Add copyright notice. Every. File.

jxtx · Aug 20, 2015 · 6950cb7 · 6950cb7
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diff --git a/kmer/libkmer/driver-existDB.C b/kmer/libkmer/driver-existDB.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-FEB-20 to 2003-OCT-20
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-30 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-DEC-04 to 2014-APR-11
+ *      are Copyright 2005,2007-2008,2011,2013-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/kmer/libkmer/driver-posDB.C b/kmer/libkmer/driver-posDB.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-AUG-14 to 2003-SEP-18
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-30 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAY-19 to 2014-APR-11
+ *      are Copyright 2005,2007-2008,2011,2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -123,7 +156,7 @@ test2(char *filename, char *query) {
 //  Builds a positionDB possibly using a subset of the file.
 //
 //  Subset on entire sequences:
-//    -use x-y,a,b  
+//    -use x-y,a,b
 //
 //  Subset on a range of mers, in this case, use only the 1000th
 //  through 1999th (inclusive) mer:

diff --git a/kmer/libkmer/existDB-create-from-fasta.C b/kmer/libkmer/existDB-create-from-fasta.C
@@ -1,3 +1,40 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-SEP-08 to 2003-OCT-20
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-21 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAR-20 to 2014-APR-11
+ *      are Copyright 2005,2007-2008,2012-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz beginning on 2014-AUG-31
+ *      are Copyright 2014 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/kmer/libkmer/existDB-create-from-meryl.C b/kmer/libkmer/existDB-create-from-meryl.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-SEP-08 to 2003-OCT-20
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz on 2004-APR-12
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAR-20 to 2014-APR-11
+ *      are Copyright 2005,2007,2010-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/kmer/libkmer/existDB-create-from-sequence.C b/kmer/libkmer/existDB-create-from-sequence.C
@@ -1,3 +1,32 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2012-MAY-08 to 2014-APR-11
+ *      are Copyright 2012-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz beginning on 2014-AUG-31
+ *      are Copyright 2014 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/kmer/libkmer/existDB-state.C b/kmer/libkmer/existDB-state.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz on 2003-SEP-08
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-12 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAR-20 to 2014-APR-11
+ *      are Copyright 2005,2007,2013-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -6,7 +39,7 @@
 #include "bio++.H"
 
 
-const char  magic[16] = { 'e', 'x', 'i', 's', 't', 'D', 'B', '2', 
+const char  magic[16] = { 'e', 'x', 'i', 's', 't', 'D', 'B', '2',
                           ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '  };
 
 

diff --git a/kmer/libkmer/existDB.C b/kmer/libkmer/existDB.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-JAN-02 to 2003-OCT-20
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-12 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAR-20 to 2014-APR-11
+ *      are Copyright 2005-2008,2012-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/kmer/libkmer/existDB.H b/kmer/libkmer/existDB.H
@@ -1,3 +1,40 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-JAN-02 to 2003-OCT-20
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-21 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-MAR-20 to 2014-APR-11
+ *      are Copyright 2005,2007,2012-2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Liliana Florea on 2010-DEC-06
+ *      are Copyright 2010 Liliana Florea, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #ifndef EXISTDB_H
 #define EXISTDB_H
 

diff --git a/kmer/libkmer/percentCovered.C b/kmer/libkmer/percentCovered.C
@@ -1,3 +1,32 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2006-MAY-09 to 2014-APR-11
+ *      are Copyright 2006-2008,2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz beginning on 2014-OCT-07
+ *      are Copyright 2014 Battelle National Biodefense Institute, and
+ *      are subject to the BSD 3-Clause License
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include "util++.H"
 #include "bio++.H"
 #include "existDB.H"

diff --git a/kmer/libkmer/positionDB-access.C b/kmer/libkmer/positionDB-access.C
@@ -1,3 +1,36 @@
+
+/******************************************************************************
+ *
+ *  This file is part of canu, a software program that assembles whole-genome
+ *  sequencing reads into contigs.
+ *
+ *  This software is based on:
+ *    'Celera Assembler' (http://wgs-assembler.sourceforge.net)
+ *    the 'kmer package' (http://kmer.sourceforge.net)
+ *  both originally distributed by Applera Corporation under the GNU General
+ *  Public License, version 2.
+ *
+ *  Canu branched from Celera Assembler at its revision 4587.
+ *  Canu branched from the kmer project at its revision 1994.
+ *
+ *  Modifications by:
+ *
+ *    Brian P. Walenz from 2003-JAN-02 to 2003-AUG-14
+ *      are Copyright 2003 Applera Corporation, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2004-APR-21 to 2004-OCT-10
+ *      are Copyright 2004 Brian P. Walenz, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *    Brian P. Walenz from 2005-FEB-07 to 2014-APR-11
+ *      are Copyright 2005-2008,2014 J. Craig Venter Institute, and
+ *      are subject to the GNU General Public License version 2
+ *
+ *  File 'README.licenses' in the root directory of this distribution contains
+ *  full conditions and disclaimers for each license.
+ */
+
 #include "bio++.H"
 #include "positionDB.H"
 
@@ -7,7 +40,7 @@ positionDB::reallocateSpace(uint64*&    posn,
                             uint64&     posnMax,
                             uint64&     posnLen,
                             uint64      len) {
- 
+
   if (posnMax < posnLen + len) {
     uint64  *pp;