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-compress-1.18.jar
  25 commons-logging-1.1.1.jar
  26 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
  27 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
  28 htsjdk-2.12.0.jar       built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
  29 httpclient-4.0.3.jar
  30 httpcore-4.0.1.jar
  31 httpmime-4.0.3.jar
  32 intervalstore-v1.0.jar
  33 jabaws-min-client-2.2.0.jar
  34 java-json.jar
  35 jaxrpc.jar
  36 jersey-client-1.19.4.jar        CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  37 jersey-core-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  38 jersey-json-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  39 jetty-http-9.2.10.v20150310.jar
  40 jetty-io-9.2.10.v20150310.jar
  41 jetty-server-9.2.10.v20150310.jar
  42 jetty-util-9.2.10.v20150310.jar
  43 jfreesvg-2.1.jar        GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
  44 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
  45 jhall.jar
  46 Jmol-14.6.4_2016.10.26.jar      GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
  47 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)
  48 jsoup-1.8.1.jar
  49 jsr311-api-1.1.1.jar
  50 jswingreader-0.3.jar    Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
  51 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/
  52 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/
  53 log4j-1.2.8.jar
  54 mail.jar
  55 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
  56 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/
  57 regex.jar
  58 saaj.jar
  59 servlet-api-3.1.jar
  60 slf4j-api-1.7.7.jar
  61 slf4j-log4j12-1.7.7.jar
  62 vamsas-client.jar
  63 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.
  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 Jmol-14.6.4_2016.10.26-no_netscape.jar  GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
 116 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
 117 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 118 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 119 slf4j-api-1.7.26.jar    MIT License - https://opensource.org/licenses/mit-license.php
 120 slf4j-log4j12-1.7.26.jar        MIT License - https://opensource.org/licenses/mit-license.php
 121 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 122 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
 123 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 124 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 125 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
 126