sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-win_amd64.whl

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

@@ -1,862 +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_SKYLINEMATRIX_H
-#define EIGEN_SKYLINEMATRIX_H
-
-#include "SkylineStorage.h"
-#include "SkylineMatrixBase.h"
-
-namespace Eigen { 
-
-/** \ingroup Skyline_Module
- *
- * \class SkylineMatrix
- *
- * \brief The main skyline matrix class
- *
- * This class implements a skyline matrix using the very uncommon storage
- * scheme.
- *
- * \param _Scalar the scalar type, i.e. the type of the coefficients
- * \param _Options Union of bit flags controlling the storage scheme. Currently the only possibility
- *                 is RowMajor. The default is 0 which means column-major.
- *
- *
- */
-namespace internal {
-template<typename _Scalar, int _Options>
-struct traits<SkylineMatrix<_Scalar, _Options> > {
-    typedef _Scalar Scalar;
-    typedef Sparse StorageKind;
-
-    enum {
-        RowsAtCompileTime = Dynamic,
-        ColsAtCompileTime = Dynamic,
-        MaxRowsAtCompileTime = Dynamic,
-        MaxColsAtCompileTime = Dynamic,
-        Flags = SkylineBit | _Options,
-        CoeffReadCost = NumTraits<Scalar>::ReadCost,
-    };
-};
-}
-
-template<typename _Scalar, int _Options>
-class SkylineMatrix
-: public SkylineMatrixBase<SkylineMatrix<_Scalar, _Options> > {
-public:
-    EIGEN_SKYLINE_GENERIC_PUBLIC_INTERFACE(SkylineMatrix)
-    EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(SkylineMatrix, +=)
-    EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(SkylineMatrix, -=)
-
-    using Base::IsRowMajor;
-
-protected:
-
-    typedef SkylineMatrix<Scalar, (Flags&~RowMajorBit) | (IsRowMajor ? RowMajorBit : 0) > TransposedSkylineMatrix;
-
-    Index m_outerSize;
-    Index m_innerSize;
-
-public:
-    Index* m_colStartIndex;
-    Index* m_rowStartIndex;
-    SkylineStorage<Scalar> m_data;
-
-public:
-
-    inline Index rows() const {
-        return IsRowMajor ? m_outerSize : m_innerSize;
-    }
-
-    inline Index cols() const {
-        return IsRowMajor ? m_innerSize : m_outerSize;
-    }
-
-    inline Index innerSize() const {
-        return m_innerSize;
-    }
-
-    inline Index outerSize() const {
-        return m_outerSize;
-    }
-
-    inline Index upperNonZeros() const {
-        return m_data.upperSize();
-    }
-
-    inline Index lowerNonZeros() const {
-        return m_data.lowerSize();
-    }
-
-    inline Index upperNonZeros(Index j) const {
-        return m_colStartIndex[j + 1] - m_colStartIndex[j];
-    }
-
-    inline Index lowerNonZeros(Index j) const {
-        return m_rowStartIndex[j + 1] - m_rowStartIndex[j];
-    }
-
-    inline const Scalar* _diagPtr() const {
-        return &m_data.diag(0);
-    }
-
-    inline Scalar* _diagPtr() {
-        return &m_data.diag(0);
-    }
-
-    inline const Scalar* _upperPtr() const {
-        return &m_data.upper(0);
-    }
-
-    inline Scalar* _upperPtr() {
-        return &m_data.upper(0);
-    }
-
-    inline const Scalar* _lowerPtr() const {
-        return &m_data.lower(0);
-    }
-
-    inline Scalar* _lowerPtr() {
-        return &m_data.lower(0);
-    }
-
-    inline const Index* _upperProfilePtr() const {
-        return &m_data.upperProfile(0);
-    }
-
-    inline Index* _upperProfilePtr() {
-        return &m_data.upperProfile(0);
-    }
-
-    inline const Index* _lowerProfilePtr() const {
-        return &m_data.lowerProfile(0);
-    }
-
-    inline Index* _lowerProfilePtr() {
-        return &m_data.lowerProfile(0);
-    }
-
-    inline Scalar coeff(Index row, Index col) const {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-
-        if (outer == inner)
-            return this->m_data.diag(outer);
-
-        if (IsRowMajor) {
-            if (inner > outer) //upper matrix
-            {
-                const Index minOuterIndex = inner - m_data.upperProfile(inner);
-                if (outer >= minOuterIndex)
-                    return this->m_data.upper(m_colStartIndex[inner] + outer - (inner - m_data.upperProfile(inner)));
-                else
-                    return Scalar(0);
-            }
-            if (inner < outer) //lower matrix
-            {
-                const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-                if (inner >= minInnerIndex)
-                    return this->m_data.lower(m_rowStartIndex[outer] + inner - (outer - m_data.lowerProfile(outer)));
-                else
-                    return Scalar(0);
