j8lib:
-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
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
+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
+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/
-
-vaqua5-patch: 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.
-
-lib/htsjdk-2.12.jar: 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
-
-lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
Libraries for Test Suite
-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/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
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.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md
-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
+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
-slf4j-api-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.php
-slf4j-log4j12-1.7.26.jar MIT License - https://opensource.org/licenses/mit-license.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
git://source.jalview.org / jalview.git / blobdiff