X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=THIRDPARTYLIBS;h=a202e9778a1c4289637d488dff069e53366103c7;hp=bbef8686155dca735e40d42e1212ed6f09d142d9;hb=729e39d052a71602d82f7808fdb3862b9d893ce8;hpb=64fb69927bb37d8773a75b684a3e7ab3f0c5c212 diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index bbef868..a202e97 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -6,51 +6,120 @@ A number of sources have also been adapted for incorporation into Jalview's sour 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 -Licencing information for each library is given below: +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/ -VARNAv3-91.jar GPL licenced software by Kévin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr 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 -commons-net-3.3.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 -jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012) +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 -jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 -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 -spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven -spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven +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 -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) -jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/ -quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ + +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: -Tools not bundled with Jalview source -jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory. +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