sequenzo 0.1.18__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h

@@ -1,274 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.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_COMPRESSED_STORAGE_H
-#define EIGEN_COMPRESSED_STORAGE_H
-
-namespace Eigen { 
-
-namespace internal {
-
-/** \internal
-  * Stores a sparse set of values as a list of values and a list of indices.
-  *
-  */
-template<typename _Scalar,typename _StorageIndex>
-class CompressedStorage
-{
-  public:
-
-    typedef _Scalar Scalar;
-    typedef _StorageIndex StorageIndex;
-
-  protected:
-
-    typedef typename NumTraits<Scalar>::Real RealScalar;
-
-  public:
-
-    CompressedStorage()
-      : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
-    {}
-
-    explicit CompressedStorage(Index size)
-      : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
-    {
-      resize(size);
-    }
-
-    CompressedStorage(const CompressedStorage& other)
-      : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
-    {
-      *this = other;
-    }
-
-    CompressedStorage& operator=(const CompressedStorage& other)
-    {
-      resize(other.size());
-      if(other.size()>0)
-      {
-        internal::smart_copy(other.m_values,  other.m_values  + m_size, m_values);
-        internal::smart_copy(other.m_indices, other.m_indices + m_size, m_indices);
-      }
-      return *this;
-    }
-
-    void swap(CompressedStorage& other)
-    {
-      std::swap(m_values, other.m_values);
-      std::swap(m_indices, other.m_indices);
-      std::swap(m_size, other.m_size);
-      std::swap(m_allocatedSize, other.m_allocatedSize);
-    }
-
-    ~CompressedStorage()
-    {
-      delete[] m_values;
-      delete[] m_indices;
-    }
-
-    void reserve(Index size)
-    {
-      Index newAllocatedSize = m_size + size;
-      if (newAllocatedSize > m_allocatedSize)
-        reallocate(newAllocatedSize);
-    }
-
-    void squeeze()
-    {
-      if (m_allocatedSize>m_size)
-        reallocate(m_size);
-    }
-
-    void resize(Index size, double reserveSizeFactor = 0)
-    {
-      if (m_allocatedSize<size)
-      {
-        Index realloc_size = (std::min<Index>)(NumTraits<StorageIndex>::highest(),  size + Index(reserveSizeFactor*double(size)));
-        if(realloc_size<size)
-          internal::throw_std_bad_alloc();
-        reallocate(realloc_size);
-      }
-      m_size = size;
-    }
-
-    void append(const Scalar& v, Index i)
-    {
-      Index id = m_size;
-      resize(m_size+1, 1);
-      m_values[id] = v;
-      m_indices[id] = internal::convert_index<StorageIndex>(i);
-    }
-
-    inline Index size() const { return m_size; }
-    inline Index allocatedSize() const { return m_allocatedSize; }
-    inline void clear() { m_size = 0; }
-
-    const Scalar* valuePtr() const { return m_values; }
-    Scalar* valuePtr() { return m_values; }
-    const StorageIndex* indexPtr() const { return m_indices; }
-    StorageIndex* indexPtr() { return m_indices; }
-
-    inline Scalar& value(Index i) { eigen_internal_assert(m_values!=0); return m_values[i]; }
-    inline const Scalar& value(Index i) const { eigen_internal_assert(m_values!=0); return m_values[i]; }
-
-    inline StorageIndex& index(Index i) { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
-    inline const StorageIndex& index(Index i) const { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
-
-    /** \returns the largest \c k such that for all \c j in [0,k) index[\c j]\<\a key */
-    inline Index searchLowerIndex(Index key) const
-    {
-      return searchLowerIndex(0, m_size, key);
-    }
-
-    /** \returns the largest \c k in [start,end) such that for all \c j in [start,k) index[\c j]\<\a key */
-    inline Index searchLowerIndex(Index start, Index end, Index key) const
-    {
-      while(end>start)
-      {
-        Index mid = (end+start)>>1;
-        if (m_indices[mid]<key)
-          start = mid+1;
-        else
-          end = mid;
-      }
-      return start;
-    }
-
-    /** \returns the stored value at index \a key
-      * If the value does not exist, then the value \a defaultValue is returned without any insertion. */
-    inline Scalar at(Index key, const Scalar& defaultValue = Scalar(0)) const
-    {
-      if (m_size==0)
-        return defaultValue;
-      else if (key==m_indices[m_size-1])
-        return m_values[m_size-1];
-      // ^^  optimization: let's first check if it is the last coefficient
-      // (very common in high level algorithms)
-      const Index id = searchLowerIndex(0,m_size-1,key);
-      return ((id<m_size) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
-    }
-
-    /** Like at(), but the search is performed in the range [start,end) */