-            }
-            return m_data.upper(m_colStartIndex[inner] + outer - inner);
-        } else {
-            if (outer > inner) //upper matrix
-            {
-                const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-                if (outer <= maxOuterIndex)
-                    return this->m_data.upper(m_colStartIndex[inner] + (outer - inner));
-                else
-                    return Scalar(0);
-            }
-            if (outer < inner) //lower matrix
-            {
-                const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-
-                if (inner <= maxInnerIndex)
-                    return this->m_data.lower(m_rowStartIndex[outer] + (inner - outer));
-                else
-                    return Scalar(0);
-            }
-        }
-    }
-
-    inline Scalar& coeffRef(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-
-        if (outer == inner)
-            return this->m_data.diag(outer);
-
-        if (IsRowMajor) {
-            if (col > row) //upper matrix
-            {
-                const Index minOuterIndex = inner - m_data.upperProfile(inner);
-                eigen_assert(outer >= minOuterIndex && "You tried to access a coeff that does not exist in the storage");
-                return this->m_data.upper(m_colStartIndex[inner] + outer - (inner - m_data.upperProfile(inner)));
-            }
-            if (col < row) //lower matrix
-            {
-                const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-                eigen_assert(inner >= minInnerIndex && "You tried to access a coeff that does not exist in the storage");
-                return this->m_data.lower(m_rowStartIndex[outer] + inner - (outer - m_data.lowerProfile(outer)));
-            }
-        } else {
-            if (outer > inner) //upper matrix
-            {
-                const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-                eigen_assert(outer <= maxOuterIndex && "You tried to access a coeff that does not exist in the storage");
-                return this->m_data.upper(m_colStartIndex[inner] + (outer - inner));
-            }
-            if (outer < inner) //lower matrix
-            {
-                const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-                eigen_assert(inner <= maxInnerIndex && "You tried to access a coeff that does not exist in the storage");
-                return this->m_data.lower(m_rowStartIndex[outer] + (inner - outer));
-            }
-        }
-    }
-
-    inline Scalar coeffDiag(Index idx) const {
-        eigen_assert(idx < outerSize());
-        eigen_assert(idx < innerSize());
-        return this->m_data.diag(idx);
-    }
-
-    inline Scalar coeffLower(Index row, Index col) const {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-            if (inner >= minInnerIndex)
-                return this->m_data.lower(m_rowStartIndex[outer] + inner - (outer - m_data.lowerProfile(outer)));
-            else
-                return Scalar(0);
-
-        } else {
-            const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-            if (inner <= maxInnerIndex)
-                return this->m_data.lower(m_rowStartIndex[outer] + (inner - outer));
-            else
-                return Scalar(0);
-        }
-    }
-
-    inline Scalar coeffUpper(Index row, Index col) const {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minOuterIndex = inner - m_data.upperProfile(inner);
-            if (outer >= minOuterIndex)
-                return this->m_data.upper(m_colStartIndex[inner] + outer - (inner - m_data.upperProfile(inner)));
-            else
-                return Scalar(0);
-        } else {
-            const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-            if (outer <= maxOuterIndex)
-                return this->m_data.upper(m_colStartIndex[inner] + (outer - inner));
-            else
-                return Scalar(0);
-        }
-    }
-
-    inline Scalar& coeffRefDiag(Index idx) {
-        eigen_assert(idx < outerSize());
-        eigen_assert(idx < innerSize());
-        return this->m_data.diag(idx);
-    }
-
-    inline Scalar& coeffRefLower(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-            eigen_assert(inner >= minInnerIndex && "You tried to access a coeff that does not exist in the storage");
-            return this->m_data.lower(m_rowStartIndex[outer] + inner - (outer - m_data.lowerProfile(outer)));
-        } else {
