/usr/include/oxli/traversal.hh is in liboxli-dev 2.0+dfsg-10.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2015, The Regents of the University of California.
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 the Michigan State 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 THE COPYRIGHT
HOLDER 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.
LICENSE (END)
Contact: khmer-project@idyll.org
*/
#ifndef TRAVERSAL_HH
#define TRAVERSAL_HH
#include <queue>
#include <functional>
#include "khmer.hh"
#include "khmer_exception.hh"
#include "read_parsers.hh"
#include "kmer_hash.hh"
#include "hashtable.hh"
namespace khmer
{
class Hashtable;
class Traverser: public KmerFactory
{
friend class Hashtable;
protected:
HashIntoType bitmask;
unsigned int rc_left_shift;
public:
const Hashtable * graph;
explicit Traverser(const Hashtable * ht);
Kmer get_left(Kmer& node, const char ch);
Kmer get_right(Kmer& node, const char ch);
unsigned int traverse_left(Kmer& node,
KmerQueue &node_q,
std::function<bool (Kmer&)> filter);
unsigned int traverse_right(Kmer& node,
KmerQueue &node_q,
std::function<bool (Kmer&)> filter);
unsigned int degree_left(Kmer& node);
unsigned int degree_right(Kmer& node);
unsigned int degree(Kmer& node);
};
}
#endif
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