JAL-3484 unit test for restoring two views' annotation ordering

[jalview.git] / THIRDPARTYLIBS

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index ea44193..728711e 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -6,12 +6,16 @@ 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:
 
 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
+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
@@ -20,11 +24,12 @@ 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
 httpclient-4.0.3.jar
 httpcore-4.0.1.jar
 httpmime-4.0.3.jar
 jaxrpc.jar
-jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012)
 jhall.jar
 jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
 log4j-1.2.8.jar
@@ -33,8 +38,6 @@ miglayout-4.0-swing.jar       BSD http://www.migcalendar.com/miglayout/versions/4.0/li
 min-jaba-client.jar
 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
 vamsas-client.jar
 wsdl4j.jar
 xercesImpl.jar
@@ -42,12 +45,27 @@ 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
+
+
 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
-
-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.
+examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php