-            const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-            eigen_assert(inner <= maxInnerIndex && "You tried to access a coeff that does not exist in the storage");
-            return this->m_data.lower(m_rowStartIndex[outer] + (inner - outer));
-        }
-    }
-
-    inline bool coeffExistLower(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-            return inner >= minInnerIndex;
-        } else {
-            const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-            return inner <= maxInnerIndex;
-        }
-    }
-
-    inline Scalar& coeffRefUpper(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minOuterIndex = inner - m_data.upperProfile(inner);
-            eigen_assert(outer >= minOuterIndex && "You tried to access a coeff that does not exist in the storage");
-            return this->m_data.upper(m_colStartIndex[inner] + outer - (inner - m_data.upperProfile(inner)));
-        } else {
-            const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-            eigen_assert(outer <= maxOuterIndex && "You tried to access a coeff that does not exist in the storage");
-            return this->m_data.upper(m_colStartIndex[inner] + (outer - inner));
-        }
-    }
-
-    inline bool coeffExistUpper(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-        eigen_assert(inner != outer);
-
-        if (IsRowMajor) {
-            const Index minOuterIndex = inner - m_data.upperProfile(inner);
-            return outer >= minOuterIndex;
-        } else {
-            const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-            return outer <= maxOuterIndex;
-        }
-    }
-
-
-protected:
-
-public:
-    class InnerUpperIterator;
-    class InnerLowerIterator;
-
-    class OuterUpperIterator;
-    class OuterLowerIterator;
-
-    /** Removes all non zeros */
-    inline void setZero() {
-        m_data.clear();
-        memset(m_colStartIndex, 0, (m_outerSize + 1) * sizeof (Index));
-        memset(m_rowStartIndex, 0, (m_outerSize + 1) * sizeof (Index));
-    }
-
-    /** \returns the number of non zero coefficients */
-    inline Index nonZeros() const {
-        return m_data.diagSize() + m_data.upperSize() + m_data.lowerSize();
-    }
-
-    /** Preallocates \a reserveSize non zeros */
-    inline void reserve(Index reserveSize, Index reserveUpperSize, Index reserveLowerSize) {
-        m_data.reserve(reserveSize, reserveUpperSize, reserveLowerSize);
-    }
-
-    /** \returns a reference to a novel non zero coefficient with coordinates \a row x \a col.
-
-     *
-     * \warning This function can be extremely slow if the non zero coefficients
-     * are not inserted in a coherent order.
-     *
-     * After an insertion session, you should call the finalize() function.
-     */
-    EIGEN_DONT_INLINE Scalar & insert(Index row, Index col) {
-        const Index outer = IsRowMajor ? row : col;
-        const Index inner = IsRowMajor ? col : row;
-
-        eigen_assert(outer < outerSize());
-        eigen_assert(inner < innerSize());
-
-        if (outer == inner)
-            return m_data.diag(col);
-
-        if (IsRowMajor) {
-            if (outer < inner) //upper matrix
-            {
-                Index minOuterIndex = 0;
-                minOuterIndex = inner - m_data.upperProfile(inner);
-
-                if (outer < minOuterIndex) //The value does not yet exist
-                {
-                    const Index previousProfile = m_data.upperProfile(inner);
-
-                    m_data.upperProfile(inner) = inner - outer;
-
-
-                    const Index bandIncrement = m_data.upperProfile(inner) - previousProfile;
-                    //shift data stored after this new one
-                    const Index stop = m_colStartIndex[cols()];
-                    const Index start = m_colStartIndex[inner];
-
-
-                    for (Index innerIdx = stop; innerIdx >= start; innerIdx--) {
-                        m_data.upper(innerIdx + bandIncrement) = m_data.upper(innerIdx);
-                    }
-
-                    for (Index innerIdx = cols(); innerIdx > inner; innerIdx--) {
-                        m_colStartIndex[innerIdx] += bandIncrement;
-                    }
-
-                    //zeros new data
-                    memset(this->_upperPtr() + start, 0, (bandIncrement - 1) * sizeof (Scalar));
-
-                    return m_data.upper(m_colStartIndex[inner]);
-                } else {
