X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=THIRDPARTYLIBS;h=a202e9778a1c4289637d488dff069e53366103c7;hp=2671d8cc150ee9fa8c511ab709b774b9a07c483d;hb=729e39d052a71602d82f7808fdb3862b9d893ce8;hpb=df05b75cc541ddf6a0a6fa62e50bbff53df03e30 diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index 2671d8c..a202e97 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -2,31 +2,124 @@ The Jalview Desktop relies on a number of third-party libraries. These can be found in the lib directory, with additional compile time dependencies in the utils directory. -Licencing information for each library is given below: +A number of sources have also been adapted for incorporation into Jalview's source tree + +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 + and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081. + + jalview.ext.android includes code taken from the Android Open Source Project (https://android.googlesource.com/platform/frameworks/base/+/master/core/java/android/util). + The Apache 2.0 Licence (http://www.apache.org/licenses/LICENSE-2.0) is acknowledged in the source code. + org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java + +Licensing information for each library is given below: + +j8lib: -JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ -Jmol-12.1.13.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ activation.jar apache-mime4j-0.6.jar axis.jar -castor-1.1-cycle-xml.jar +biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE +biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE commons-codec-1.3.jar -commons-discovery.jar commons-logging-1.1.1.jar -commons-logging.jar +getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE +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 +htsjdk-2.12.0.jar built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute httpclient-4.0.3.jar httpcore-4.0.1.jar httpmime-4.0.3.jar +intervalstore-v1.0.jar +jabaws-min-client-NO_LOG4J-2.2.0.jar Apache license +java-json.jar jaxrpc.jar +jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jetty-http-9.2.10.v20150310.jar +jetty-io-9.2.10.v20150310.jar +jetty-server-9.2.10.v20150310.jar +jetty-util-9.2.10.v20150310.jar +jfreesvg-2.1.jar GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/ +JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ jhall.jar -log4j-1.2.8.jar +Jmol-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile) +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) +jsoup-1.8.1.jar +jsr311-api-1.1.1.jar +jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 +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/ +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/ +log4j-1.2-api-2.16.0.jar Apache license version 2.0 +log4j-api-2.16.0.jar Apache license version 2.0 +log4j-core-2.16.0.jar Apache license version 2.0 +log4j-slf4j18-impl-2.16.0.jar Apache license version 2.0 mail.jar -miglayout-4.0-swing.jar BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt -min-jaba-client.jar +miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt +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/ regex.jar saaj.jar +servlet-api-3.1.jar +slf4j-api-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php +slf4j-log4j12-1.7.32.jar MIT license - https://opensource.org/licenses/mit-license.php vamsas-client.jar +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. +VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr wsdl4j.jar xercesImpl.jar xml-apis.jar + +Libraries for Test Suite + +utils/axis-ant.jar +utils/ant-contrib-1.0b3.jar +utils/hamcrest-core-1.3.jar +utils/roxes-ant-tasks-1.2-2004-01-30.jar +utils/proguard_5.3.3.jar +utils/jhindexer.jar +utils/junit-4.12.jar +utils/jhall.jar +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 +utils/testnglibs/guava-base-r03.jar +utils/testnglibs/guava-collections-r03.jar +utils/testnglibs/bsh-2.0b4.jar +utils/testnglibs/snakeyaml.jar +utils/testnglibs/testng-sources.jar +utils/testnglibs/testng.jar +utils/testnglibs/junit-4.12.jar +utils/testnglibs/jcommander.jar +utils/wsdl4j.jar + + +Additional dependencies + +examples/javascript/deployJava.js : http://java.com/js/deployJava.js +examples/javascript/jquery*.js : BSD license +examples/javascript/jshashtable-2.1.js : Apache License +examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php + + +New in j11lib: + +FastInfoset.jar CDDL Version 1.1 - https://javaee.github.io/metro-fi/LICENSE +getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE +groovy-*2.5.7.jar Apache License, Version 2.0 - http://www.apache.org/licenses/LICENSE-2.0.html +istack-commons-runtime.jar CDDL Version 1.1 - https://glassfish.java.net/public/CDDL+GPL_1_1.html +javax.activation-api-1.2.0.jar CDDL/GPLv2+CE - https://github.com/javaee/activation/blob/master/LICENSE.txt +javax.annotation-api-1.3.2.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.annotation/blob/master/LICENSE +javax.jws-api-1.1.jar CDDL + GPLv2 with classpath exception - https://glassfish.dev.java.net/nonav/public/CDDL+GPL.html +javax.servlet-api-4.0.1.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1 +javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss.oracle.com/licenses/CDDL+GPL-1.1 +javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE +jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1 +jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md +jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php +mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +stax-ex-1.8.1.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +stax2-api-4.2.jar The BSD License - http://www.opensource.org/licenses/bsd-license.php +streambuffer-1.5.7.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +txw2-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php +wsdl4j-1.6.3.jar CPL - http://www.opensource.org/licenses/cpl1.0.txt +