-    inline Scalar atInRange(Index start, Index end, Index key, const Scalar &defaultValue = Scalar(0)) const
-    {
-      if (start>=end)
-        return defaultValue;
-      else if (end>start && key==m_indices[end-1])
-        return m_values[end-1];
-      // ^^  optimization: let's first check if it is the last coefficient
-      // (very common in high level algorithms)
-      const Index id = searchLowerIndex(start,end-1,key);
-      return ((id<end) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
-    }
-
-    /** \returns a reference to the value at index \a key
-      * If the value does not exist, then the value \a defaultValue is inserted
-      * such that the keys are sorted. */
-    inline Scalar& atWithInsertion(Index key, const Scalar& defaultValue = Scalar(0))
-    {
-      Index id = searchLowerIndex(0,m_size,key);
-      if (id>=m_size || m_indices[id]!=key)
-      {
-        if (m_allocatedSize<m_size+1)
-        {
-          m_allocatedSize = 2*(m_size+1);
-          internal::scoped_array<Scalar> newValues(m_allocatedSize);
-          internal::scoped_array<StorageIndex> newIndices(m_allocatedSize);
-
-          // copy first chunk
-          internal::smart_copy(m_values,  m_values +id, newValues.ptr());
-          internal::smart_copy(m_indices, m_indices+id, newIndices.ptr());
-
-          // copy the rest
-          if(m_size>id)
-          {
-            internal::smart_copy(m_values +id,  m_values +m_size, newValues.ptr() +id+1);
-            internal::smart_copy(m_indices+id,  m_indices+m_size, newIndices.ptr()+id+1);
-          }
-          std::swap(m_values,newValues.ptr());
-          std::swap(m_indices,newIndices.ptr());
-        }
-        else if(m_size>id)
-        {
-          internal::smart_memmove(m_values +id, m_values +m_size, m_values +id+1);
-          internal::smart_memmove(m_indices+id, m_indices+m_size, m_indices+id+1);
-        }
-        m_size++;
-        m_indices[id] = internal::convert_index<StorageIndex>(key);
-        m_values[id] = defaultValue;
-      }
-      return m_values[id];
-    }
-
-    void moveChunk(Index from, Index to, Index chunkSize)
-    {
-      eigen_internal_assert(to+chunkSize <= m_size);
-      if(to>from && from+chunkSize>to)
-      {
-        // move backward
-        internal::smart_memmove(m_values+from,  m_values+from+chunkSize,  m_values+to);
-        internal::smart_memmove(m_indices+from, m_indices+from+chunkSize, m_indices+to);
-      }
-      else
-      {
-        internal::smart_copy(m_values+from,  m_values+from+chunkSize,  m_values+to);
-        internal::smart_copy(m_indices+from, m_indices+from+chunkSize, m_indices+to);
-      }
-    }
-
-    void prune(const Scalar& reference, const RealScalar& epsilon = NumTraits<RealScalar>::dummy_precision())
-    {
-      Index k = 0;
-      Index n = size();
-      for (Index i=0; i<n; ++i)
-      {
-        if (!internal::isMuchSmallerThan(value(i), reference, epsilon))
-        {
-          value(k) = value(i);
-          index(k) = index(i);
-          ++k;
-        }
-      }
-      resize(k,0);
-    }
-
-  protected:
-
-    inline void reallocate(Index size)
-    {
-      #ifdef EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
-        EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
-      #endif
-      eigen_internal_assert(size!=m_allocatedSize);
-      internal::scoped_array<Scalar> newValues(size);
-      internal::scoped_array<StorageIndex> newIndices(size);
-      Index copySize = (std::min)(size, m_size);
-      if (copySize>0) {
-        internal::smart_copy(m_values, m_values+copySize, newValues.ptr());
-        internal::smart_copy(m_indices, m_indices+copySize, newIndices.ptr());
-      }
-      std::swap(m_values,newValues.ptr());
-      std::swap(m_indices,newIndices.ptr());
-      m_allocatedSize = size;
-    }
-
-  protected:
-    Scalar* m_values;
-    StorageIndex* m_indices;
-    Index m_size;
-    Index m_allocatedSize;
-
-};
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_COMPRESSED_STORAGE_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h

@@ -1,352 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.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_CONSERVATIVESPARSESPARSEPRODUCT_H
-#define EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H
-
-namespace Eigen {
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, typename ResultType>
-static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false)
-{
-  typedef typename remove_all<Lhs>::type::Scalar LhsScalar;
-  typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
-  typedef typename remove_all<ResultType>::type::Scalar ResScalar;
-
-  // make sure to call innerSize/outerSize since we fake the storage order.