-                    return m_data.upper(m_colStartIndex[inner] + outer - (inner - m_data.upperProfile(inner)));
-                }
-            }
-
-            if (outer > inner) //lower matrix
-            {
-                const Index minInnerIndex = outer - m_data.lowerProfile(outer);
-                if (inner < minInnerIndex) //The value does not yet exist
-                {
-                    const Index previousProfile = m_data.lowerProfile(outer);
-                    m_data.lowerProfile(outer) = outer - inner;
-
-                    const Index bandIncrement = m_data.lowerProfile(outer) - previousProfile;
-                    //shift data stored after this new one
-                    const Index stop = m_rowStartIndex[rows()];
-                    const Index start = m_rowStartIndex[outer];
-
-
-                    for (Index innerIdx = stop; innerIdx >= start; innerIdx--) {
-                        m_data.lower(innerIdx + bandIncrement) = m_data.lower(innerIdx);
-                    }
-
-                    for (Index innerIdx = rows(); innerIdx > outer; innerIdx--) {
-                        m_rowStartIndex[innerIdx] += bandIncrement;
-                    }
-
-                    //zeros new data
-                    memset(this->_lowerPtr() + start, 0, (bandIncrement - 1) * sizeof (Scalar));
-                    return m_data.lower(m_rowStartIndex[outer]);
-                } else {
-                    return m_data.lower(m_rowStartIndex[outer] + inner - (outer - m_data.lowerProfile(outer)));
-                }
-            }
-        } else {
-            if (outer > inner) //upper matrix
-            {
-                const Index maxOuterIndex = inner + m_data.upperProfile(inner);
-                if (outer > maxOuterIndex) //The value does not yet exist
-                {
-                    const Index previousProfile = m_data.upperProfile(inner);
-                    m_data.upperProfile(inner) = outer - inner;
-
-                    const Index bandIncrement = m_data.upperProfile(inner) - previousProfile;
-                    //shift data stored after this new one
-                    const Index stop = m_rowStartIndex[rows()];
-                    const Index start = m_rowStartIndex[inner + 1];
-
-                    for (Index innerIdx = stop; innerIdx >= start; innerIdx--) {
-                        m_data.upper(innerIdx + bandIncrement) = m_data.upper(innerIdx);
-                    }
-
-                    for (Index innerIdx = inner + 1; innerIdx < outerSize() + 1; innerIdx++) {
-                        m_rowStartIndex[innerIdx] += bandIncrement;
-                    }
-                    memset(this->_upperPtr() + m_rowStartIndex[inner] + previousProfile + 1, 0, (bandIncrement - 1) * sizeof (Scalar));
-                    return m_data.upper(m_rowStartIndex[inner] + m_data.upperProfile(inner));
-                } else {
-                    return m_data.upper(m_rowStartIndex[inner] + (outer - inner));
-                }
-            }
-
-            if (outer < inner) //lower matrix
-            {
-                const Index maxInnerIndex = outer + m_data.lowerProfile(outer);
-                if (inner > maxInnerIndex) //The value does not yet exist
-                {
-                    const Index previousProfile = m_data.lowerProfile(outer);
-                    m_data.lowerProfile(outer) = inner - outer;
-
-                    const Index bandIncrement = m_data.lowerProfile(outer) - previousProfile;
-                    //shift data stored after this new one
-                    const Index stop = m_colStartIndex[cols()];
-                    const Index start = m_colStartIndex[outer + 1];
-
-                    for (Index innerIdx = stop; innerIdx >= start; innerIdx--) {
-                        m_data.lower(innerIdx + bandIncrement) = m_data.lower(innerIdx);
-                    }
-
-                    for (Index innerIdx = outer + 1; innerIdx < outerSize() + 1; innerIdx++) {
-                        m_colStartIndex[innerIdx] += bandIncrement;
-                    }
-                    memset(this->_lowerPtr() + m_colStartIndex[outer] + previousProfile + 1, 0, (bandIncrement - 1) * sizeof (Scalar));
-                    return m_data.lower(m_colStartIndex[outer] + m_data.lowerProfile(outer));
-                } else {
-                    return m_data.lower(m_colStartIndex[outer] + (inner - outer));
-                }
-            }
-        }
-    }
-
-    /** Must be called after inserting a set of non zero entries.
