sequenzo 0.1.18__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h

@@ -1,212 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Guillaume Saupin <guillaume.saupin@cea.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SKYLINEMATRIXBASE_H
-#define EIGEN_SKYLINEMATRIXBASE_H
-
-#include "SkylineUtil.h"
-
-namespace Eigen {
-
-/** \ingroup Skyline_Module
- *
- * \class SkylineMatrixBase
- *
- * \brief Base class of any skyline matrices or skyline expressions
- *
- * \param Derived
- *
- */
-template<typename Derived> class SkylineMatrixBase : public EigenBase<Derived> {
-public:
-
-    typedef typename internal::traits<Derived>::Scalar Scalar;
-    typedef typename internal::traits<Derived>::StorageKind StorageKind;
-    typedef typename internal::index<StorageKind>::type Index;
-
-    enum {
-        RowsAtCompileTime = internal::traits<Derived>::RowsAtCompileTime,
-        /**< The number of rows at compile-time. This is just a copy of the value provided
-         * by the \a Derived type. If a value is not known at compile-time,
-         * it is set to the \a Dynamic constant.
-         * \sa MatrixBase::rows(), MatrixBase::cols(), ColsAtCompileTime, SizeAtCompileTime */
-
-        ColsAtCompileTime = internal::traits<Derived>::ColsAtCompileTime,
-        /**< The number of columns at compile-time. This is just a copy of the value provided
-         * by the \a Derived type. If a value is not known at compile-time,
-         * it is set to the \a Dynamic constant.
-         * \sa MatrixBase::rows(), MatrixBase::cols(), RowsAtCompileTime, SizeAtCompileTime */
-
-
-        SizeAtCompileTime = (internal::size_at_compile_time<internal::traits<Derived>::RowsAtCompileTime,
-        internal::traits<Derived>::ColsAtCompileTime>::ret),
-        /**< This is equal to the number of coefficients, i.e. the number of
-         * rows times the number of columns, or to \a Dynamic if this is not
-         * known at compile-time. \sa RowsAtCompileTime, ColsAtCompileTime */
-
-        MaxRowsAtCompileTime = RowsAtCompileTime,
-        MaxColsAtCompileTime = ColsAtCompileTime,
-
-        MaxSizeAtCompileTime = (internal::size_at_compile_time<MaxRowsAtCompileTime,
-        MaxColsAtCompileTime>::ret),
-
-        IsVectorAtCompileTime = RowsAtCompileTime == 1 || ColsAtCompileTime == 1,
-        /**< This is set to true if either the number of rows or the number of
-         * columns is known at compile-time to be equal to 1. Indeed, in that case,
-         * we are dealing with a column-vector (if there is only one column) or with
-         * a row-vector (if there is only one row). */
-
-        Flags = internal::traits<Derived>::Flags,
-        /**< This stores expression \ref flags flags which may or may not be inherited by new expressions
-         * constructed from this one. See the \ref flags "list of flags".
-         */
-
-        CoeffReadCost = internal::traits<Derived>::CoeffReadCost,
-        /**< This is a rough measure of how expensive it is to read one coefficient from
-         * this expression.
-         */
-
-        IsRowMajor = Flags & RowMajorBit ? 1 : 0
-    };
-
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-    /** This is the "real scalar" type; if the \a Scalar type is already real numbers
-     * (e.g. int, float or double) then \a RealScalar is just the same as \a Scalar. If
-     * \a Scalar is \a std::complex<T> then RealScalar is \a T.
-     *
-     * \sa class NumTraits
-     */
-    typedef typename NumTraits<Scalar>::Real RealScalar;
-
-    /** type of the equivalent square matrix */
-    typedef Matrix<Scalar, EIGEN_SIZE_MAX(RowsAtCompileTime, ColsAtCompileTime),
-                           EIGEN_SIZE_MAX(RowsAtCompileTime, ColsAtCompileTime) > SquareMatrixType;
-
-    inline const Derived& derived() const {
-        return *static_cast<const Derived*> (this);
-    }
-
-    inline Derived& derived() {
-        return *static_cast<Derived*> (this);
-    }
-
-    inline Derived& const_cast_derived() const {
-        return *static_cast<Derived*> (const_cast<SkylineMatrixBase*> (this));
-    }
-#endif // not EIGEN_PARSED_BY_DOXYGEN
-
-    /** \returns the number of rows. \sa cols(), RowsAtCompileTime */
-    inline EIGEN_CONSTEXPR Index rows() const EIGEN_NOEXCEPT {
-        return derived().rows();
-    }
-
-    /** \returns the number of columns. \sa rows(), ColsAtCompileTime*/
-    inline EIGEN_CONSTEXPR Index cols() const EIGEN_NOEXCEPT {
-        return derived().cols();
-    }
-
-    /** \returns the number of coefficients, which is \a rows()*cols().