-  Index rows = lhs.innerSize();
-  Index cols = rhs.outerSize();
-  eigen_assert(lhs.outerSize() == rhs.innerSize());
-
-  ei_declare_aligned_stack_constructed_variable(bool,   mask,     rows, 0);
-  ei_declare_aligned_stack_constructed_variable(ResScalar, values,   rows, 0);
-  ei_declare_aligned_stack_constructed_variable(Index,  indices,  rows, 0);
-
-  std::memset(mask,0,sizeof(bool)*rows);
-
-  evaluator<Lhs> lhsEval(lhs);
-  evaluator<Rhs> rhsEval(rhs);
-
-  // estimate the number of non zero entries
-  // given a rhs column containing Y non zeros, we assume that the respective Y columns
-  // of the lhs differs in average of one non zeros, thus the number of non zeros for
-  // the product of a rhs column with the lhs is X+Y where X is the average number of non zero
-  // per column of the lhs.
-  // Therefore, we have nnz(lhs*rhs) = nnz(lhs) + nnz(rhs)
-  Index estimated_nnz_prod = lhsEval.nonZerosEstimate() + rhsEval.nonZerosEstimate();
-
-  res.setZero();
-  res.reserve(Index(estimated_nnz_prod));
-  // we compute each column of the result, one after the other
-  for (Index j=0; j<cols; ++j)
-  {
-
-    res.startVec(j);
-    Index nnz = 0;
-    for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
-    {
-      RhsScalar y = rhsIt.value();
-      Index k = rhsIt.index();
-      for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, k); lhsIt; ++lhsIt)
-      {
-        Index i = lhsIt.index();
-        LhsScalar x = lhsIt.value();
-        if(!mask[i])
-        {
-          mask[i] = true;
-          values[i] = x * y;
-          indices[nnz] = i;
-          ++nnz;
-        }
-        else
-          values[i] += x * y;
-      }
-    }
-    if(!sortedInsertion)
-    {
-      // unordered insertion
-      for(Index k=0; k<nnz; ++k)
-      {
-        Index i = indices[k];
-        res.insertBackByOuterInnerUnordered(j,i) = values[i];
-        mask[i] = false;
-      }
-    }
-    else
-    {
-      // alternative ordered insertion code:
-      const Index t200 = rows/11; // 11 == (log2(200)*1.39)
-      const Index t = (rows*100)/139;
-
-      // FIXME reserve nnz non zeros
-      // FIXME implement faster sorting algorithms for very small nnz
-      // if the result is sparse enough => use a quick sort
-      // otherwise => loop through the entire vector
-      // In order to avoid to perform an expensive log2 when the
-      // result is clearly very sparse we use a linear bound up to 200.