-     */
-    inline void finalize() {
-        if (IsRowMajor) {
-            if (rows() > cols())
-                m_data.resize(cols(), cols(), rows(), m_colStartIndex[cols()] + 1, m_rowStartIndex[rows()] + 1);
-            else
-                m_data.resize(rows(), cols(), rows(), m_colStartIndex[cols()] + 1, m_rowStartIndex[rows()] + 1);
-
-            //            eigen_assert(rows() == cols() && "memory reorganisatrion only works with suare matrix");
-            //
-            //            Scalar* newArray = new Scalar[m_colStartIndex[cols()] + 1 + m_rowStartIndex[rows()] + 1];
-            //            Index dataIdx = 0;
-            //            for (Index row = 0; row < rows(); row++) {
-            //
-            //                const Index nbLowerElts = m_rowStartIndex[row + 1] - m_rowStartIndex[row];
-            //                //                std::cout << "nbLowerElts" << nbLowerElts << std::endl;
-            //                memcpy(newArray + dataIdx, m_data.m_lower + m_rowStartIndex[row], nbLowerElts * sizeof (Scalar));
-            //                m_rowStartIndex[row] = dataIdx;
-            //                dataIdx += nbLowerElts;
-            //
-            //                const Index nbUpperElts = m_colStartIndex[row + 1] - m_colStartIndex[row];
-            //                memcpy(newArray + dataIdx, m_data.m_upper + m_colStartIndex[row], nbUpperElts * sizeof (Scalar));
-            //                m_colStartIndex[row] = dataIdx;
-            //                dataIdx += nbUpperElts;
-            //
-            //
-            //            }
-            //            //todo : don't access m_data profile directly : add an accessor from SkylineMatrix
-            //            m_rowStartIndex[rows()] = m_rowStartIndex[rows()-1] + m_data.lowerProfile(rows()-1);
-            //            m_colStartIndex[cols()] = m_colStartIndex[cols()-1] + m_data.upperProfile(cols()-1);
-            //
-            //            delete[] m_data.m_lower;
-            //            delete[] m_data.m_upper;
-            //
-            //            m_data.m_lower = newArray;
-            //            m_data.m_upper = newArray;
-        } else {
-            if (rows() > cols())
-                m_data.resize(cols(), rows(), cols(), m_rowStartIndex[cols()] + 1, m_colStartIndex[cols()] + 1);
-            else
-                m_data.resize(rows(), rows(), cols(), m_rowStartIndex[rows()] + 1, m_colStartIndex[rows()] + 1);
-        }
-    }
-
-    inline void squeeze() {
-        finalize();
-        m_data.squeeze();
-    }
-
-    void prune(Scalar reference, RealScalar epsilon = dummy_precision<RealScalar > ()) {
-        //TODO
-    }
-
-    /** Resizes the matrix to a \a rows x \a cols matrix and initializes it to zero
-     * \sa resizeNonZeros(Index), reserve(), setZero()
-     */
-    void resize(size_t rows, size_t cols) {
-        const Index diagSize = rows > cols ? cols : rows;
-        m_innerSize = IsRowMajor ? cols : rows;
-
-        eigen_assert(rows == cols && "Skyline matrix must be square matrix");
-
-        if (diagSize % 2) { // diagSize is odd
-            const Index k = (diagSize - 1) / 2;
-
-            m_data.resize(diagSize, IsRowMajor ? cols : rows, IsRowMajor ? rows : cols,
-                    2 * k * k + k + 1,
-                    2 * k * k + k + 1);
-
-        } else // diagSize is even
-        {
-            const Index k = diagSize / 2;
-            m_data.resize(diagSize, IsRowMajor ? cols : rows, IsRowMajor ? rows : cols,
-                    2 * k * k - k + 1,
-                    2 * k * k - k + 1);
-        }
-
-        if (m_colStartIndex && m_rowStartIndex) {
-            delete[] m_colStartIndex;
-            delete[] m_rowStartIndex;
-        }
-        m_colStartIndex = new Index [cols + 1];
-        m_rowStartIndex = new Index [rows + 1];
-        m_outerSize = diagSize;
-
