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-2.1.jar        GPL v3 licensed library from the JFree suite - 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-1.7.32.jar    MIT license - https://opensource.org/licenses/mit-license.php
  62 vamsas-client.jar
  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 jsr311-api-1.1.1.jar    CDDL License - http://www.opensource.org/licenses/cddl1.php
 115 mimepull-1.9.11.jar     Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 116 policy-2.7.6.jar        Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 117 stax-ex-1.8.1.jar       Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 118 stax2-api-4.2.jar       The BSD License - http://www.opensource.org/licenses/bsd-license.php
 119 streambuffer-1.5.7.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 120 txw2-2.3.2.jar  Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php
 121 wsdl4j-1.6.3.jar        CPL - http://www.opensource.org/licenses/cpl1.0.txt
 122