This file contains descriptions and license information for all libraries referenced by SeqCode

Copies of applicable license are stored in ./licenses.


SeqCode
-----------------
http://seqcode.org
License: MIT.


AffxFusion
----------
Library used for loading affymetrix expression array data from CEL files.
http://www.affymetrix.com/estore/partners_programs/programs/developer/fusion/index.affx?terms=no
License: LGPL v2.1
Packages: affymetrix.*
Jars:
	./affxfusion/AffxFusion-1.09.jar


Apache Commons
--------------
Broad collection of reusable components.
	CLI = command-line args parser
	Lang = extra functionality for classes in java.lang
	Math = Math & stats components
https://commons.apache.org/
License: Apache v2.0
Packages: org.apache.commons.*
Jars:
 ./apache-commons/commons-cli-1.5.0.jar
 ./apache-commons/commons-lang3-3.13.0.jar
 ./apache-commons/commons-math4-core-4.0-beta1.jar
 ./apache-commons/commons-math4-legacy-4.0-beta1.jar
 ./apache-commons/commons-math4-legacy-core-4.0-beta1.jar
 ./apache-commons/commons-math4-legacy-exception-4.0-beta1.jar
 ./apache-commons/commons-math4-neuralnet-4.0-beta1.jar
 ./apache-commons/commons-math4-transform-4.0-beta1.jar

Apache HTTP Components
----------------------
Toolset of low level Java components focused on HTTP and associated protocols.
https://hc.apache.org/
License: Apache v2.0
Packages: org.apache.http.*
Jars:
 ./apache-httpcomponents/httpclient5-5.2.1.jar
 ./apache-httpcomponents/httpcore5-5.2.2.jar

Apache Logging
--------------
Application logging services.
https://logging.apache.org/
License: Apache v2.0
Packages: org.apache.logging.*
Jars:
 ./apache-logging/log4j-api-2.20.0.jar
 ./apache-logging/log4j-core-2.20.0.jar


Batik
-----
Apache toolset for images in the Scalable Vector Graphics (SVG) format
http://xmlgraphics.apache.org/batik/
License: Apache v2.0
Packages: org.apache.batik.*
Jars:
	./batik/batik*-1.17.jar


BioJava
-------
http://biojava.org
License: LGPL
Packages: org.biojava.*
Jars:
 ./biojava/biojava-1.5.jar
NOTE: newer versions are very different and would require migration


COLT
----
Libraries for High Performance Scientific and Technical Computing
https://dst.lbl.gov/ACSSoftware/colt/
License:
    Packages cern.colt* , cern.jet*, cern.clhep
        Copyright (c) 1999 CERN - European Organization for Nuclear
        Research.
        Permission to use, copy, modify, distribute and sell this
        software and its documentation for any purpose is hereby granted
        without fee, provided that the above copyright notice appear in
        all copies and that both that copyright notice and this
        permission notice appear in supporting documentation. CERN makes
        no representations about the suitability of this software for
        any purpose. It is provided "as is" without expressed or implied
        warranty.
    Packages hep.aida.*
        Written by Pavel Binko, Dino Ferrero Merlino, Wolfgang Hoschek,
        Tony Johnson, Andreas Pfeiffer, and others. Check the FreeHEP
        home page for more info. Permission to use and/or redistribute
        this work is granted under the terms of the LGPL License, with
        the exception that any usage related to military applications is
        expressly forbidden. The software and documentation made
        available under the terms of this license are provided with no
        warranty.
Packages: cern.colt.*, cern.jet.*, cern.clhep.*
Jars:
	./colt/colt-1.2.0.jar


HTSJDK
------
Java API for high-throughput sequencing data (HTS) formats.
https://github.com/samtools/htsjdk
License: MIT
Packages: htsjdk.*
Jars:
	./htsjdk/htsjdk-3.0.5-SNAPSHOT.jar


JAHMM
-----
Java Hidden Markov Model implementation
http://www.run.montefiore.ulg.ac.be/~francois/software/jahmm/
Packages: be.ac.ulg.montefiore.*
Jars:
	./jahmm/jahmm-0.6.1-with-mvg.jar


JAMA
----
Basic linear algebra package
http://math.nist.gov/javanumerics/jama/
License: Public Domain
Packages: Jama.*
Jars:
	./jama/Jama-1.0.3.jar


JavaML
------
Java machine-learning library
http://java-ml.sourceforge.net/
License: GPL v2
Packages: net.sf.javaml.*
Jars:
	./javaml/javaml-0.1.7.jar