-        m_data.reset();
-        m_data.clear();
-
-        m_outerSize = diagSize;
-        memset(m_colStartIndex, 0, (cols + 1) * sizeof (Index));
-        memset(m_rowStartIndex, 0, (rows + 1) * sizeof (Index));
-    }
-
-    void resizeNonZeros(Index size) {
-        m_data.resize(size);
-    }
-
-    inline SkylineMatrix()
-    : m_outerSize(-1), m_innerSize(0), m_colStartIndex(0), m_rowStartIndex(0) {
-        resize(0, 0);
-    }
-
-    inline SkylineMatrix(size_t rows, size_t cols)
-    : m_outerSize(0), m_innerSize(0), m_colStartIndex(0), m_rowStartIndex(0) {
-        resize(rows, cols);
-    }
-
-    template<typename OtherDerived>
-    inline SkylineMatrix(const SkylineMatrixBase<OtherDerived>& other)
-    : m_outerSize(0), m_innerSize(0), m_colStartIndex(0), m_rowStartIndex(0) {
-        *this = other.derived();
-    }
-
-    inline SkylineMatrix(const SkylineMatrix & other)
-    : Base(), m_outerSize(0), m_innerSize(0), m_colStartIndex(0), m_rowStartIndex(0) {
-        *this = other.derived();
-    }
-
-    inline void swap(SkylineMatrix & other) {
-        //EIGEN_DBG_SKYLINE(std::cout << "SkylineMatrix:: swap\n");
-        std::swap(m_colStartIndex, other.m_colStartIndex);
-        std::swap(m_rowStartIndex, other.m_rowStartIndex);
-        std::swap(m_innerSize, other.m_innerSize);
-        std::swap(m_outerSize, other.m_outerSize);
-        m_data.swap(other.m_data);
-    }
-
-    inline SkylineMatrix & operator=(const SkylineMatrix & other) {
-        std::cout << "SkylineMatrix& operator=(const SkylineMatrix& other)\n";
-        if (other.isRValue()) {
-            swap(other.const_cast_derived());
-        } else {
-            resize(other.rows(), other.cols());
-            memcpy(m_colStartIndex, other.m_colStartIndex, (m_outerSize + 1) * sizeof (Index));
-            memcpy(m_rowStartIndex, other.m_rowStartIndex, (m_outerSize + 1) * sizeof (Index));
-            m_data = other.m_data;
-        }
-        return *this;
-    }
-
-    template<typename OtherDerived>
-            inline SkylineMatrix & operator=(const SkylineMatrixBase<OtherDerived>& other) {
-        const bool needToTranspose = (Flags & RowMajorBit) != (OtherDerived::Flags & RowMajorBit);
-        if (needToTranspose) {
-            //         TODO
-            //            return *this;
-        } else {
-            // there is no special optimization
-            return SkylineMatrixBase<SkylineMatrix>::operator=(other.derived());
-        }
-    }
-
-    friend std::ostream & operator <<(std::ostream & s, const SkylineMatrix & m) {
-
-        EIGEN_DBG_SKYLINE(
-        std::cout << "upper elements : " << std::endl;
-        for (Index i = 0; i < m.m_data.upperSize(); i++)
-            std::cout << m.m_data.upper(i) << "\t";
-        std::cout << std::endl;
-        std::cout << "upper profile : " << std::endl;
-        for (Index i = 0; i < m.m_data.upperProfileSize(); i++)
-            std::cout << m.m_data.upperProfile(i) << "\t";
-        std::cout << std::endl;
-        std::cout << "lower startIdx : " << std::endl;
-        for (Index i = 0; i < m.m_data.upperProfileSize(); i++)
-            std::cout << (IsRowMajor ? m.m_colStartIndex[i] : m.m_rowStartIndex[i]) << "\t";
-        std::cout << std::endl;
-
-
-        std::cout << "lower elements : " << std::endl;
-        for (Index i = 0; i < m.m_data.lowerSize(); i++)
-            std::cout << m.m_data.lower(i) << "\t";
-        std::cout << std::endl;
-        std::cout << "lower profile : " << std::endl;
-        for (Index i = 0; i < m.m_data.lowerProfileSize(); i++)
-            std::cout << m.m_data.lowerProfile(i) << "\t";
-        std::cout << std::endl;
-        std::cout << "lower startIdx : " << std::endl;
-        for (Index i = 0; i < m.m_data.lowerProfileSize(); i++)
-            std::cout << (IsRowMajor ? m.m_rowStartIndex[i] : m.m_colStartIndex[i]) << "\t";
-        std::cout << std::endl;