-     * \sa rows(), cols(), SizeAtCompileTime. */
-    inline EIGEN_CONSTEXPR Index size() const EIGEN_NOEXCEPT {
-        return rows() * cols();
-    }
-
-    /** \returns the number of nonzero coefficients which is in practice the number
-     * of stored coefficients. */
-    inline Index nonZeros() const {
-        return derived().nonZeros();
-    }
-
-    /** \returns the size of the storage major dimension,
-     * i.e., the number of columns for a columns major matrix, and the number of rows otherwise */
-    Index outerSize() const {
-        return (int(Flags) & RowMajorBit) ? this->rows() : this->cols();
-    }
-
-    /** \returns the size of the inner dimension according to the storage order,
-     * i.e., the number of rows for a columns major matrix, and the number of cols otherwise */
-    Index innerSize() const {
-        return (int(Flags) & RowMajorBit) ? this->cols() : this->rows();
-    }
-
-    bool isRValue() const {
-        return m_isRValue;
-    }
-
-    Derived& markAsRValue() {
-        m_isRValue = true;
-        return derived();
-    }
-
-    SkylineMatrixBase() : m_isRValue(false) {
-        /* TODO check flags */
-    }
-
-    inline Derived & operator=(const Derived& other) {
-        this->operator=<Derived > (other);
-        return derived();
-    }
-
-    template<typename OtherDerived>
-    inline void assignGeneric(const OtherDerived& other) {
-        derived().resize(other.rows(), other.cols());
-        for (Index row = 0; row < rows(); row++)
-            for (Index col = 0; col < cols(); col++) {
-                if (other.coeff(row, col) != Scalar(0))
-                    derived().insert(row, col) = other.coeff(row, col);
-            }
-        derived().finalize();
-    }
-
-    template<typename OtherDerived>
-            inline Derived & operator=(const SkylineMatrixBase<OtherDerived>& other) {
-        //TODO
-    }
-
-    template<typename Lhs, typename Rhs>
-            inline Derived & operator=(const SkylineProduct<Lhs, Rhs, SkylineTimeSkylineProduct>& product);
-
-    friend std::ostream & operator <<(std::ostream & s, const SkylineMatrixBase& m) {
-        s << m.derived();
-        return s;
-    }
-
-    template<typename OtherDerived>
-    const typename SkylineProductReturnType<Derived, OtherDerived>::Type
-    operator*(const MatrixBase<OtherDerived> &other) const;
-
-    /** \internal use operator= */
-    template<typename DenseDerived>
-    void evalTo(MatrixBase<DenseDerived>& dst) const {
-        dst.setZero();
-        for (Index i = 0; i < rows(); i++)
-            for (Index j = 0; j < rows(); j++)
-                dst(i, j) = derived().coeff(i, j);
-    }
-
-    Matrix<Scalar, RowsAtCompileTime, ColsAtCompileTime> toDense() const {
-        return derived();
-    }
-
-    /** \returns the matrix or vector obtained by evaluating this expression.
-     *
-     * Notice that in the case of a plain matrix or vector (not an expression) this function just returns
-     * a const reference, in order to avoid a useless copy.
