/usr/include/seqan/find/find_simple.h is in seqan-dev 1.3.1-1.
This file is owned by root:root, with mode 0o644.
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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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_FIND_SIMPLE_H
#define SEQAN_HEADER_FIND_SIMPLE_H
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
// Simple Finder
//////////////////////////////////////////////////////////////////////////////
/**
.Spec.Simple Finder:
..summary:A brute force online searching algorithm.
..general:Class.Pattern
..cat:Searching
..signature:Pattern<TNeedle, Simple>
..param.TNeedle:The needle type.
...type:Class.String
..remarks:This specialization should only be used if no other is applicable.
..include:seqan/find.h
*/
///.Class.Pattern.param.TSpec.type:Spec.Simple Finder
//////////////////////////////////////////////////////////////////////////////
template <typename TNeedle>
class Pattern<TNeedle, Simple> {
//____________________________________________________________________________
public:
Holder<TNeedle> data_host;
//____________________________________________________________________________
Pattern() {}
Pattern(Pattern const & other):
data_host(other.data_host)
{
}
template <typename TNeedle2>
Pattern(TNeedle2 const & ndl)
{
setHost(*this, ndl);
}
~Pattern(){}
Pattern const &
operator = (Pattern const & other)
{
data_host = other.data_host;
return *this;
}
//____________________________________________________________________________
};
//////////////////////////////////////////////////////////////////////////////
// Functions
//////////////////////////////////////////////////////////////////////////////
template <typename TNeedle, typename TNeedle2>
void setHost (Pattern<TNeedle, Simple> & me,
TNeedle2 & needle)
{
setValue(me.data_host, needle);
}
template <typename TNeedle, typename TNeedle2>
void setHost (Pattern<TNeedle, Simple> & me,
TNeedle2 const & needle)
{
setValue(me.data_host, needle);
}
//____________________________________________________________________________
template <typename TFinder, typename TNeedle>
inline bool find(TFinder & finder,
Pattern<TNeedle, Simple> & me)
{
SEQAN_CHECKPOINT
typedef typename Haystack<TFinder>::Type THaystack;
typedef typename Size<THaystack>::Type TSize;
typedef typename Iterator<THaystack, Standard>::Type THaystackIterator;
if (empty(finder))
{
_setFinderLength(finder, length(needle(me)));
_finderSetNonEmpty(finder);
}
else ++finder;
THaystack const & hstk = haystack(finder);
TNeedle const & ndl = needle(me);
THaystackIterator res = ::std::search(begin(hstk, Standard())+position(finder), end(hstk, Standard()), begin(ndl, Standard()), end(ndl, Standard()));
if (res == end(hstk)) return false;
_setFinderEnd(finder, (res - begin(hstk, Standard())) + length(ndl));
setPosition(finder, beginPosition(finder));
return true;
/*
TSize n = length(hstk);
TSize m = length(ndl);
while (position(finder)+m <= n)
{
if (ndl == infix(hstk, position(finder), position(finder)+m))
{
_setFinderEnd(finder, position(finder)+m);
return true;
}
++finder;
}
return false;
*/
}
//____________________________________________________________________________
}// namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
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