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
  24 commons-logging-1.1.1.jar
  25 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
  26 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
  27 htsjdk-2.12.0.jar       built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
  28 httpclient-4.0.3.jar
  29 httpcore-4.0.1.jar
  30 httpmime-4.0.3.jar
  31 intervalstore-v1.1.jar
  32 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
  33 java-json.jar
  34 jaxrpc.jar
  35 jersey-client-1.19.4.jar        CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  36 jersey-core-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  37 jersey-json-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  38 jetty-http-9.2.10.v20150310.jar
  39 jetty-io-9.2.10.v20150310.jar
  40 jetty-server-9.2.10.v20150310.jar
  41 jetty-util-9.2.10.v20150310.jar
  42 jfreesvg-2.1.jar        GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
  43 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
  44 jhall.jar
  45 Jmol-14.31.53.jar       GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
  46 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)
  47 jsoup-1.8.1.jar
  48 jsr311-api-1.1.1.jar
  49 jswingreader-0.3.jar    Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
  50 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/
  51 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/
  52 log4j-1.2-api-2.16.0.jar        Apache license version 2.0
  53 log4j-api-2.16.0.jar    Apache license version 2.0
  54 log4j-core-2.16.0.jar   Apache license version 2.0
  55 log4j-slf4j18-impl-2.16.0.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 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/
  59 regex.jar
  60 saaj.jar
  61 servlet-api-3.1.jar
  62 slf4j-api-1.7.32.jar    MIT license - https://opensource.org/licenses/mit-license.php
  63 slf4j-log4j12-1.7.32.jar        MIT license - https://opensource.org/licenses/mit-license.php
  64 vamsas-client.jar
  65 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.
  66 VARNAv3-93.jar  GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr
  67 wsdl4j.jar
  68 xercesImpl.jar
  69 xml-apis.jar
  70
  71
  72 Libraries for Test Suite
  73
  74 utils/axis-ant.jar
  75 utils/ant-contrib-1.0b3.jar
  76 utils/hamcrest-core-1.3.jar
  77 utils/roxes-ant-tasks-1.2-2004-01-30.jar
  78 utils/proguard_5.3.3.jar
  79 utils/jhindexer.jar
  80 utils/junit-4.12.jar
  81 utils/jhall.jar
  82 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
  83 utils/testnglibs/guava-base-r03.jar
  84 utils/testnglibs/guava-collections-r03.jar
  85 utils/testnglibs/bsh-2.0b4.jar
  86 utils/testnglibs/snakeyaml.jar
  87 utils/testnglibs/testng-sources.jar
  88 utils/testnglibs/testng.jar
  89 utils/testnglibs/junit-4.12.jar
  90 utils/testnglibs/jcommander.jar
  91 utils/wsdl4j.jar
  92
  93
  94 Additional dependencies
  95
  96 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
  97 examples/javascript/jquery*.js : BSD license
  98 examples/javascript/jshashtable-2.1.js : Apache License
  99 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
 100
 101
 102 New in j11lib:
 103
 104 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
 105 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
 106 groovy-*2.5.7.jar       Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
 107 istack-commons-runtime.jar      CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
 108 javax.activation-api-1.2.0.jar  CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
 109 javax.annotation-api-1.3.2.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
 110 javax.jws-api-1.1.jar   CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
 111 javax.servlet-api-4.0.1.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
 112 javax.xml.rpc-api-1.1.2.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
 113 javax.xml.soap-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
 114 jaxb-api-2.3.1.jar      CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
 115 jaxb-runtime-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 116 jaxws-api-2.3.1.jar     CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
 117 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
 118 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 119 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 120 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 121 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
 122 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 123 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 124 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
 125