Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: BioJava
Source: http://www.biojava.org/download/source
Files-Excluded: core/src/test/resources/org/biojava/bio/program/indexdb/part?.swiss
                core/src/test/resources/AAC4_HUMAN.sp
Comment: Those files are under non-free SWISS-PROT license.

Files: *
Copyright: 1999-2008 the Individual authors who contributed the code,
    as identified by the @authors tag of the respective source file.
    BioJava Developers <biojava-l@biojava.org>
    Namely: Alan Li, Andreas Dräger <andreas.draeger@uni-tuebingen.de>, Andreas Prlic,
    Andy Hammer, Andy Yates, Andy Yates, Aroul Ramadass, Bradford Powell,
    Brian Gilman, Brian King, Bubba Puryear, Colin Hardman , David Allen,
    David H. Klatte, David Huen, David Scott, David Waring, Eric Haugen,
    Ewan Birney, Francois Pepin, Frans Verhoef, Frederik Decouttere, Gerald
    Loeffler <Gerald.Loeffler@vienna.at>, Greg Cox, G. Waldon, Hanning
    Ni ,, Horvath Tamas, Jason Stajich, Jim Balhoff, John Day Richter,
    Jolyon Holdstock, Jonathan Warren, Jules Jacobsen, Kalle Naslund,
    Keith James <kdj@sanger.ac.uk>, Lachlan Coin, Laurent Jourdren, Leen
    Ammeraal, Lei Lai, Len Trigg, Lorna Morris, Lukas Kall, Mark Schreiber
    <mark.schreiber@agresearch.co.nz>, Mark Southern, Markus Brosch, Martin
    Senger <senger@ebi.ac.uk>, Martin Szugat <Martin.Szugat@GMX.net>, Mathew
    Pocock, Mathieu Wiepert , Matthew Pocock, Mayo Foundation, Michael Heuer,
    Michael Jones, Michael L Heuer, Mike Jones, Moses Hohman, Nimesh Singh,
    Paul Seed, Peter Lackner, raemig, Rahul Karnik, Rhett Sutphin, Richard
    Holland, Ronald Tschalar, Ron Kuhn, Russell Smithies, Samiul Hasan,
    Shuvankar Mukherjee, Simon Brocklehurst, Simon Foote, Stuart Johnston ,
    Susanne Merz, Tamas Horvath, Tanya Vavouri, Thad Welch, Thomas Down,
    Tim Dilks , Tobias Thierer, Todd Riley
License: LGPL-2.1+

Files: blast/src/main/java/org/biojava/bio/program/PdbToXMLConverter.java
Copyright: 2000-2002 Cambridge Antibody Technology.
License: LGPL-2.1+

Files: blast/src/main/java/org/biojava/bio/program/sax/*
       blast/src/main/java/org/biojava/bio/program/sax/BaseXMLWriterTestHelper.java
       blast/src/main/java/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/FastaSequenceSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/GenericSAXParserTest.java
       blast/src/main/java/org/biojava/bio/program/sax/PdbSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/SequenceAlignmentSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/SimpleXMLEmitterTestHelper.java
Copyright: 2000-2002 Cambridge Antibody Technology.
License: LGPL-2.1+

Files: blast/src/main/java/org/biojava/bio/program/sax/AbstractNativeAppSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/BlastLikeSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/FastaSearchParser.java
       blast/src/main/java/org/biojava/bio/program/sax/FastaSearchSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/NeedleAlignmentSAXParser.java
       blast/src/main/java/org/biojava/bio/program/sax/blastxml/*
Copyright: 1999-2008 the Individual authors who contributed the code,
    as identified by the @authors tag of the respective source file.
License: LGPL-2.1+

Files: blast/src/main/java/org/biojava/bio/program/sax/GCGBlastSummaryLineHelper.java
Copyright: 2001 Mayo Foundation
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/program/blast2html/*
       core/src/main/java/org/biojava/bio/program/blast2html/AlignmentMarker.java
       core/src/main/java/org/biojava/bio/program/blast2html/BlastMatrixAlignmentStyler.java
       core/src/main/java/org/biojava/bio/program/blast2html/SimpleAlignmentStyler.java
Copyright: 2000-2001 Cambridge Antibody Technology Group plc.
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/program/phred/*
       core/src/main/java/org/biojava/bio/seq/Frame.java
       core/src/main/java/org/biojava/bio/seq/FramedFeature.java
       core/src/main/java/org/biojava/bio/seq/impl/SimpleFramedFeature.java
Copyright: 2001 Mark Schreiber
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/program/phred/PhredTools.java
Copyright: 2001 Mark Schreiber
           2001 Matthew Pocock
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/program/xml/*
Copyright: 2000-2002 Cambridge Antibody Technology.
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/symbol/MergeLocation.java
Copyright: 2002 Mark Schreiber
           2002 François Pepin
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/bio/symbol/SoftMaskedAlphabet.java
Copyright: 2004 Novartis Institute for Tropical Diseases
License: LGPL-2.1+

Files: core/src/main/java/org/biojava/utils/ExecRunner.java
Copyright: 2002 Scott McCrory
License: LGPL-2+

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

Files: core/src/test/java/org/biojava/bio/proteomics/aaindex/AAindexStreamReaderTest.java
Copyright: 2005 BioWeka.org
License: GPL-2+

Files: core/src/test/java/org/biojava/bio/symbol/AlphabetSerializationTest.java
       core/src/test/java/org/biojava/bio/symbol/MergeLocationTest.java
       gui/src/main/java/org/biojava/bio/gui/FeatureTree.java
Copyright: 2002 Mark Schreiber
License: LGPL-2.1+

Files: sequencing/src/main/java/org/biojava/bio/program/abi/ABITrace.java
Copyright: 2001 David H. Klatte, Ph.D.
License: LGPL-2.1+

Files: debian/*
Copyright: 2007-2010 Steffen Moeller <moeller@debian.org>
           2011-2017 Andreas Tille <tille@debian.org>
           2022      Pierre Gruet <pgt@debian.org>
License: LGPL-2.1+

License: LGPL-2.1+
    BioJava is an open source project. The project is distributed under the GNU
    Lesser General Public Licence. We do not consider Java class loading to
    constitute the production of a derivative work. We do not consider
    sub-classing of Java classes or implementations of Java interfaces to constitute
    the production of a derivative work.
 .
    All .java source files should include the following comment which implies the
    author's agreement to the tearms of the license.
 .
    /*
     *                    BioJava development code
     *
     * This code may be freely distributed and modified under the
     * terms of the GNU Lesser General Public Licence.  This should
     * be distributed with the code.  If you do not have a copy,
     * see:
     *
     *      http://www.gnu.org/copyleft/lesser.html
     *
     * Copyright for this code is held jointly by the individual
     * authors.  These should be listed in @author doc comments.
     *
     * For more information on the BioJava project and its aims,
     * or to join the biojava-l mailing list, visit the home page
     * at:
     *
     *      http://www.biojava.org/
     *
     */
 .
    This package is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    Lesser General Public License for more details.
 .
    You should have received a copy of the GNU Lesser General Public
    License along with this package; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
 .
 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+
 On Debian systems the full text of the LGPL-2 can be found in
 /usr/share/common-licenses/LGPL-2

License: GPL-2+
 On Debian systems the full text of the GPL-2 can be found in
 /usr/share/common-licenses/GPL-2
