X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=THIRDPARTYLIBS;h=a202e9778a1c4289637d488dff069e53366103c7;hp=e0be9046f006070549a79aef37f7ad4643f0f1d3;hb=729e39d052a71602d82f7808fdb3862b9d893ce8;hpb=4d22ba3918844213aaf4c3f58da43f93146159d4 diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index e0be904..a202e97 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -9,51 +9,86 @@ ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Mor 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: -JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ -Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ -VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr +j8lib: + 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 -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 +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/ -lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute -lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE +Libraries for Test Suite -lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE +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 @@ -63,3 +98,28 @@ 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 +