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-v1.0.jar
  32 jabaws-min-client-2.2.0.jar
  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-1.2.8.jar
  53 mail.jar
  54 miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt
  55 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/
  56 regex.jar
  57 saaj.jar
  58 servlet-api-3.1.jar
  59 slf4j-api-1.7.7.jar
  60 slf4j-log4j12-1.7.7.jar
  61 vamsas-client.jar
  62 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.
  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 Jmol-14.6.4_2016.10.26-no_netscape.jar  GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
 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 slf4j-api-1.7.26.jar    MIT License - https://opensource.org/licenses/mit-license.php
 119 slf4j-log4j12-1.7.26.jar        MIT License - https://opensource.org/licenses/mit-license.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