JAL-2931 patch IA paths for new build box

[jalview.git] / THIRDPARTYLIBS

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 5918fc2..e2baa85 100644 (file)
--- 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
@@ -14,10 +23,13 @@ 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
@@ -26,8 +38,30 @@ 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
 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