JAL-3066 Read parameters directly from args list allowing for multiple values.
[jalview.git] / THIRDPARTYLIBS
1 The Jalview Desktop relies on a number of third-party libraries.
2 These can be found in the lib directory, with additional compile
3 time dependencies in the utils directory.
4
5 A number of sources have also been adapted for incorporation into Jalview's source tree
6
7 ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Morris and Nadezhda Doncheva for the Cytoscape StructureViz2 plugin. It is released under the Berkley license and we hereby acknowledge its original copyright is held by the UCSF Computer Graphics Laboratory
8  and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081. 
9  
10  jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util).
11  The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code.
12  org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java 
13
14 Licensing information for each library is given below:
15
16 j8lib:
17
18 activation.jar  
19 apache-mime4j-0.6.jar
20 axis.jar
21 biojava-core-4.1.0.jar  LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
22 biojava-ontology-4.1.0.jar      LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
23 commons-codec-1.3.jar
24 commons-compress-1.18.jar
25 commons-logging-1.1.1.jar
26 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
27 groovy-all-2.4.12-indy.jar      APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
28 htsjdk-2.12.0.jar       built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
29 httpclient-4.0.3.jar
30 httpcore-4.0.1.jar
31 httpmime-4.0.3.jar
32 intervalstore-v1.0.jar
33 jabaws-min-client-2.2.0.jar
34 java-json.jar
35 jaxrpc.jar
36 jersey-client-1.19.4.jar        CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
37 jersey-core-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
38 jersey-json-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
39 jetty-http-9.2.10.v20150310.jar
40 jetty-io-9.2.10.v20150310.jar
41 jetty-server-9.2.10.v20150310.jar
42 jetty-util-9.2.10.v20150310.jar
43 jfreesvg-2.1.jar        GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
44 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
45 jhall.jar
46 Jmol-14.6.4_2016.10.26.jar      GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
47 json_simple-1.1.jar     Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
48 jsoup-1.8.1.jar
49 jsr311-api-1.1.1.jar
50 jswingreader-0.3.jar    Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
51 libquaqua64-8.0.jnilib.jar      quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
52 libquaqua-8.0.jnilib.jar        quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
53 log4j-1.2.8.jar
54 mail.jar
55 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
56 quaqua-filechooser-only-8.0.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
57 regex.jar
58 saaj.jar
59 servlet-api-3.1.jar
60 slf4j-api-1.7.7.jar
61 slf4j-log4j12-1.7.7.jar
62 vamsas-client.jar
63 VAqua5-patch.jar        This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses.
64 VARNAv3-93.jar  GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
65 wsdl4j.jar
66 xercesImpl.jar
67 xml-apis.jar
68
69
70 Libraries for Test Suite
71
72 utils/axis-ant.jar
73 utils/ant-contrib-1.0b3.jar
74 utils/hamcrest-core-1.3.jar
75 utils/roxes-ant-tasks-1.2-2004-01-30.jar
76 utils/proguard_5.3.3.jar
77 utils/jhindexer.jar
78 utils/junit-4.12.jar
79 utils/jhall.jar
80 utils/classgraph-4.1.6.jar      BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
81 utils/testnglibs/guava-base-r03.jar
82 utils/testnglibs/guava-collections-r03.jar
83 utils/testnglibs/bsh-2.0b4.jar
84 utils/testnglibs/snakeyaml.jar
85 utils/testnglibs/testng-sources.jar
86 utils/testnglibs/testng.jar
87 utils/testnglibs/junit-4.12.jar
88 utils/testnglibs/jcommander.jar
89 utils/wsdl4j.jar
90
91
92 Additional dependencies
93
94 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
95 examples/javascript/jquery*.js : BSD license
96 examples/javascript/jshashtable-2.1.js : Apache License
97 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
98
99
100 New in j11lib:
101
102 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
103 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
104 groovy-*2.5.7.jar       Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
105 istack-commons-runtime.jar      CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
106 javax.activation-api-1.2.0.jar  CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
107 javax.annotation-api-1.3.2.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
108 javax.jws-api-1.1.jar   CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
109 javax.servlet-api-4.0.1.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
110 javax.xml.rpc-api-1.1.2.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
111 javax.xml.soap-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
112 jaxb-api-2.3.1.jar      CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
113 jaxb-runtime-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
114 jaxws-api-2.3.1.jar     CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
115 Jmol-14.6.4_2016.10.26-no_netscape.jar  GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
116 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
117 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
118 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
119 slf4j-api-1.7.26.jar    MIT License - https://opensource.org/licenses/mit-license.php
120 slf4j-log4j12-1.7.26.jar        MIT License - https://opensource.org/licenses/mit-license.php
121 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
122 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
123 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
124 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
125 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
126