JAL-3878 update branch from 2.12 merge from 2.11.2
[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-logging-1.1.1.jar
25 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
26 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
27 htsjdk-2.12.0.jar       built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
28 httpclient-4.0.3.jar
29 httpcore-4.0.1.jar
30 httpmime-4.0.3.jar
31 intervalstore-v1.1.jar
32 jabaws-min-client-NO_LOG4J-2.2.1.jar    Apache license - pre-release of JABAWS 2.2.1 client built from https://source.jalview.org/crucible/changelog/jabaws?cs=586260b9f877e0954513fcffb0aa27eaddc5d0ff 
33 java-json.jar
34 jaxrpc.jar
35 jersey-client-1.19.4.jar        CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
36 jersey-core-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
37 jersey-json-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
38 jetty-http-9.2.10.v20150310.jar
39 jetty-io-9.2.10.v20150310.jar
40 jetty-server-9.2.10.v20150310.jar
41 jetty-util-9.2.10.v20150310.jar
42 jfreesvg-2.1.jar        GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
43 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
44 jhall.jar
45 Jmol-14.31.53.jar       GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
46 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)
47 jsoup-1.8.1.jar
48 jsr311-api-1.1.1.jar
49 jswingreader-0.3.jar    Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
50 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/ 
51 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/ 
52 log4j-1.2-api-2.16.0.jar        Apache license version 2.0
53 log4j-api-2.16.0.jar    Apache license version 2.0
54 log4j-core-2.16.0.jar   Apache license version 2.0
55 log4j-slf4j18-impl-2.16.0.jar   Apache license version 2.0
56 mail.jar
57 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
58 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/ 
59 regex.jar
60 saaj.jar
61 servlet-api-3.1.jar
62 slf4j-api-1.7.32.jar    MIT license - https://opensource.org/licenses/mit-license.php
63 slf4j-log4j12-1.7.32.jar        MIT license - https://opensource.org/licenses/mit-license.php
64 vamsas-client.jar
65 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.
66 VARNAv3-93.jar  GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
67 wsdl4j.jar
68 xercesImpl.jar
69 xml-apis.jar
70
71
72 Libraries for Test Suite
73
74 utils/axis-ant.jar
75 utils/ant-contrib-1.0b3.jar
76 utils/hamcrest-core-1.3.jar
77 utils/roxes-ant-tasks-1.2-2004-01-30.jar
78 utils/proguard_5.3.3.jar
79 utils/jhindexer.jar
80 utils/junit-4.12.jar
81 utils/jhall.jar
82 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
83 utils/testnglibs/guava-base-r03.jar
84 utils/testnglibs/guava-collections-r03.jar
85 utils/testnglibs/bsh-2.0b4.jar
86 utils/testnglibs/snakeyaml.jar
87 utils/testnglibs/testng-sources.jar
88 utils/testnglibs/testng.jar
89 utils/testnglibs/junit-4.12.jar
90 utils/testnglibs/jcommander.jar
91 utils/wsdl4j.jar
92
93
94 Additional dependencies
95
96 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
97 examples/javascript/jquery*.js : BSD license
98 examples/javascript/jshashtable-2.1.js : Apache License
99 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
100
101
102 New in j11lib:
103
104 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
105 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
106 groovy-*2.5.7.jar       Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
107 istack-commons-runtime.jar      CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
108 javax.activation-api-1.2.0.jar  CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
109 javax.annotation-api-1.3.2.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
110 javax.jws-api-1.1.jar   CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
111 javax.servlet-api-4.0.1.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
112 javax.xml.rpc-api-1.1.2.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
113 javax.xml.soap-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
114 jaxb-api-2.3.1.jar      CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
115 jaxb-runtime-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
116 jaxws-api-2.3.1.jar     CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
117 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
118 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
119 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
120 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
121 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
122 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
123 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
124 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
125