking an arrow on one icon |
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| 234 | an putting it on another. |
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| 235 | |
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| 236 | More info : http://www.famfamfam.com/lab/icons/silk/ |
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| 237 | Version : 1.3 |
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| 238 | License : Creative Commons Attribution 2.5 License |
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| 239 | (http://creativecommons.org/licenses/by/2.5/) |
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| 240 | |
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| 241 | |
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| 242 | SvnAnt |
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| 243 | ------ |
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| 244 | An 'ant' task implementation for accessing subversion from the ant buildfile. |
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| 245 | |
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| 246 | More info : http://subclipse.tigris.org/svnant.html |
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| 247 | Version : 1.3.0 |
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| 248 | License : Apache Software License 1.1 (apache.license.txt) |
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| 249 | Jar files : svnant.jar, svnkit.jar, svnClientAdapter.jar, svnjavahl.jar |
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| 250 | ganymed.jar |
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| 251 | |
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| 252 | |
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| 253 | Docbook |
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| 254 | ------- |
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| 255 | A set of DTD:s and stylesheets for creating documentation. We use |
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| 256 | the DocBook styler suite (see below) but has upgraded it to Docbook 4.5. |
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| 257 | |
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| 258 | More info: http://www.docbook.org/ |
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| 259 | Version : 4.5 |
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| 260 | License : docbook.license.txt |
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| 261 | Files : Everything in lib/docbook/docbook and dist/commons-logging-1.1.jar |
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| 262 | |
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| 263 | |
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| 264 | Docbook styler guide |
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| 265 | -------------------- |
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| 266 | An extension to docbook created by Dawid Weiss which simplifies |
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| 267 | file inclusion and building from ant. |
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| 268 | |
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| 269 | More info: http://www.cs.put.poznan.pl/dweiss/xml/projects/ant-docbook-styler/index.xml?lang=en |
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| 270 | Version : 2004_06_22-21_12 |
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| 271 | License : docbook.styler.guide.txt |
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| 272 | Files : Everything in lib/docbook except the 'docbook' subdirectory |
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| 273 | |
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| 274 | Example code syntax highlighter |
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| 275 | ------------------------------- |
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| 276 | A javascript library that can be used to dynamically highlight |
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| 277 | the syntax in program examples. We have made minor changes to |
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| 278 | make it support the HTML produced by Docbook (ie. find the language |
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| 279 | from the 'language' attribute instead of the 'class' attribute). |
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| 280 | |
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| 281 | More info: http://alexgorbatchev.com/SyntaxHighlighter/ |
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| 282 | Version : 1.5.1 |
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| 283 | License : LGPL (lgpl.txt) |
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| 284 | Files : Everything in the /doc/src/docbook/script and |
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| 285 | /doc/src/docbook/css directories |
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| 286 | |
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| 287 | Affymetrix Fusion SDK |
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| 288 | --------------------- |
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| 289 | Package for reading various Affymetrix file formats. We use a modified |
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| 290 | version that for some file formats can read from an InputStream instead |
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| 291 | of from a File object. This avoids a lot of copying and decompressing. |
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| 292 | |
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| 293 | More info: http://www.affymetrix.com/support/developer/fusion/index.affx |
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| 294 | : (original version) |
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| 295 | : http://dev.thep.lu.se/basehacks/wiki/AffxFusion |
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| 296 | : (modified version) |
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| 297 | Version : 1.09 |
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| 298 | License : LGPL (lgpl.txt) |
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| 299 | Files : AffxFusion.jar |
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| 300 | |
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| 301 | TAR file support |
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| 302 | ---------------- |
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| 303 | Package for reading and writing TAR files. |
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| 304 | |
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| 305 | More info: http://www.trustice.com/java/tar/ |
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| 306 | Version : 2.5 |
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| 307 | License : tar.license.txt |
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| 308 | Files : tar.jar |
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| 309 | |
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| 310 | BZIP file support |
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| 311 | ----------------- |
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| 312 | Package for reading and writing BZIP files. |
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| 313 | |
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| 314 | More info: http://www.kohsuke.org/bzip2/ |
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| 315 | Version : unknown |
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| 316 | License : Apache software license (apache.license.txt) |
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| 317 | Files : bzip2.jar |
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| 318 | |
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| 319 | Axis2 |
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| 320 | ----- |
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| 321 | A core engine for webservices from Apache. |
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| 322 | |
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| 323 | More info : http://ws.apache.org/axis2/ |
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| 324 | Version : 1.3 |
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| 325 | License : Apache License 2.0 (apache.license-2.0.txt) |
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| 326 | Files : Everything in the /lib/webservices directory |
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| 327 | |
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| 328 | SecondString |
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| 329 | ------------ |
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| 330 | A package with some fuzzy string matching algorithms developed |
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| 331 | by researchers at Carnegie Mellon University. |
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| 332 | |
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| 333 | More info : http://secondstring.sourceforge.net/ |
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| 334 | Version : CVS trunk checkout (2008-08-25) |
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| 335 | License : University of Illinois/NCSA Open Source (secondstring-LICENSE.txt) |
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| 336 | Files : secondstring.jar |
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| 337 | |
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| 338 | |
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| 339 | jsDraw2D |
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| 340 | -------- |
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| 341 | A vector graphics package for JavaScript. |
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| 342 | |
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| 343 | More info : http://jsdraw2d.jsfiction.com/ |
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| 344 | Version : 1.1.0 |
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| 345 | License : LGPL v3 |
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| 346 | Files : www/include/scripts/js-draw.js |
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| 347 | |
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| 348 | JavaSysMon |
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| 349 | ---------- |
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| 350 | A library for accessing CPU and memory information on some selected |
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| 351 | operating systems (including Linux, Windows and Mac OSX). It uses |
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| 352 | native libraries targeted for each platform |
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| 353 | |
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| 354 | More info : http://github.com/jezhumble/javasysmon |
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| 355 | Version : 0.3.1 |
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| 356 | License : javasysmon-LICENSE.txt |
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| 357 | Files : javasysmon-0.3.1.jar |
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