The Jalview Desktop relies on a number of third-party libraries.
These can be found in the lib directory, with additional compile
time dependencies in the utils directory.

A number of sources have also been adapted for incorporation into Jalview's source tree

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
 and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081. 
 
 jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util).
 The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code.
 org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java 

Licensing information for each library is given below:

j8lib:

activation.jar	
apache-mime4j-0.6.jar
axis.jar
biojava-core-4.1.0.jar	LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
biojava-ontology-4.1.0.jar	LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
commons-codec-1.3.jar
commons-logging-1.1.1.jar
getdown-core.jar	Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
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
htsjdk-2.12.0.jar	built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
httpclient-4.0.3.jar
httpcore-4.0.1.jar
httpmime-4.0.3.jar
intervalstore-v1.0.jar
jabaws-min-client-NO_LOG4J-2.2.0.jar	Apache license
java-json.jar
jaxrpc.jar
jersey-client-1.19.4.jar	CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
jersey-core-1.19.4.jar	CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
jersey-json-1.19.4.jar	CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
jetty-http-9.2.10.v20150310.jar
jetty-io-9.2.10.v20150310.jar
jetty-server-9.2.10.v20150310.jar
jetty-util-9.2.10.v20150310.jar
jfreesvg-2.1.jar	GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
JGoogleAnalytics_0.3.jar	APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
jhall.jar
Jmol-14.31.53.jar	GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
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)
jsoup-1.8.1.jar
jsr311-api-1.1.1.jar
jswingreader-0.3.jar	Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
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/ 
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/ 
log4j-1.2-api-2.16.0.jar	Apache license version 2.0
log4j-api-2.16.0.jar	Apache license version 2.0
log4j-core-2.16.0.jar	Apache license version 2.0
log4j-slf4j18-impl-2.16.0.jar	Apache license version 2.0
mail.jar
miglayout-4.0-swing.jar	BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
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/ 
regex.jar
saaj.jar
servlet-api-3.1.jar
slf4j-api-1.7.32.jar	MIT license - https://opensource.org/licenses/mit-license.php
slf4j-log4j12-1.7.32.jar	MIT license - https://opensource.org/licenses/mit-license.php
vamsas-client.jar
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.
VARNAv3-93.jar	GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
wsdl4j.jar
xercesImpl.jar
xml-apis.jar


Libraries for Test Suite

utils/axis-ant.jar
utils/ant-contrib-1.0b3.jar
utils/hamcrest-core-1.3.jar
utils/roxes-ant-tasks-1.2-2004-01-30.jar
utils/proguard_5.3.3.jar
utils/jhindexer.jar
utils/junit-4.12.jar
utils/jhall.jar
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
utils/testnglibs/guava-base-r03.jar
utils/testnglibs/guava-collections-r03.jar
utils/testnglibs/bsh-2.0b4.jar
utils/testnglibs/snakeyaml.jar
utils/testnglibs/testng-sources.jar
utils/testnglibs/testng.jar
utils/testnglibs/junit-4.12.jar
utils/testnglibs/jcommander.jar
utils/wsdl4j.jar


Additional dependencies

examples/javascript/deployJava.js : http://java.com/js/deployJava.js
examples/javascript/jquery*.js : BSD license
examples/javascript/jshashtable-2.1.js : Apache License
examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php


New in j11lib:

FastInfoset.jar	CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
getdown-core.jar	Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
groovy-*2.5.7.jar	Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
istack-commons-runtime.jar	CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
javax.activation-api-1.2.0.jar	CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
javax.annotation-api-1.3.2.jar	CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
javax.jws-api-1.1.jar	CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
javax.servlet-api-4.0.1.jar	CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
javax.xml.rpc-api-1.1.2.jar	CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
javax.xml.soap-api.jar	CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
jaxb-api-2.3.1.jar	CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
jaxb-runtime-2.3.2.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
jaxws-api-2.3.1.jar	CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
jsr311-api-1.1.1.jar	CDDL License - http://www.opensource.org/licenses/cddl1.php
mimepull-1.9.11.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
policy-2.7.6.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
stax-ex-1.8.1.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
stax2-api-4.2.jar	The BSD License - http://www.opensource.org/licenses/bsd-license.php
streambuffer-1.5.7.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
txw2-2.3.2.jar	Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
wsdl4j-1.6.3.jar	CPL - http://www.opensource.org/licenses/cpl1.0.txt

