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-compress-1.18.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-2.2.0.jar 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-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ 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-1.2.8.jar 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-1.7.7.jar slf4j-log4j12-1.7.7.jar 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 Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ 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 slf4j-api-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php slf4j-log4j12-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.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