-      if((nnz<200 && nnz<t200) || nnz * numext::log2(int(nnz)) < t)
-      {
-        if(nnz>1) std::sort(indices,indices+nnz);
-        for(Index k=0; k<nnz; ++k)
-        {
-          Index i = indices[k];
-          res.insertBackByOuterInner(j,i) = values[i];
-          mask[i] = false;
-        }
-      }
-      else
-      {
-        // dense path
-        for(Index i=0; i<rows; ++i)
-        {
-          if(mask[i])
-          {
-            mask[i] = false;
-            res.insertBackByOuterInner(j,i) = values[i];
-          }
-        }
-      }
-    }
-  }
-  res.finalize();
-}
-
-
-} // end namespace internal
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, typename ResultType,
-  int LhsStorageOrder = (traits<Lhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
-  int RhsStorageOrder = (traits<Rhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
-  int ResStorageOrder = (traits<ResultType>::Flags&RowMajorBit) ? RowMajor : ColMajor>
-struct conservative_sparse_sparse_product_selector;
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,ColMajor>
-{
-  typedef typename remove_all<Lhs>::type LhsCleaned;
-  typedef typename LhsCleaned::Scalar Scalar;
-
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
-    typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrixAux;
-    typedef typename sparse_eval<ColMajorMatrixAux,ResultType::RowsAtCompileTime,ResultType::ColsAtCompileTime,ColMajorMatrixAux::Flags>::type ColMajorMatrix;
-
-    // If the result is tall and thin (in the extreme case a column vector)
-    // then it is faster to sort the coefficients inplace instead of transposing twice.
-    // FIXME, the following heuristic is probably not very good.
-    if(lhs.rows()>rhs.cols())
-    {
-      ColMajorMatrix resCol(lhs.rows(),rhs.cols());
-      // perform sorted insertion
-      internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrix>(lhs, rhs, resCol, true);
-      res = resCol.markAsRValue();
-    }
-    else
-    {
-      ColMajorMatrixAux resCol(lhs.rows(),rhs.cols());
-      // resort to transpose to sort the entries
-      internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrixAux>(lhs, rhs, resCol, false);
-      RowMajorMatrix resRow(resCol);
-      res = resRow.markAsRValue();
-    }
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,ColMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Rhs::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRhs;
-    typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRes;
-    RowMajorRhs rhsRow = rhs;
-    RowMajorRes resRow(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<RowMajorRhs,Lhs,RowMajorRes>(rhsRow, lhs, resRow);
-    res = resRow;
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,ColMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Lhs::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorLhs;
-    typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRes;
-    RowMajorLhs lhsRow = lhs;
-    RowMajorRes resRow(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<Rhs,RowMajorLhs,RowMajorRes>(rhs, lhsRow, resRow);
-    res = resRow;
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,ColMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
-    RowMajorMatrix resRow(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<Rhs,Lhs,RowMajorMatrix>(rhs, lhs, resRow);
-    res = resRow;
-  }
-};
-
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,RowMajor>
-{
-  typedef typename traits<typename remove_all<Lhs>::type>::Scalar Scalar;
-
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrix;
-    ColMajorMatrix resCol(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrix>(lhs, rhs, resCol);
-    res = resCol;
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,RowMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorLhs;
-    typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRes;
-    ColMajorLhs lhsCol = lhs;
-    ColMajorRes resCol(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<ColMajorLhs,Rhs,ColMajorRes>(lhsCol, rhs, resCol);
-    res = resCol;
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,RowMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRhs;
-    typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRes;
-    ColMajorRhs rhsCol = rhs;
-    ColMajorRes resCol(lhs.rows(), rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<Lhs,ColMajorRhs,ColMajorRes>(lhs, rhsCol, resCol);
-    res = resCol;
