X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=THIRDPARTYLIBS;h=7d4ffc71ca33e6f469a17c3a6c2d90838719a2df;hb=60068a9887dba34c9e7cf49b2f5f53a6fdc15931;hp=52214b28a318b1b2a5b1b907d26dea8d95009c55;hpb=516cbeec2ab5eb61f1767720258d896920f2db4d;p=jalview.git

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 52214b2..7d4ffc7 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -6,11 +6,15 @@ 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/
+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
@@ -21,6 +25,7 @@ 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
@@ -45,12 +50,19 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 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-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
-
-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