// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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>
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// TODO(holtgrew): Switch to Host interface.
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// Internally used tag for creating iterators at the begin of containers.
struct Begin__;
typedef Tag<Begin__> Begin_;
// Internally used tag for creating iterators at the end of containers.
struct End__;
typedef Tag<End__> End_;
// Internally used tag for creating iterators inside of containers.
struct Position__;
typedef Tag<Position__> Position_;
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
/*!
* @class GapsIterator
* @implements RandomAccessIteratorConcept
*
* @brief Iterator class for @link Gaps @endlink.
*
* @signature template <typename TGaps, typename TSpec>
* class Iter<TGaps, GapsIterator<TSpec> >;
*
* @tparam TGaps The @link Gaps @endlink object for the iterator.
* @tparam TSpec The specializing tag.
*/
template <typename TSpec>
struct GapsIterator;
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction Position
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
struct Position<Iter<TGaps, GapsIterator<TSpec> > > :
Position<TGaps>
{};
template <typename TGaps, typename TSpec>
struct Position<Iter<TGaps, GapsIterator<TSpec> > const> :
Position<Iter<TGaps, GapsIterator<TSpec> > >
{};
// ----------------------------------------------------------------------------
// Metafunction Difference
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
struct Difference<Iter<TGaps, GapsIterator<TSpec> > > :
Difference<TGaps>
{};
template <typename TGaps, typename TSpec>
struct Difference<Iter<TGaps, GapsIterator<TSpec> > const> :
Difference<Iter<TGaps, GapsIterator<TSpec> > >
{};
// ----------------------------------------------------------------------------
// Metafunction Source
// ----------------------------------------------------------------------------
// TODO(holtgrew): Should this be Host? or SourceIterator?
template <typename TGaps, typename TSpec>
struct Source<Iter<TGaps, GapsIterator<TSpec> > >
{
typedef typename Source<TGaps>::Type TSource_;
typedef typename Iterator<TSource_, Rooted>::Type Type;
};
template <typename TGaps, typename TSpec>
struct Source<Iter<TGaps, GapsIterator<TSpec> > const>
{
typedef typename Source<TGaps>::Type TSource_;
typedef typename Iterator<TSource_, Rooted>::Type Type;
};
// ----------------------------------------------------------------------------
// Metafunction Value
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
struct Value<Iter<TGaps, GapsIterator<TSpec> > >
{
typedef typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type TSource_;
typedef typename Value<TSource_>::Type TSourceValue_;
//typedef TSourceValue_ Type;
// TODO(holtgrew): We really want gapped values here but there are issues...
typedef typename GappedValueType<TSourceValue_>::Type Type;
};
template <typename TGaps, typename TSpec>
struct Value<Iter<TGaps, GapsIterator<TSpec> > const> :
Value<Iter<TGaps, GapsIterator<TSpec> > > {};
// ----------------------------------------------------------------------------
// Metafunction GetValue
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
struct GetValue<Iter<TGaps, GapsIterator<TSpec> > > :
Value<Iter<TGaps, GapsIterator<TSpec> > >
{
};
template <typename TGaps, typename TSpec>
struct GetValue<Iter<TGaps, GapsIterator<TSpec> > const> :
Value<Iter<TGaps, GapsIterator<TSpec> > const>
{
};
// ----------------------------------------------------------------------------
// Metafunction Reference
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
struct Reference<Iter<TGaps, GapsIterator<TSpec> > >
{
typedef Iter<TGaps, GapsIterator<TSpec> > TIterator_;
typedef Proxy<IteratorProxy<TIterator_> > Type;
};
template <typename TGaps, typename TSpec>
struct Reference<Iter<TGaps, GapsIterator<TSpec> > const>
{
typedef Iter<TGaps, GapsIterator<TSpec> const > TIterator_;
typedef Proxy<IteratorProxy<TIterator_> > Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function operator++
// ----------------------------------------------------------------------------
// TODO(holtgrew): Could be general forward
template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator++(Iter<TGaps, GapsIterator<TSpec> > & it)
{
goNext(it);
return it;
}
template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> >
operator++(Iter<TGaps, GapsIterator<TSpec> > & it, int)
{
Iter<TGaps, GapsIterator<TSpec> > ret = it;
goNext(it);
return ret;
}
// ----------------------------------------------------------------------------
// Function operator--
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator--(Iter<TGaps, GapsIterator<TSpec> > & it)
{
goPrevious(it);
return it;
}
template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> >
operator--(Iter<TGaps, GapsIterator<TSpec> > & it, int)
{
Iter<TGaps, GapsIterator<TSpec> > ret = it;
goPrevious(it);
return ret;
}
// ----------------------------------------------------------------------------
// Function insertGap()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#insertGap
* @brief Insert gap at the current position.
*
* @signature void insertGap(it);
*
* @param[in,out] it The iterator to insert gaps at.
*/
// Forward to insertGaps() which has to be implemented by the specific gap
// iterator.
template <typename TGaps, typename TSpec>
inline void
insertGap(Iter<TGaps, GapsIterator<TSpec> > & it)
{
insertGaps(it, 1);
}
// ----------------------------------------------------------------------------
// Function isCharacter()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#isCharacter
* @brief Query an iterator for being at a character
*
* @signature bool isCharacter(it);
*
* @param[in] it Iterator to query for pointing at a character.
*
* @return bool <tt>true</tt> if <tt>it</tt> is at a character and <tt>false</tt> otherwise.
