JAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 72ff49e..3ec73d3 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -20,15 +20,18 @@ 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
+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
@@ -42,27 +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-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
+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-1.7.32.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