JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

[jalview.git] / THIRDPARTYLIBS

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 38d5b93..c7c9b5d 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -6,8 +6,12 @@ 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-14.6.4_2016.10.26.jar     GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
@@ -26,7 +30,6 @@ 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
@@ -35,8 +38,8 @@ 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
+spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
+spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven - TODO: JAL-3035 remove if no longer needed ?
 vamsas-client.jar
 wsdl4j.jar
 xercesImpl.jar
@@ -46,7 +49,9 @@ 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/ 
 
-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
+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
 
@@ -58,4 +63,5 @@ 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