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 commons-codec-1.3.jar Apache license - https://www.apache.org/licenses/
24 commons-discovery.jar Apache license - https://www.apache.org/licenses/
25 commons-logging-1.1.1.jar Apache license - https://www.apache.org/licenses/
26 flatlaf-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license
27 flatlaf-extras-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license
28 getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
29 groovy-all-2.4.21-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
30 htsjdk-2.23.0.jar built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
34 intervalstore-v1.1.jar
35 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
38 jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
39 jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
40 jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
41 jetty-http-9.2.10.v20150310.jar
42 jetty-io-9.2.10.v20150310.jar
43 jetty-server-9.2.10.v20150310.jar
44 jetty-util-9.2.10.v20150310.jar
45 jfreesvg-3.4.3.jar GPL v3 licensed library from the JFree suite - last release with Java 1.8 compatibility http://www.jfree.org/jfreesvg/
46 JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
48 Jmol-NO_LOG4J-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
49 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)
52 jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
53 log4j-api-2.17.1.jar Apache license version 2.0
54 log4j-core-2.17.1.jar Apache license version 2.0
55 log4j-slf4j18-impl-2.17.1.jar Apache license version 2.0
57 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
61 slf4j-api-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/
62 slf4j-nop-1.7.36.jar MIT license - https://opensource.org/licenses/mit-license.php - downloaded from https://repo1.maven.org/maven2/org/slf4j/
64 VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
70 Libraries for Test Suite
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
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
92 Additional dependencies
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
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 jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php
116 mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
117 policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
118 stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
119 stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php
120 streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
121 txw2-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
122 wsdl4j-1.6.3.jar CPL - http://www.opensource.org/licenses/cpl1.0.txt