*/
template <typename TGaps, typename TSpec>
bool isCharacter(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
return !isGap(it);
}
// ----------------------------------------------------------------------------
// Function countCharacters()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#countCharacters
* @brief Count characters at iterator.
*
* @signature TSize countCharacters(it[, dir]);
*
* @param[in] it Iterator for counting characters at.
* @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink.
* Defaults to @link GapDirectionTags#RightOfViewPos @endlink.
*
* @return TSize Number of characters.
*
* If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be
* included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected.
*/
template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
countCharacters(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
return countCharacters(it, RightOfViewPos());
}
// ----------------------------------------------------------------------------
// Function isGap()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#isGap
* @brief Query an iterator for being at a gap
*
* @signature bool isGap(it);
*
* @param[in] it Iterator to query for pointing at a gap.
*
* @return bool <tt>true</tt> if <tt>it</tt> is at a gap and <tt>false</tt> otherwise.
*/
// ----------------------------------------------------------------------------
// Function countGaps()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#countGaps
* @brief Count gaps at iterator.
*
* @signature TSize countGaps(it[, dir]);
*
* @param[in] it Iterator for counting gaps at.
* @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink.
* Defaults to @link GapDirectionTags#RightOfViewPos @endlink.
*
* @return TSize Number of gaps.
*
* If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be
* included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected.
*/
template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
countGaps(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
return countGaps(it, RightOfViewPos());
}
// ----------------------------------------------------------------------------
// Function insertGaps()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#insertGaps
* @brief Insert gaps at the current position.
*
* @signature void insertGaps(it, num);
*
* @param[in,out] it Remove gap at the given position (if any).
* @param[in] num Number of gaps to insert.
*/
// ----------------------------------------------------------------------------
// Function removeGap()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#removeGap
* @brief Insert gap at the current position.
*
* @signature TSize removeGap(it);
*
* @param[in,out] it Remove gap at the given position (if any).
*
* @return TSize Number of removed gaps.
*/
// Forward to removeGaps() which has to be implemented by the specific gap
// iterator.
template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
removeGap(Iter<TGaps, GapsIterator<TSpec> > & it)
{
return removeGaps(it, 1);
}
// ----------------------------------------------------------------------------
// Function removeGaps()
// ----------------------------------------------------------------------------
/*!
* @fn GapsIterator#removeGaps
* @brief Remove gaps from the current position.
*
* @signature TSize removeGaps(it, num);
*
* @param[in,out] it Remove gap at the given position (if any).
* @param[in] num Number of gaps to remove.
*
* @return TSize Number of removed gaps.
*/
// ----------------------------------------------------------------------------
// Function assignValue()
// ----------------------------------------------------------------------------
// TODO(holtgrew): Const consistency problems.
template <typename TGaps, typename TSpec, typename TValue>
inline void
assignValue(Iter<TGaps, GapsIterator<TSpec> > & me,
TValue const & val)
{
if (!isGap(me))
{
assignValue(source(me), val);
}
// TODO(holtgrew): Else, inserting gaps is problematic...
}
template <typename TGaps, typename TSpec, typename TValue>
inline void
assignValue(Iter<TGaps, GapsIterator<TSpec> > const & me,
TValue const & val)
{
if (!isGap(me))
{
assignValue(source(me), val);
}
}
// ----------------------------------------------------------------------------
// Function container()
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
inline TGaps &
container(Iter<TGaps, GapsIterator<TSpec> > & me)
{
return *me._container;
}
template <typename TGaps, typename TSpec>
inline TGaps &
container(Iter<TGaps, GapsIterator<TSpec> > const & me)
{
return *me._container;
}
// ----------------------------------------------------------------------------
// Function source
// ----------------------------------------------------------------------------
// Returns host iterator.
// TODO(holtgrew): Non-const version is superfluous.
template <typename TGaps, typename TSpec>
inline typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type /*returns copy*/
source(Iter<TGaps, GapsIterator<TSpec> > & it)
{
return iter(container(it), toSourcePosition(container(it), position(it)));
}
template <typename TGaps, typename TSpec>
inline typename Source<Iter<TGaps, GapsIterator<TSpec> > const>::Type /*returns copy*/
source(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
return iter(container(source(it)), toSourcePosition(container(it), position(it)));
}
// TODO(holtgrew): setSource? setContainer?
// ----------------------------------------------------------------------------
// Function operator+=
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec, typename TDiff>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator+=(Iter<TGaps, GapsIterator<TSpec> > & it, TDiff diff)
{
goFurther(it, diff);
return it;
}
// ----------------------------------------------------------------------------
// Function operator-=
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec, typename TDiff>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator-=(Iter<TGaps, GapsIterator<TSpec> > & it, TDiff diff)
{
goFurther(it, -(int64_t)(diff));
return it;
}
// ----------------------------------------------------------------------------
// Function goFurther
// ----------------------------------------------------------------------------
// TODO(holtgrew): Implementation could be faster.
template <typename TGaps, typename TSpec, typename TDifference>
inline void
goFurther(Iter<TGaps, GapsIterator<TSpec> > & it,
TDifference steps)
{
typedef typename MakeSigned<TDifference>::Type TSignedDifference;
if (steps > TDifference(0))
for (; steps; --steps)
goNext(it);
else
for (; -static_cast<TSignedDifference>(steps); ++steps)
goPrevious(it);
}
// ----------------------------------------------------------------------------
// Function isClipped()
// ----------------------------------------------------------------------------
template <typename TGaps, typename TSpec>
inline bool
isClipped(Iter<TGaps, GapsIterator<TSpec> > const &)
{
return false;
}
} // namespace seqan
#endif // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
