X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=THIRDPARTYLIBS;h=e2baa858fe96c0d3a899c2bbb4a0439d87597490;hp=57aad05ad35a86c686b4ea8fc00cd07109cfe06f;hb=019b7e5c1193bc78ddb667bfa1f4a68724b4b2cf;hpb=9d75efeeb9a6e51bd328f56e376dca4e007b635c

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 57aad05..e2baa85 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -2,10 +2,19 @@ The Jalview Desktop relies on a number of third-party libraries.
 These can be found in the lib directory, with additional compile
 time dependencies in the utils directory.
 
-Licencing information for each library is given below:
+A number of sources have also been adapted for incorporation into Jalview's source tree
+
+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.
+
+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/
+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
@@ -14,6 +23,8 @@ 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
@@ -34,8 +45,23 @@ 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/ 
+
+vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html
+
+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
+
+lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
+
+
 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
+examples/javascript/facebox-1.3.js : MTI License - http://www.opensource.org/licenses/mit-license.php
+