X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=THIRDPARTYLIBS;h=3ec73d38c8c01f1028be5f78809e5adc9a250b8d;hb=refs%2Fheads%2Fnew_feature%2FJAL-4019_ambiguous_base_colourscheme;hp=c26858d827e97be04679e3e7b89d75a28b29b22f;hpb=f2134a990625e5d9190daa31b7771fcafff58c96;p=jalview.git diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index c26858d..3ec73d3 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -20,16 +20,19 @@ apache-mime4j-0.6.jar axis.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-logging-1.1.1.jar +commons-codec-1.3.jar Apache license - https://www.apache.org/licenses/ +commons-discovery.jar Apache license - https://www.apache.org/licenses/ +commons-logging-1.1.1.jar Apache license - https://www.apache.org/licenses/ +flatlaf-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license +flatlaf-extras-3.0.jar Apache 2.0 License - https://www.formdev.com/flatlaf/#license 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 +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 +htsjdk-2.23.0.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-2.2.0.jar +intervalstore-v1.1.jar +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 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 @@ -42,24 +45,21 @@ 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 -Jmol-14.31.53.jar GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile) +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) 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-1.2.8.jar +log4j-api-2.17.1.jar Apache license version 2.0 +log4j-core-2.17.1.jar Apache license version 2.0 +log4j-slf4j18-impl-2.17.1.jar Apache license version 2.0 mail.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-1.7.7.jar -slf4j-log4j12-1.7.7.jar +slf4j-api-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 @@ -111,12 +111,9 @@ javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.co 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 -Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ 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