-     */
-    EIGEN_STRONG_INLINE const typename internal::eval<Derived, IsSkyline>::type eval() const {
-        return typename internal::eval<Derived>::type(derived());
-    }
-
-protected:
-    bool m_isRValue;
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_SKYLINEMATRIXBASE_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h

@@ -1,295 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Guillaume Saupin <guillaume.saupin@cea.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SKYLINEPRODUCT_H
-#define EIGEN_SKYLINEPRODUCT_H
-
-namespace Eigen { 
-
-template<typename Lhs, typename Rhs, int ProductMode>
-struct SkylineProductReturnType {
-    typedef const typename internal::nested_eval<Lhs, Rhs::RowsAtCompileTime>::type LhsNested;
-    typedef const typename internal::nested_eval<Rhs, Lhs::RowsAtCompileTime>::type RhsNested;
-
-    typedef SkylineProduct<LhsNested, RhsNested, ProductMode> Type;
-};
-
-template<typename LhsNested, typename RhsNested, int ProductMode>
-struct internal::traits<SkylineProduct<LhsNested, RhsNested, ProductMode> > {
-    // clean the nested types:
-    typedef typename internal::remove_all<LhsNested>::type _LhsNested;
-    typedef typename internal::remove_all<RhsNested>::type _RhsNested;
-    typedef typename _LhsNested::Scalar Scalar;
-
-    enum {
-        LhsCoeffReadCost = _LhsNested::CoeffReadCost,
-        RhsCoeffReadCost = _RhsNested::CoeffReadCost,
-        LhsFlags = _LhsNested::Flags,
-        RhsFlags = _RhsNested::Flags,
-
-        RowsAtCompileTime = _LhsNested::RowsAtCompileTime,
-        ColsAtCompileTime = _RhsNested::ColsAtCompileTime,
-        InnerSize = EIGEN_SIZE_MIN_PREFER_FIXED(_LhsNested::ColsAtCompileTime, _RhsNested::RowsAtCompileTime),
-
-        MaxRowsAtCompileTime = _LhsNested::MaxRowsAtCompileTime,
-        MaxColsAtCompileTime = _RhsNested::MaxColsAtCompileTime,
-
-        EvalToRowMajor = (RhsFlags & LhsFlags & RowMajorBit),
-        ResultIsSkyline = ProductMode == SkylineTimeSkylineProduct,
-
-        RemovedBits = ~((EvalToRowMajor ? 0 : RowMajorBit) | (ResultIsSkyline ? 0 : SkylineBit)),
-
-        Flags = (int(LhsFlags | RhsFlags) & HereditaryBits & RemovedBits)
-        | EvalBeforeAssigningBit
-        | EvalBeforeNestingBit,
-
-        CoeffReadCost = HugeCost
-    };
-
-    typedef typename internal::conditional<ResultIsSkyline,
-            SkylineMatrixBase<SkylineProduct<LhsNested, RhsNested, ProductMode> >,
-            MatrixBase<SkylineProduct<LhsNested, RhsNested, ProductMode> > >::type Base;
-};
-
-namespace internal {
-template<typename LhsNested, typename RhsNested, int ProductMode>
-class SkylineProduct : no_assignment_operator,
-public traits<SkylineProduct<LhsNested, RhsNested, ProductMode> >::Base {
-public:
-
-    EIGEN_GENERIC_PUBLIC_INTERFACE(SkylineProduct)
-
-private:
-
-    typedef typename traits<SkylineProduct>::_LhsNested _LhsNested;
-    typedef typename traits<SkylineProduct>::_RhsNested _RhsNested;
-
-public:
-
-    template<typename Lhs, typename Rhs>
-    EIGEN_STRONG_INLINE SkylineProduct(const Lhs& lhs, const Rhs& rhs)
-    : m_lhs(lhs), m_rhs(rhs) {
-        eigen_assert(lhs.cols() == rhs.rows());
-
-        enum {
-            ProductIsValid = _LhsNested::ColsAtCompileTime == Dynamic
-            || _RhsNested::RowsAtCompileTime == Dynamic
-            || int(_LhsNested::ColsAtCompileTime) == int(_RhsNested::RowsAtCompileTime),
-            AreVectors = _LhsNested::IsVectorAtCompileTime && _RhsNested::IsVectorAtCompileTime,
-            SameSizes = EIGEN_PREDICATE_SAME_MATRIX_SIZE(_LhsNested, _RhsNested)
-        };
-        // note to the lost user:
-        //    * for a dot product use: v1.dot(v2)
-        //    * for a coeff-wise product use: v1.cwise()*v2
-        EIGEN_STATIC_ASSERT(ProductIsValid || !(AreVectors && SameSizes),
-                INVALID_VECTOR_VECTOR_PRODUCT__IF_YOU_WANTED_A_DOT_OR_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTIONS)
