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 JGoogleAnalytics_0.3.jar        APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
  19 Jmol-14.6.4_2016.10.26.jar      GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
  20 VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr
  21 activation.jar
  22 apache-mime4j-0.6.jar
  23 axis.jar
  24 castor-1.1-cycle-xml.jar
  25 commons-codec-1.3.jar
  26 commons-discovery.jar
  27 commons-logging-1.1.1.jar
  28 commons-logging.jar
  29 commons-net-3.3.jar
  30 groovy-all-2.4.6-indy.jar       APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip
  31 httpclient-4.0.3.jar
  32 httpcore-4.0.1.jar
  33 httpmime-4.0.3.jar
  34 jaxrpc.jar
  35 jhall.jar
  36 jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
  37 log4j-1.2.8.jar
  38 mail.jar
  39 miglayout-4.0-swing.jar BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
  40 min-jaba-client.jar
  41 regex.jar
  42 saaj.jar
  43 vamsas-client.jar
  44 wsdl4j.jar
  45 xercesImpl.jar
  46 xml-apis.jar
  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 jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/
  49
  50 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
  51
  52 vaqua5-patch: 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.
  53
  54 lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
  55
  56 lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
  57
  58 lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
  59
  60
  61 Libraries for Test Suite
  62
  63 utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview
  64                       version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6
  65
  66
  67 Additional dependencies
  68
  69 examples/javascript/deployJava.js : http://java.com/js/deployJava.js
  70 examples/javascript/jquery*.js : BSD license
  71 examples/javascript/jshashtable-2.1.js : Apache License
  72 examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
  73
  74
  75 New in j11lib:
  76
  77 FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE
  78 getdown-core.jar        Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE
  79 groovy-*2.5.7.jar       Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html
  80 istack-commons-runtime.jar      CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html
  81 javax.activation-api-1.2.0.jar  CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt
  82 javax.annotation-api-1.3.2.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE
  83 javax.jws-api-1.1.jar   CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html
  84 javax.servlet-api-4.0.1.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
  85 javax.xml.rpc-api-1.1.2.jar     CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1
  86 javax.xml.soap-api.jar  CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE
  87 jaxb-api-2.3.1.jar      CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1
  88 jaxb-runtime-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
  89 jaxws-api.jar   CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
  90 jersey-client-1.19.4.jar        CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  91 jersey-core-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  92 jersey-json-1.19.4.jar  CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html
  93 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
  94 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
  95 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
  96 slf4j-api-1.7.26.jar    MIT License - https://opensource.org/licenses/mit-license.php
  97 slf4j-log4j12-1.7.26.jar        MIT License - https://opensource.org/licenses/mit-license.php
  98 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
  99 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
 100 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 101 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 102 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
 103