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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// SubstituteAlignConfig_
// ----------------------------------------------------------------------------
template <typename TAlignConfig>
struct SubstituteAlignConfig_;
// 0000
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, false, false, false, TSpec> >
{
typedef FreeEndGaps_<False, False, False, False> Type;
};
// 0001
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, false, false, true, TSpec> >
{
typedef FreeEndGaps_<False, False, True, False> Type;
};
// 0010
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, false, true, false, TSpec> >
{
typedef FreeEndGaps_<False, False, False, True> Type;
};
// 0011
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, false, true, true, TSpec> >
{
typedef FreeEndGaps_<False, False, True, True> Type;
};
// 0100
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, true, false, false, TSpec> >
{
typedef FreeEndGaps_<False, True, False, False> Type;
};
// 0101
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, true, false, true, TSpec> >
{
typedef FreeEndGaps_<False, True, True, False> Type;
};
// 0110
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, true, true, false, TSpec> >
{
typedef FreeEndGaps_<False, True, False, True> Type;
};
// 0111
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<false, true, true, true, TSpec> >
{
typedef FreeEndGaps_<False, True, True, True> Type;
};
// 1000
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, false, false, false, TSpec> >
{
typedef FreeEndGaps_<True, False, False, False> Type;
};
// 1001
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, false, false, true, TSpec> >
{
typedef FreeEndGaps_<True, False, True, False> Type;
};
// 1010
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, false, true, false, TSpec> >
{
typedef FreeEndGaps_<True, False, False, True> Type;
};
// 1011
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, false, true, true, TSpec> >
{
typedef FreeEndGaps_<True, False, True, True> Type;
};
// 1100
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, true, false, false, TSpec> >
{
typedef FreeEndGaps_<True, True, False, False> Type;
};
// 1101
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, true, false, true, TSpec> >
{
typedef FreeEndGaps_<True, True, True, False> Type;
};
// 1110
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, true, true, false, TSpec> >
{
typedef FreeEndGaps_<True, True, False, True> Type;
};
// 1111
template <typename TSpec>
struct SubstituteAlignConfig_<AlignConfig<true, true, true, true, TSpec> >
{
typedef FreeEndGaps_<True, True, True, True> Type;
};
// ----------------------------------------------------------------------------
// Metafunction SubstituteAlgoTag_
// ----------------------------------------------------------------------------
// NOTE(rmaerker): Needed to substitute the global alingment algo tags to the correct gap model.
template <typename TTag>
struct SubstituteAlgoTag_
{
typedef TTag Type;
};
template <>
struct SubstituteAlgoTag_<NeedlemanWunsch>
{
typedef LinearGaps Type;
};
template <>
struct SubstituteAlgoTag_<Gotoh>
{
typedef AffineGaps Type;
};
// ----------------------------------------------------------------------------
// SetUpAlignmentProfile
// ----------------------------------------------------------------------------
template <typename TDPType, typename TAlignConfig, typename TTraceSwitch, typename TGapCosts>
struct SetupAlignmentProfile_;
// Profile for Needleman-Wunsch algorithm.
template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
struct SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapCosts, TTraceSwitch>
{
typedef DPProfile_<GlobalAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch> Type;
};
// Profile for Smith-Waterman algorithm.
template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
struct SetupAlignmentProfile_<DPLocal, TFreeEndGaps, TGapCosts, TTraceSwitch>
{
typedef DPProfile_<LocalAlignment_<>, TGapCosts, TTraceSwitch> Type;
};
// Profile for Waterman-Eggert algorithm
template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch>
struct SetupAlignmentProfile_<DPLocalEnumerate, TFreeEndGaps, TGapCosts, TTraceSwitch>
{
typedef DPProfile_<LocalAlignment_<SuboptimalAlignment>, TGapCosts, TracebackOn<TracebackConfig_<SingleTrace, GapsLeft> > > Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _usesAffineGaps()
// ----------------------------------------------------------------------------
template <typename TScoringScheme, typename TSeqH, typename TSeqV>
inline bool
_usesAffineGaps(TScoringScheme const & scoringScheme,
TSeqH const & seqH,
TSeqV const & seqV)
{
typedef typename SequenceEntryForScore<TScoringScheme, TSeqH>::Type TSequenceHEntry;
typedef typename SequenceEntryForScore<TScoringScheme, TSeqV>::Type TSequenceVEntry;
TSequenceHEntry seqHEntry = sequenceEntryForScore(scoringScheme, seqH, 0);
TSequenceVEntry seqVEntry = sequenceEntryForScore(scoringScheme, seqV, 0);
return (scoreGapExtendHorizontal(scoringScheme, seqHEntry, seqVEntry) !=
scoreGapOpenHorizontal(scoringScheme, seqHEntry, seqVEntry)) ||
(scoreGapExtendVertical(scoringScheme, seqHEntry, seqVEntry) !=
scoreGapOpenVertical(scoringScheme, seqHEntry, seqVEntry));
}
// ----------------------------------------------------------------------------
// Function _setUpAndRunAlignment()
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapModel,
typename TDPScoutStateSpec,
typename TTrace,
typename TSequenceH,
typename TSequenceV,
typename TScoreValue2, typename TScoreSpec,
typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig>
typename Value<Score<TScoreValue2, TScoreSpec> >::Type
_setUpAndRunAlignment(DPContext<TScoreValue, TGapModel> & dpContext,
TTrace & traceSegments,
DPScoutState_<TDPScoutStateSpec> & dpScoutState,
TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue2, TScoreSpec> const & scoringScheme,
AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
{
SEQAN_ASSERT_GEQ(length(seqH), 1u);
SEQAN_ASSERT_GEQ(length(seqV), 1u);
typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, TGapModel, TTraceConfig>::Type TDPProfile;
return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band,
TDPProfile());
}
template <typename TTrace,
typename TDPScoutStateSpec,
typename TSequenceH,
typename TSequenceV,
typename TScoreValue2, typename TScoreSpec,
typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig,
typename TGapModel>
typename Value<Score<TScoreValue2, TScoreSpec> >::Type
_setUpAndRunAlignment(TTrace & traceSegments,
DPScoutState_<TDPScoutStateSpec> & dpScoutState,
TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue2, TScoreSpec> const & scoringScheme,
AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig,
TGapModel const & /**/)
{
DPContext<TScoreValue2, TGapModel> dpContext;
return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig);
}
template <typename TTrace,
typename TDPScoutStateSpec,
typename TSequenceH,
typename TSequenceV,
typename TScoreValue2, typename TScoreSpec,
typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig>
typename Value<Score<TScoreValue2, TScoreSpec> >::Type
_setUpAndRunAlignment(TTrace & traceSegments,
DPScoutState_<TDPScoutStateSpec> & dpScoutState,
TSequenceH const & seqH,
TSequenceV const & seqV,
Score<TScoreValue2, TScoreSpec> const & scoringScheme,
AlignConfig2<TDPType, TBand, TFreeEndGaps, TTraceConfig> const & alignConfig)
{
if (_usesAffineGaps(scoringScheme, seqH, seqV))
return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, AffineGaps());
else
return _setUpAndRunAlignment(traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig, LinearGaps());
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_SETUP_H_
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