-                EIGEN_STATIC_ASSERT(ProductIsValid || !(SameSizes && !AreVectors),
-                INVALID_MATRIX_PRODUCT__IF_YOU_WANTED_A_COEFF_WISE_PRODUCT_YOU_MUST_USE_THE_EXPLICIT_FUNCTION)
-                EIGEN_STATIC_ASSERT(ProductIsValid || SameSizes, INVALID_MATRIX_PRODUCT)
-    }
-
-    EIGEN_STRONG_INLINE Index rows() const {
-        return m_lhs.rows();
-    }
-
-    EIGEN_STRONG_INLINE Index cols() const {
-        return m_rhs.cols();
-    }
-
-    EIGEN_STRONG_INLINE const _LhsNested& lhs() const {
-        return m_lhs;
-    }
-
-    EIGEN_STRONG_INLINE const _RhsNested& rhs() const {
-        return m_rhs;
-    }
-
-protected:
-    LhsNested m_lhs;
-    RhsNested m_rhs;
-};
-
-// dense = skyline * dense
-// Note that here we force no inlining and separate the setZero() because GCC messes up otherwise
-
-template<typename Lhs, typename Rhs, typename Dest>
-EIGEN_DONT_INLINE void skyline_row_major_time_dense_product(const Lhs& lhs, const Rhs& rhs, Dest& dst) {
-    typedef typename remove_all<Lhs>::type _Lhs;
-    typedef typename remove_all<Rhs>::type _Rhs;
-    typedef typename traits<Lhs>::Scalar Scalar;
-
-    enum {
-        LhsIsRowMajor = (_Lhs::Flags & RowMajorBit) == RowMajorBit,
-        LhsIsSelfAdjoint = (_Lhs::Flags & SelfAdjointBit) == SelfAdjointBit,
-        ProcessFirstHalf = LhsIsSelfAdjoint
-        && (((_Lhs::Flags & (UpperTriangularBit | LowerTriangularBit)) == 0)
-        || ((_Lhs::Flags & UpperTriangularBit) && !LhsIsRowMajor)
-        || ((_Lhs::Flags & LowerTriangularBit) && LhsIsRowMajor)),
-        ProcessSecondHalf = LhsIsSelfAdjoint && (!ProcessFirstHalf)
-    };
-
-    //Use matrix diagonal part <- Improvement : use inner iterator on dense matrix.
-    for (Index col = 0; col < rhs.cols(); col++) {
-        for (Index row = 0; row < lhs.rows(); row++) {
-            dst(row, col) = lhs.coeffDiag(row) * rhs(row, col);
-        }
-    }
-    //Use matrix lower triangular part
-    for (Index row = 0; row < lhs.rows(); row++) {
-        typename _Lhs::InnerLowerIterator lIt(lhs, row);
-        const Index stop = lIt.col() + lIt.size();
-        for (Index col = 0; col < rhs.cols(); col++) {
-
-            Index k = lIt.col();
-            Scalar tmp = 0;
-            while (k < stop) {
-                tmp +=
-                        lIt.value() *
-                        rhs(k++, col);
-                ++lIt;
-            }
-            dst(row, col) += tmp;
-            lIt += -lIt.size();
-        }
-
-    }
-
-    //Use matrix upper triangular part
-    for (Index lhscol = 0; lhscol < lhs.cols(); lhscol++) {
-        typename _Lhs::InnerUpperIterator uIt(lhs, lhscol);
-        const Index stop = uIt.size() + uIt.row();
-        for (Index rhscol = 0; rhscol < rhs.cols(); rhscol++) {
-
-
-            const Scalar rhsCoeff = rhs.coeff(lhscol, rhscol);
-            Index k = uIt.row();
-            while (k < stop) {
-                dst(k++, rhscol) +=
-                        uIt.value() *
-                        rhsCoeff;
-                ++uIt;
-            }
-            uIt += -uIt.size();
-        }
-    }
-
-}
-
-template<typename Lhs, typename Rhs, typename Dest>
-EIGEN_DONT_INLINE void skyline_col_major_time_dense_product(const Lhs& lhs, const Rhs& rhs, Dest& dst) {
-    typedef typename remove_all<Lhs>::type _Lhs;
-    typedef typename remove_all<Rhs>::type _Rhs;
-    typedef typename traits<Lhs>::Scalar Scalar;
-
-    enum {
-        LhsIsRowMajor = (_Lhs::Flags & RowMajorBit) == RowMajorBit,
-        LhsIsSelfAdjoint = (_Lhs::Flags & SelfAdjointBit) == SelfAdjointBit,
-        ProcessFirstHalf = LhsIsSelfAdjoint
-        && (((_Lhs::Flags & (UpperTriangularBit | LowerTriangularBit)) == 0)
-        || ((_Lhs::Flags & UpperTriangularBit) && !LhsIsRowMajor)
-        || ((_Lhs::Flags & LowerTriangularBit) && LhsIsRowMajor)),
-        ProcessSecondHalf = LhsIsSelfAdjoint && (!ProcessFirstHalf)
-    };
-
-    //Use matrix diagonal part <- Improvement : use inner iterator on dense matrix.
