/usr/include/seqan/index/index_shawarma.h is in seqan-dev 1.3.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// 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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_INDEX_SHAWARMA_H
#define SEQAN_HEADER_INDEX_SHAWARMA_H
namespace SEQAN_NAMESPACE_MAIN {
namespace shawarma {
extern void ds_ssort(unsigned char *t, int *sa, int n);
extern int init_ds_ssort(int adist, int bs_ratio);
}
//////////////////////////////////////////////////////////////////////////////
// SeqAn interface
template <typename TSpec>
struct Shawarma {};
struct MSufSort{}; // MSufSort
struct DivSufSort{}; // DivSufSort
struct DeepShallow{}; // Deep-Shallow sort
struct QSufSort{}; // QSufSort
// WARNING:
// 1. text value must have char size
// 2. SA value must have int size
// 3. Deep-Shallow sort expects overshoot bytes behind the text
// 4. SA must be contiguous
//
template < typename TSA,
typename TText >
void createSuffixArray(
TSA &SA,
TText &s,
Shawarma<DeepShallow> const)
{
typedef typename Value<TText>::Type TValue;
typedef typename Value<TSA>::Type TSAValue;
SEQAN_ASSERT(sizeof(TValue) == sizeof(unsigned char));
SEQAN_ASSERT(sizeof(TSAValue) == sizeof(int));
SEQAN_ASSERT(IsContiguous<TSA>::VALUE);
int overshoot = shawarma::init_ds_ssort(500, 2000);
SEQAN_ASSERT(overshoot > 0);
reserve(s, length(s) + overshoot);
shawarma::ds_ssort(
(unsigned char*)toCString(s), // text
(int*)begin(SA, Standard()), // SA
length(s)); // n
}
} // namespace SEQAN_NAMESPACE_MAIN
#endif // SEQAN_HEADER_INDEX_PIZZACHILI_H
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