-        );
-        for (Index rowIdx = 0; rowIdx < m.rows(); rowIdx++) {
-            for (Index colIdx = 0; colIdx < m.cols(); colIdx++) {
-                s << m.coeff(rowIdx, colIdx) << "\t";
-            }
-            s << std::endl;
-        }
-        return s;
-    }
-
-    /** Destructor */
-    inline ~SkylineMatrix() {
-        delete[] m_colStartIndex;
-        delete[] m_rowStartIndex;
-    }
-
-    /** Overloaded for performance */
-    Scalar sum() const;
-};
-
-template<typename Scalar, int _Options>
-class SkylineMatrix<Scalar, _Options>::InnerUpperIterator {
-public:
-
-    InnerUpperIterator(const SkylineMatrix& mat, Index outer)
-    : m_matrix(mat), m_outer(outer),
-    m_id(_Options == RowMajor ? mat.m_colStartIndex[outer] : mat.m_rowStartIndex[outer] + 1),
-    m_start(m_id),
-    m_end(_Options == RowMajor ? mat.m_colStartIndex[outer + 1] : mat.m_rowStartIndex[outer + 1] + 1) {
-    }
-
-    inline InnerUpperIterator & operator++() {
-        m_id++;
-        return *this;
-    }
-
-    inline InnerUpperIterator & operator+=(Index shift) {
-        m_id += shift;
-        return *this;
-    }
-
-    inline Scalar value() const {
-        return m_matrix.m_data.upper(m_id);
-    }
-
-    inline Scalar* valuePtr() {
-        return const_cast<Scalar*> (&(m_matrix.m_data.upper(m_id)));
-    }
-
-    inline Scalar& valueRef() {
-        return const_cast<Scalar&> (m_matrix.m_data.upper(m_id));
-    }
-
-    inline Index index() const {
-        return IsRowMajor ? m_outer - m_matrix.m_data.upperProfile(m_outer) + (m_id - m_start) :
-                m_outer + (m_id - m_start) + 1;
-    }
-
-    inline Index row() const {
-        return IsRowMajor ? index() : m_outer;
-    }
-
-    inline Index col() const {
-        return IsRowMajor ? m_outer : index();
-    }
-
-    inline size_t size() const {
-        return m_matrix.m_data.upperProfile(m_outer);
-    }
-
-    inline operator bool() const {
-        return (m_id < m_end) && (m_id >= m_start);
-    }
-
-protected:
-    const SkylineMatrix& m_matrix;
-    const Index m_outer;
-    Index m_id;
-    const Index m_start;
-    const Index m_end;
-};
-
-template<typename Scalar, int _Options>
-class SkylineMatrix<Scalar, _Options>::InnerLowerIterator {
-public:
-
-    InnerLowerIterator(const SkylineMatrix& mat, Index outer)
-    : m_matrix(mat),
-    m_outer(outer),
-    m_id(_Options == RowMajor ? mat.m_rowStartIndex[outer] : mat.m_colStartIndex[outer] + 1),
-    m_start(m_id),
-    m_end(_Options == RowMajor ? mat.m_rowStartIndex[outer + 1] : mat.m_colStartIndex[outer + 1] + 1) {
-    }
-
-    inline InnerLowerIterator & operator++() {
-        m_id++;
-        return *this;
-    }
-
-    inline InnerLowerIterator & operator+=(Index shift) {
-        m_id += shift;
-        return *this;
-    }
-
-    inline Scalar value() const {
-        return m_matrix.m_data.lower(m_id);
-    }
-
-    inline Scalar* valuePtr() {
-        return const_cast<Scalar*> (&(m_matrix.m_data.lower(m_id)));
-    }
-
-    inline Scalar& valueRef() {
-        return const_cast<Scalar&> (m_matrix.m_data.lower(m_id));
-    }
-
-    inline Index index() const {
-        return IsRowMajor ? m_outer - m_matrix.m_data.lowerProfile(m_outer) + (m_id - m_start) :
-                m_outer + (m_id - m_start) + 1;
-        ;
-    }
-
-    inline Index row() const {
-        return IsRowMajor ? m_outer : index();
-    }
-
-    inline Index col() const {
-        return IsRowMajor ? index() : m_outer;
-    }
-
-    inline size_t size() const {
-        return m_matrix.m_data.lowerProfile(m_outer);
-    }
-
-    inline operator bool() const {
-        return (m_id < m_end) && (m_id >= m_start);
-    }
-
-protected:
-    const SkylineMatrix& m_matrix;
-    const Index m_outer;
-    Index m_id;
-    const Index m_start;
-    const Index m_end;
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_SKYLINEMATRIX_H