-    for (Index col = 0; col < rhs.cols(); col++) {
-        for (Index row = 0; row < lhs.rows(); row++) {
-            dst(row, col) = lhs.coeffDiag(row) * rhs(row, col);
-        }
-    }
-
-    //Use matrix upper triangular part
-    for (Index row = 0; row < lhs.rows(); row++) {
-        typename _Lhs::InnerUpperIterator uIt(lhs, row);
-        const Index stop = uIt.col() + uIt.size();
-        for (Index col = 0; col < rhs.cols(); col++) {
-
-            Index k = uIt.col();
-            Scalar tmp = 0;
-            while (k < stop) {
-                tmp +=
-                        uIt.value() *
-                        rhs(k++, col);
-                ++uIt;
-            }
-
-
-            dst(row, col) += tmp;
-            uIt += -uIt.size();
-        }
-    }
-
-    //Use matrix lower triangular part
-    for (Index lhscol = 0; lhscol < lhs.cols(); lhscol++) {
-        typename _Lhs::InnerLowerIterator lIt(lhs, lhscol);
-        const Index stop = lIt.size() + lIt.row();
-        for (Index rhscol = 0; rhscol < rhs.cols(); rhscol++) {
-
-            const Scalar rhsCoeff = rhs.coeff(lhscol, rhscol);
-            Index k = lIt.row();
-            while (k < stop) {
-                dst(k++, rhscol) +=
-                        lIt.value() *
-                        rhsCoeff;
-                ++lIt;
-            }
-            lIt += -lIt.size();
-        }
-    }
-
-}
-
-template<typename Lhs, typename Rhs, typename ResultType,
-        int LhsStorageOrder = traits<Lhs>::Flags&RowMajorBit>
-        struct skyline_product_selector;
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct skyline_product_selector<Lhs, Rhs, ResultType, RowMajor> {
-    typedef typename traits<typename remove_all<Lhs>::type>::Scalar Scalar;
-
-    static void run(const Lhs& lhs, const Rhs& rhs, ResultType & res) {
-        skyline_row_major_time_dense_product<Lhs, Rhs, ResultType > (lhs, rhs, res);
-    }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct skyline_product_selector<Lhs, Rhs, ResultType, ColMajor> {
-    typedef typename traits<typename remove_all<Lhs>::type>::Scalar Scalar;
-
-    static void run(const Lhs& lhs, const Rhs& rhs, ResultType & res) {
-        skyline_col_major_time_dense_product<Lhs, Rhs, ResultType > (lhs, rhs, res);
-    }
-};
-
-} // end namespace internal
-
-// template<typename Derived>
-// template<typename Lhs, typename Rhs >
-// Derived & MatrixBase<Derived>::lazyAssign(const SkylineProduct<Lhs, Rhs, SkylineTimeDenseProduct>& product) {
-//     typedef typename internal::remove_all<Lhs>::type _Lhs;
-//     internal::skyline_product_selector<typename internal::remove_all<Lhs>::type,
-//             typename internal::remove_all<Rhs>::type,
-//             Derived>::run(product.lhs(), product.rhs(), derived());
-// 
-//     return derived();
-// }
-
-// skyline * dense
-
-template<typename Derived>
-template<typename OtherDerived >
-EIGEN_STRONG_INLINE const typename SkylineProductReturnType<Derived, OtherDerived>::Type
-SkylineMatrixBase<Derived>::operator*(const MatrixBase<OtherDerived> &other) const {
-
-    return typename SkylineProductReturnType<Derived, OtherDerived>::Type(derived(), other.derived());
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_SKYLINEPRODUCT_H