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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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>
// ==========================================================================
// Code for score matrices with data from files or built-in data.
// ==========================================================================
#ifndef SEQAN_SSCORE_MATRIX_H_
#define SEQAN_SSCORE_MATRIX_H_
// TODO(holtgrew): If the complex type conversions are necessary, a static_cast<> is more C++ and explicit.
namespace seqan2 {
template <typename TValue, typename TSequenceValue, typename TSpec>
struct ScoringMatrixData_;
template <typename TSequenceValue = AminoAcid, typename TSpec = Default>
struct ScoreMatrix;
/*!
* @class MatrixScore
* @headerfile <seqan/score.h>
* @extends Score
* @brief A general scoring matrix.
*
* @signature template <typename TValue, typename TSeqValue, typename TSpec>
* class Score<TValue, ScoreMatrix<[TSeqValue[, TSpec]]> >;
*
* @tparam TValue The score value.
* @tparam TSeqValue The alphabet type, defaults to AminoAcid.
* @tparam TSpec Further specialization, defaults to Default.
*
* The TSpec argument can be used to obtain a predefined matrix.
* Specify one of the following tags:
*
* ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80,
* ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.
*
* This will internally call @link MatrixScore#setDefaultScoreMatrix setDefaultScoreMatrix@endlink.
*
* In order to provide a more user-friendly access to the predefined scoring matrixes, typedefs exist:
* @link Blosum30 @endlink, @link Blosum45 @endlink, @link Blosum62 @endlink,
* @link Blosum80 @endlink, @link Pam40 @endlink, @link Pam120 @endlink,
* @link Pam200 @endlink, @link Pam250 @endlink and @link Vtml200 @endlink.
*
* @fn MatrixScore::Score
* @brief Constructor
*
* @signature MatrixScore::Score(gapExtend[, gapOpen]);
* @signature MatrixScore::Score(fileName, gapExtend[, gapOpen]);
*
* @param[in] fileName Path to load the matrix from, type is <tt>char const *</tt>.
* @param[in] gapExtend Gap extension score, type is TValue.
* @param[in] gapOpen Gap open score, defaults to gapExtend, type is TValue.
*/
template <typename TValue, typename TSequenceValue, typename TSpec>
class Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > {
public:
// Static computation of the required array size.
enum {
VALUE_SIZE = ValueSize<TSequenceValue>::VALUE,
TAB_SIZE = VALUE_SIZE * VALUE_SIZE
};
// The data table.
TValue data_tab[TAB_SIZE];
// The gap extension score.
TValue data_gap_extend;
// The gap open score.
TValue data_gap_open;
explicit Score(TValue _gap_extend = -1)
: data_gap_extend(_gap_extend),
data_gap_open(_gap_extend) {
setDefaultScoreMatrix(*this, TSpec());
}
Score(TValue _gap_extend, TValue _gap_open)
: data_gap_extend(_gap_extend), data_gap_open(_gap_open) {
setDefaultScoreMatrix(*this, TSpec());
}
explicit Score(char const * filename, TValue _gap_extend = -1)
: data_gap_extend(_gap_extend), data_gap_open(_gap_extend) {
loadScoreMatrix(*this, filename);
}
Score(char const * filename, TValue _gap_extend, TValue _gap_open)
: data_gap_extend(_gap_extend), data_gap_open(_gap_open) {
loadScoreMatrix(*this, filename);
}
Score(Score const &) = default;
Score(Score &&) = default;
Score & operator=(Score const &) = default;
Score & operator=(Score &&) = default;
~Score() = default;
};
// ----------------------------------------------------------------------------
// Metafunction IsScoreMatrix_
// ----------------------------------------------------------------------------
template <typename TSpec>
struct IsScoreMatrix_ : False
{};
template <typename TAlphabet, typename TSpec>
struct IsScoreMatrix_<ScoreMatrix<TAlphabet, TSpec> > : True
{};
template <typename TValue, typename TSpec>
struct IsScoreMatrix_<Score<TValue, TSpec> > : IsScoreMatrix_<TSpec>
{};
// ----------------------------------------------------------------------------
// Function score()
// ----------------------------------------------------------------------------
// TODO(holtgrew): Does it make sense to document each Score specialization? Should dddoc show a list of all specializations of a class?
template <typename TValue, typename TSequenceValue, typename TSpec, typename TVal1, typename TVal2>
inline TValue
score(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > const & sc, TVal1 val1, TVal2 val2) {
typedef Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > TScore;
// TODO(holtgrew): Why not implicit cast?
unsigned int i = (TSequenceValue) val1; // conversion TVal1 => TSequenceValue => integral
unsigned int j = (TSequenceValue) val2; // conversion TVal2 => TSequenceValue => integral
return sc.data_tab[i * TScore::VALUE_SIZE + j];
}
/*!
* @fn MatrixScore#setScore
* @brief Set the substitution score between to values.
*
* @signature void setScore(score, x, y, v);
*
* @param[in,out] score The MatrixScore to set the value for.
* @param[in] x The substituted alphabet value.
* @param[in] y The alphabet value to substitute x for.
* @param[in] v The score value to set.
*/
template <typename TValue, typename TSequenceValue, typename TSpec, typename TVal1, typename TVal2, typename T>
inline void
setScore(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, TVal1 val1, TVal2 val2, T score) {
typedef Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > TScore;
// TODO(holtgrew): Why not implicit cast?
unsigned int i = (TSequenceValue) val1; // conversion TVal1 => TSequenceValue => integral
unsigned int j = (TSequenceValue) val2; // conversion TVal2 => TSequenceValue => integral
sc.data_tab[i * TScore::VALUE_SIZE + j] = score;
}
/*!
* @fn MatrixScore#setDefaultScoreMatrix
* @brief Set the score matrix of a Score to one of the default matrixes.
*
* @signature void setDefaultScoreMatrix(score, tag);
*
* @param[in,out] score The MatrixScore to update.
* @param[in] tag The tag to select the default matrix, see description below.
*
* @section Remarks
*
* The tag must be one of the following:
* Default, ScoreSpecBlosum30, ScoreSpecBlosum45, ScoreSpecBlosum62, ScoreSpecBlosum80,
* ScoreSpecPam40, ScoreSpecPam120, ScoreSpecPam200, ScoreSpecPam250, ScoreSpecVtml200.
*
* If Default is used for tag then the matrix will be filled with default-constructed TValue values.
*/
template <typename TValue, typename TSequenceValue, typename TSpec, typename TTag>
inline void
setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, TTag) {
typedef Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > TScore;
TValue const * tab = ScoringMatrixData_<TValue, TSequenceValue, TTag>::getData();
arrayCopy(tab, tab + TScore::TAB_SIZE, sc.data_tab);
}
template <typename TValue, typename TSequenceValue, typename TSpec>
inline void
setDefaultScoreMatrix(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, Default) {
typedef Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > TScore;
arrayFill(sc.data_tab, sc.data_tab + TScore::TAB_SIZE, TValue());
}
} // namespace seqan2
#endif // SEQAN_SSCORE_MATRIX_H_
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