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,RowMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
-    typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrix;
-    RowMajorMatrix resRow(lhs.rows(),rhs.cols());
-    internal::conservative_sparse_sparse_product_impl<Rhs,Lhs,RowMajorMatrix>(rhs, lhs, resRow);
-    // sort the non zeros:
-    ColMajorMatrix resCol(resRow);
-    res = resCol;
-  }
-};
-
-} // end namespace internal
-
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, typename ResultType>
-static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-{
-  typedef typename remove_all<Lhs>::type::Scalar LhsScalar;
-  typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
-  Index cols = rhs.outerSize();
-  eigen_assert(lhs.outerSize() == rhs.innerSize());
-
-  evaluator<Lhs> lhsEval(lhs);
-  evaluator<Rhs> rhsEval(rhs);
-
-  for (Index j=0; j<cols; ++j)
-  {
-    for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
-    {
-      RhsScalar y = rhsIt.value();
-      Index k = rhsIt.index();
-      for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, k); lhsIt; ++lhsIt)
-      {
-        Index i = lhsIt.index();
-        LhsScalar x = lhsIt.value();
-        res.coeffRef(i,j) += x * y;
-      }
-    }
-  }
-}
-
-
-} // end namespace internal
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, typename ResultType,
-  int LhsStorageOrder = (traits<Lhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
-  int RhsStorageOrder = (traits<Rhs>::Flags&RowMajorBit) ? RowMajor : ColMajor>
-struct sparse_sparse_to_dense_product_selector;
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    internal::sparse_sparse_to_dense_product_impl<Lhs,Rhs,ResultType>(lhs, rhs, res);
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorLhs;
-    ColMajorLhs lhsCol(lhs);
-    internal::sparse_sparse_to_dense_product_impl<ColMajorLhs,Rhs,ResultType>(lhsCol, rhs, res);
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRhs;
-    ColMajorRhs rhsCol(rhs);
-    internal::sparse_sparse_to_dense_product_impl<Lhs,ColMajorRhs,ResultType>(lhs, rhsCol, res);
-  }
-};
-
-template<typename Lhs, typename Rhs, typename ResultType>
-struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor>
-{
-  static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
-  {
-    Transpose<ResultType> trRes(res);
-    internal::sparse_sparse_to_dense_product_impl<Rhs,Lhs,Transpose<ResultType> >(rhs, lhs, trRes);
-  }
-};
-
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h

@@ -1,67 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.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_MAPPED_SPARSEMATRIX_H
-#define EIGEN_MAPPED_SPARSEMATRIX_H
-
-namespace Eigen {
-
-/** \deprecated Use Map<SparseMatrix<> >
-  * \class MappedSparseMatrix
-  *
-  * \brief Sparse matrix
-  *
-  * \param _Scalar the scalar type, i.e. the type of the coefficients
-  *
-  * See http://www.netlib.org/linalg/html_templates/node91.html for details on the storage scheme.
-  *
-  */
-namespace internal {
-template<typename _Scalar, int _Flags, typename _StorageIndex>
-struct traits<MappedSparseMatrix<_Scalar, _Flags, _StorageIndex> > : traits<SparseMatrix<_Scalar, _Flags, _StorageIndex> >
-{};
-} // end namespace internal
-
-template<typename _Scalar, int _Flags, typename _StorageIndex>
-class MappedSparseMatrix
-  : public Map<SparseMatrix<_Scalar, _Flags, _StorageIndex> >
-{
-    typedef Map<SparseMatrix<_Scalar, _Flags, _StorageIndex> > Base;
-
-  public:
-    
-    typedef typename Base::StorageIndex StorageIndex;
-    typedef typename Base::Scalar Scalar;
-
-    inline MappedSparseMatrix(Index rows, Index cols, Index nnz, StorageIndex* outerIndexPtr, StorageIndex* innerIndexPtr, Scalar* valuePtr, StorageIndex* innerNonZeroPtr = 0)
-      : Base(rows, cols, nnz, outerIndexPtr, innerIndexPtr, valuePtr, innerNonZeroPtr)
-    {}
-
-    /** Empty destructor */
-    inline ~MappedSparseMatrix() {}
-};
-
-namespace internal {
-
-template<typename _Scalar, int _Options, typename _StorageIndex>
-struct evaluator<MappedSparseMatrix<_Scalar,_Options,_StorageIndex> >
-  : evaluator<SparseCompressedBase<MappedSparseMatrix<_Scalar,_Options,_StorageIndex> > >
-{
-  typedef MappedSparseMatrix<_Scalar,_Options,_StorageIndex> XprType;
-  typedef evaluator<SparseCompressedBase<XprType> > Base;
-  
-  evaluator() : Base() {}
-  explicit evaluator(const XprType &mat) : Base(mat) {}
-};
-
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_MAPPED_SPARSEMATRIX_H