JAL-4001 make page_location the same encoding as the old jgoogleanalytics
[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 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
31 httpclient-4.0.3.jar
32 httpcore-4.0.1.jar
33 httpmime-4.0.3.jar
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 
36 java-json.jar
37 jaxrpc.jar
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-2.1.jar        GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
46 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
47 jhall.jar
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)
50 jsoup-1.8.1.jar
51 jsr311-api-1.1.1.jar
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
56 mail.jar
57 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
58 regex.jar
59 saaj.jar
60 servlet-api-3.1.jar
61 slf4j-api-1.7.32.jar    MIT license - https://opensource.org/licenses/mit-license.php
62 vamsas-client.jar
63 VARNAv3-93.jar  GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
64 wsdl4j.jar
65 xercesImpl.jar
66 xml-apis.jar
67
68
69 Libraries for Test Suite
70
71 utils/axis-ant.jar
72 utils/ant-contrib-1.0b3.jar
73 utils/hamcrest-core-1.3.jar
74 utils/roxes-ant-tasks-1.2-2004-01-30.jar
75 utils/proguard_5.3.3.jar
76 utils/jhindexer.jar
77 utils/junit-4.12.jar
78 utils/jhall.jar
79 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
80 utils/testnglibs/guava-base-r03.jar
81 utils/testnglibs/guava-collections-r03.jar
82 utils/testnglibs/bsh-2.0b4.jar
83 utils/testnglibs/snakeyaml.jar
84 utils/testnglibs/testng-sources.jar
85 utils/testnglibs/testng.jar
86 utils/testnglibs/junit-4.12.jar
87 utils/testnglibs/jcommander.jar
88 utils/wsdl4j.jar
89
90
91 Additional dependencies
92
93 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
94 examples/javascript/jquery*.js : BSD license
95 examples/javascript/jshashtable-2.1.js : Apache License
96 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
97
98
99 New in j11lib:
100
101 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
102 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
103 groovy-*2.5.7.jar       Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
104 istack-commons-runtime.jar      CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
105 javax.activation-api-1.2.0.jar  CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
106 javax.annotation-api-1.3.2.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
107 javax.jws-api-1.1.jar   CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
108 javax.servlet-api-4.0.1.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
109 javax.xml.rpc-api-1.1.2.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
110 javax.xml.soap-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
111 jaxb-api-2.3.1.jar      CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
112 jaxb-runtime-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
113 jaxws-api-2.3.1.jar     CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
114 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
115 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
116 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
117 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
118 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
119 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
120 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
121 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
122