X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=THIRDPARTYLIBS;h=d0d91256259f162dab3a4ce9a4a11415c708c5b6;hb=refs%2Fheads%2Fbugs%2FJAL-3009_blockingNetworkThreads;hp=f7f3529af3c1d51f003563a540067bf73672ae75;hpb=c90c66a318c7f009bf7fe27f98d711996bfb86f1;p=jalview.git diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index f7f3529..d0d9125 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -2,10 +2,20 @@ 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. + org.stackoverflowusers.file.WindowsShortcuts was downloaded from http://github.com/codebling/WindowsShortcuts via https://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java + +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 +24,8 @@ 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 @@ -33,13 +45,24 @@ 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 - -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