JFreeChart
----------
Java chart library
http://www.jfree.org/
License: LGPL
Packages: org.jfree.*
Jars:
	./jfreechart/jfreechart-1.0.13/jfreechart-1.0.13.jar
	./jfreechart/jfreechart-1.0.13/jcommon-1.0.10.jar


JHeatChart
----------
Java HeatMap library
http://www.javaheatmap.com/
License: LGPL
Packages: org.tc33.jheatchart
Jars:
	./jheatchart/jheatchart-0.6.jar


JMathPlot
---------
Provides interactive 2D/3D plots
https://github.com/yannrichet/jmathplot
License: BSD
Packages: org.math.io.*, org.math.plot.*
Jars:
	./jmathplot/jmathplot-1.0.0.jar


JUnit
-----
Unit testing package
http://junit.org/junit4
License: Eclipse Public License v1.0
Packages: org.junit, org.hamcrest
Jars:
	./junit/junit-4.13.2.jar
	./junit/hamcrest-core-1.3.jar


LIBSVM
------
Java port of libsvm (https://www.csie.ntu.edu.tw/~cjlin/libsvm)
https://github.com/cjlin1/
License:
	Copyright (c) 2000-2014 Chih-Chung Chang and Chih-Jen Lin
	All rights reserved.
	Redistribution and use in source and binary forms, with or without
	modification, are permitted provided that the following conditions
	are met:
	1. Redistributions of source code must retain the above copyright
	notice, this list of conditions and the following disclaimer.
	2. Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in the
	documentation and/or other materials provided with the distribution.
	3. Neither name of copyright holders nor the names of its contributors
	may be used to endorse or promote products derived from this software
	without specific prior written permission.
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
	``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
	A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR
	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Packages: libsvm, liblinear
Jars:
	./libsvm/libsvm.jar
	./libsvm/liblinear-1.7.jar



MYSQL
-----
Connection management & official JDBC driver for mySQL.
http://dev.mysql.com/downloads/connector/j
License: GPL, but Oracle FOSS exception allows MIT license (described here: http://www.mysql.com/about/legal/licensing/foss-exception)
Packages: com.mysql.jdbc
Jars:
	./mysql-connector/mysql-connector-j-8.1.0.jar


OJDBC
------
Oracle Database 10g Release 2 JDBC Drivers
http://www.oracle.com/technetwork/apps-tech/jdbc-10201-088211.html
License: Oracle Technology Network Development and Distribution License
Packages: oracle.jdbc.*, oracle.sql.*
Jars:
	./ojdbc/ojdbc14.jar


SSJ
---
Stochastic Simulation in Java. Developed at Pierre L'Ecuyer's Simulation and Optimization Laboratory, Universite de Montreal.
https://github.com/umontreal-simul/ssj
License: Apache v2.0
Included dependencies:
	concurrent (http://gee.cs.oswego.edu/dl/classes/EDU/oswego/cs/dl/util/concurrent/intro.html) - Public Domain
	nonlinear optimization (http://www1.fpl.fs.fed.us/optimization.html) - Public Domain
Packages: umontreal.ssj.*
Jars:
	./ssj/ssj-3.3.1.jar


T-SNE-Java
----------
Pure Java implementation of Van Der Maaten and Hinton's t-sne clustering algorithm.
https://github.com/lejon/T-SNE-Java
License:
	This Java port of t-SNE is is Copyright (c) Leif Jonsson 2014. The original Python implementation is Copyright (c)
	Laurens van der Maaten on 20-12-08, Tilburg University. All rights reserved.
	Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
	following conditions are met:
		- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
		- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer
		  in the documentation and/or other materials provided with the distribution.
		- Neither the name of Tilburg University nor the names of its contributors may be used to endorse or promote products derived
		  from this software without specific prior written permission.
	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Leif
	Jonsson or Laurens van der Maaten BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
	HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
	ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Packages: com.jujutsu.tsne.*
Jars:
	./t-sne-java/tsne-2.6.4.jar
	./t-sne-java/tsne-demos-2.5.3.jar


Tomcat
------
Apache Tomcat: open source implementation of the Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket technologies.
http://tomcat.apache.org/
License: Apache v2.0
Packages: org.apache.tomcat.*
Jars:
	./tomcat/


Weka
----
Collection of machine learning algorithms for data mining tasks.
http://www.cs.waikato.ac.nz/ml/weka/
License: GPL
Packages: weka.*
Jars:
	./weka/weka-3-7-12.jar