JAL-4260 encapsulate logic for resolving nearest column and do better using it in...
[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-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/
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-1.7.36.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/
63 vamsas-client.jar
64 VARNAv3-93.jar  GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
65 wsdl4j.jar
66 xercesImpl.jar
67 xml-apis.jar
68
69
70 Libraries for Test Suite
71
72 utils/axis-ant.jar
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
77 utils/jhindexer.jar
78 utils/junit-4.12.jar
79 utils/jhall.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
89 utils/wsdl4j.jar
90
91
92 Additional dependencies
93
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
98
99
100 New in j11lib:
101
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
123