/usr/include/seqan/index/find_index.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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_INDEX_FIND_H
#define SEQAN_HEADER_INDEX_FIND_H
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
template < typename TText, typename TSpec, typename TSpecFinder >
struct Position< Finder< Index<TText, TSpec>, TSpecFinder > >:
SAValue< Index<TText, TSpec> > {};
//////////////////////////////////////////////////////////////////////////////
// generic Finder class for all indices containing a suffix array or
// similar table, where a query result is an interval in this table
//
// your index must specialize the function _findFirstIndex and set
// finder.range to the interval containing the query hits. See:
//
// template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
// inline void _findFirstIndex(
// Finder< Index<TText, TSpec>, TSpecFinder > &finder,
// TPattern const &pattern,
// EsaFindMlr const)
// {
// Index<TText, TSpec> &index = haystack(finder);
// indexRequire(index, EsaSA());
// finder.range = equalRangeSAIterator(indexText(index), indexSA(index), pattern);
// }
template < typename TText, typename TSpec, typename TSpecFinder >
class Finder< Index<TText, TSpec>, TSpecFinder >
{
protected:
typedef Index<TText, TSpec> TIndex;
typedef typename Fibre<TIndex, FibreSA>::Type TSA;
typedef typename Iterator<TSA const, Standard>::Type TIterator;
typedef typename Size<TIndex>::Type TSize;
public:
Holder<TIndex> index;
Pair<TIterator> range;
TIterator data_iterator;
TSize data_length;
Finder()
{
clear(*this);
}
Finder(TIndex &_index): index(_index)
{
clear(*this);
}
Finder(TIndex const &_index): index(_index)
{
clear(*this);
}
};
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Parameter_< Index<TText, TSpec> >::Type
host(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return value(me.index);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Parameter_< Index<TText, TSpec> >::Type
host(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
return value(me.index);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Parameter_< Index<TText, TSpec> >::Type
container(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return value(me.index);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Parameter_< Index<TText, TSpec> >::Type
container(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
return value(me.index);
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline void
setHost(
Finder< Index<TText, TSpec>, TSpecFinder > & me,
typename Parameter_<Index<TText, TSpec> >::Type /*container_*/)
{
SEQAN_CHECKPOINT
me.index = container;
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline void
setContainer(
Finder< Index<TText, TSpec>, TSpecFinder > & me,
typename Parameter_<Index<TText, TSpec> >::Type /*container_*/)
{
SEQAN_CHECKPOINT
me.index = container;
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type &
hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return me.data_iterator;
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Iterator< typename Fibre<Index<TText, TSpec>, FibreSA>::Type const, Standard>::Type const &
hostIterator(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
return me.data_iterator;
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline bool
empty(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return me.range.i1 == me.range.i2;
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline void
clear(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
typedef Index<TText, TSpec> TIndex;
typedef typename Fibre<TIndex, FibreSA>::Type TSA;
typedef typename Iterator<TSA const, Standard>::Type TIterator;
me.range.i1 = me.range.i2 = TIterator();
me.data_length = 0;
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline bool
atBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return (empty(me) || hostIterator(me) == me.range.i1);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline bool
atEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return (empty(me) || hostIterator(me) == me.range.i2);
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline void
goBegin(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
hostIterator(me) = me.range.i1;
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline void
goEnd(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
hostIterator(me) = me.range.i2;
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
SEQAN_ASSERT(!empty(me))
return *me.data_iterator;
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
beginPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
SEQAN_ASSERT(!empty(me))
return *me.data_iterator;
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
endPosition(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return posAdd(beginPosition(me), me.data_length);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
endPosition(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
return posAdd(beginPosition(me), me.data_length);
}
//____________________________________________________________________________
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
position(Finder< Index<TText, TSpec>, TSpecFinder > & me)
{
SEQAN_CHECKPOINT
return beginPosition(me);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline typename Position< Finder< Index<TText, TSpec>, TSpecFinder > >::Type
position(Finder< Index<TText, TSpec>, TSpecFinder > const & me)
{
SEQAN_CHECKPOINT
return beginPosition(me);
}
//////////////////////////////////////////////////////////////////////////////
// find
template < typename TText, typename TSpec, typename TSpecFinder, typename TPattern >
inline bool find(
Finder<Index<TText, TSpec>, TSpecFinder> &finder,
TPattern const &pattern)
{
if (empty(finder))
{
_findFirstIndex(finder, needle(pattern), TSpecFinder());
_setFinderLength(finder, length(needle(pattern)));
hostIterator(finder) = finder.range.i1;
} else
++hostIterator(finder);
return !atEnd(finder);
}
template < typename TText, typename TSpec, typename TSpecFinder >
inline bool find(Finder<Index<TText, TSpec>, TSpecFinder> &finder)
{
if (empty(finder)) return false;
++hostIterator(finder);
return !atEnd(finder);
}
}
#endif
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