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.
5 A number of sources have also been adapted for incorporation into Jalview's source tree
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.
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
14 Licensing information for each library is given below:
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 BrowserLauncher2-1_3.jar LGPLv2.1
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
32 intervalstore-v1.0.jar
33 jabaws-min-client-NO_LOG4J-2.2.0.jar Apache license
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/
46 Jmol-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
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)
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-api-2.16.0.jar Apache license version 2.0
54 log4j-api-2.16.0.jar Apache license version 2.0
55 log4j-core-2.16.0.jar Apache license version 2.0
56 log4j-slf4j18-impl-2.16.0.jar Apache license version 2.0
58 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
59 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/
63 slf4j-api-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
64 slf4j-log4j12-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php
66 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.
67 VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
73 Libraries for Test Suite
76 utils/ant-contrib-1.0b3.jar
77 utils/hamcrest-core-1.3.jar
78 utils/roxes-ant-tasks-1.2-2004-01-30.jar
79 utils/proguard_5.3.3.jar
83 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
84 utils/testnglibs/guava-base-r03.jar
85 utils/testnglibs/guava-collections-r03.jar
86 utils/testnglibs/bsh-2.0b4.jar
87 utils/testnglibs/snakeyaml.jar
88 utils/testnglibs/testng-sources.jar
89 utils/testnglibs/testng.jar
90 utils/testnglibs/junit-4.12.jar
91 utils/testnglibs/jcommander.jar
95 Additional dependencies
97 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
98 examples/javascript/jquery*.js : BSD license
99 examples/javascript/jshashtable-2.1.js : Apache License
100 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
105 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
106 getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
107 groovy-*2.5.7.jar Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
108 istack-commons-runtime.jar CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
109 javax.activation-api-1.2.0.jar CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
110 javax.annotation-api-1.3.2.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
111 javax.jws-api-1.1.jar CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
112 javax.servlet-api-4.0.1.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
113 javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
114 javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
115 jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
116 jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
117 jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
118 jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php
119 mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
120 policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.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