Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: biojava6
Source: http://www.biojava.org/
Files-Excluded-forester: */*.class
Comment:
 Biojava uses the forester library, which is handled within a
 MUT package.
 .
 Same for jcolorbrewer

Files: *
Copyright: 2000-2021 the Individual authors who contributed the code,
    as identified by the @authors tag of the respective source file.
    BioJava Developers <biojava-l@biojava.org>
    Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
    Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
    Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
    Jules Jacobsen <jacobsen@ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
    A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
    Spencer Bliven <sbliven@ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
    Koh Chuan Hock, Expasy4J, Benjamin Schuster-B&ouml;ckle, Peter Troshin,
    Jose Manuel Duarte, D. Myers, Andrew Yates, Ulysse Carion, M. L Heuer,
    B. T. Boyle, emckee2006, paolopavan, J. Grzebyta, G. Waldon, D. Cameron,
    A. Drager, kevinwu1, Siarhei, R. Thornton, C. Foti, sroughley, ferlan,
    parit, M. Bizzari
License: LGPL-2.1

Files: biojava-core/src/main/java/org/biojava/nbio/core/util/UncompressInputStream.java
Copyright: 1996-2001 Ronald Tschalar
License: LGPL-2+

Files: biojava-protein-disorder/src/main/java/org/*
Copyright: 2009-2010 Peter Troshin
License: LGPL-2.1

Files: biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
Copyright: 2002 Sun Microsystems, Inc.
License: BSD-3-clause+

Files: forester/*
Copyright: 2000-2014 Christian M. Zmasek
           2007-2014 Burnham Institute for Medical Research
License: LGPL-2.1+

Files: forester/org/forester/application/rio.java
       forester/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java
       forester/org/forester/io/parsers/tol/TolXmlMapping.java
       forester/org/forester/phylogeny/Phylogeny.java
       forester/org/forester/phylogeny/PhylogenyBranch.java
       forester/org/forester/phylogeny/PhylogenyNode.java
       forester/org/forester/phylogeny/data/BranchData.java
       forester/org/forester/phylogeny/data/Date.java
       forester/org/forester/phylogeny/data/Distribution.java
       forester/org/forester/phylogeny/data/NodeData.java
       forester/org/forester/phylogeny/data/Property.java
       forester/org/forester/rio/*
       forester/org/forester/sdi/*
Copyright: 2008-2009 Christian M. Zmasek
           2008-2009 Burnham Institute for Medical Research
           2000-2001 Washington University School of Medicine
License: LGPL-2.1+

Files: forester/org/forester/archaeopteryx/ColorSchemeChooser.java
       forester/org/forester/archaeopteryx/Configuration.java
       forester/org/forester/archaeopteryx/Constants.java
       forester/org/forester/archaeopteryx/MainFrameApplet.java
       forester/org/forester/archaeopteryx/MainPanel.java
       forester/org/forester/archaeopteryx/MainPanelApplets.java
       forester/org/forester/archaeopteryx/MouseListener.java
       forester/org/forester/archaeopteryx/NodeFrame.java
       forester/org/forester/archaeopteryx/PdfExporter.java
       forester/org/forester/archaeopteryx/TextFrame.java
       forester/org/forester/archaeopteryx/TreeFontSet.java
       forester/org/forester/util/SequenceAccessionTools.java
Copyright: 2008-2009 Christian M. Zmasek
           2008-2009 Burnham Institute for Medical Research
           2003-2007 Ethalinda K.S. Cannon
           2000-2001 Washington University School of Medicine
License: LGPL-2.1+

Files: forester/org/forester/archaeopteryx/MainFrame.java
       forester/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java
       forester/org/forester/evoinference/distance/*
       forester/org/forester/io/parsers/nhx/NHXParser.java
       forester/org/forester/sdi/GSDIR.java
Copyright: 2008-2014 Christian M. Zmasek
License: LGPL-2.1+

Files: forester/org/forester/archaeopteryx/MainFrameApplication.java
       forester/org/forester/archaeopteryx/TreeColorSet.java
Copyright: 2008-2010 Christian M. Zmasek
           2008-2010 Burnham Institute for Medical Research
           2003-2010 Ethalinda K.S. Cannon
License: LGPL-2.1+

Files: forester/org/forester/evoinference/distance/PairwiseDistanceCalculator.java
       forester/org/forester/sdi/GSDI.java
       forester/org/forester/sdi/TestGSDI.java
Copyright: 2008-2012 Sanford-Burnham Medical Research Institute
           2008-2012 Christian M Zmasek
License: LGPL-2.1+

Files: forester/org/forester/util/SystemCommandExecutor.java
       forester/org/forester/util/ThreadedStreamHandler.java
Copyright: 2010 alvin j. alexander, devdaily.com.
License: LGPL-3+

Files: debian/*
Copyright: 2015 Olivier Sallou <osallou@debian.org>
           2022 Pierre Gruet <pgt@debian.org>
License: GPL-2+

License: LGPL-2+
 On Debian systems, the complete text of the GNU Lesser General
 Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2".

License: LGPL-2.1
 On Debian systems, the complete text of the GNU Lesser General
 Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".

License: LGPL-2.1+
 On Debian systems, the complete text of the GNU Lesser General
 Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".

License: GPL-2+
 On Debian systems, the complete text of the GNU General
 Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".

License: BSD-3-clause+
 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.
 .
 -Redistribution in binary form must reproduct 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 Sun Microsystems, Inc. or the names of contributors
  may be used to endorse or promote products derived from this software
  without specific prior written permission.
 .
 This software is provided "AS IS," without a warranty of any kind. ALL
 EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING
 ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE
 OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND ITS LICENSORS SHALL NOT
 BE LIABLE FOR ANY DAMAGES OR LIABILITIES SUFFERED BY LICENSEE AS A RESULT
 OF OR RELATING TO USE, MODIFICATION OR DISTRIBUTION OF THE SOFTWARE OR ITS
 DERIVATIVES. IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE FOR ANY LOST
 REVENUE, PROFIT OR DATA, OR FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL,
 INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY
 OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE SOFTWARE, EVEN
 IF SUN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
 .
 You acknowledge that Software is not designed, licensed or intended for
 use in the design, construction, operation or maintenance of any nuclear
 facility.
Comment: The last paragraph is to be interpreted as a warranty disclaimer,
 see https://lists.debian.org/debian-legal/2012/09/msg00034.html

License: LGPL-3+
 On Debian systems the full text of the LGPL-3 can be found in
 /usr/share/common-licenses/LGPL-3
