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 Namely: Alan Li, Andreas Dräger , 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 , 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 , Lachlan Coin, Laurent Jourdren, Leen Ammeraal, Lei Lai, Len Trigg, Lorna Morris, Lukas Kall, Mark Schreiber , Mark Southern, Markus Brosch, Martin Senger , Martin Szugat , 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 2011-2017 Andreas Tille 2022 Pierre Gruet 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