sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h

@@ -1,152 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
-//
-// 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/.
-
-// This file is a base class plugin containing matrix specifics coefficient wise functions.
-
-/** \returns an expression of the Schur product (coefficient wise product) of *this and \a other
-  *
-  * Example: \include MatrixBase_cwiseProduct.cpp
-  * Output: \verbinclude MatrixBase_cwiseProduct.out
-  *
-  * \sa class CwiseBinaryOp, cwiseAbs2
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const EIGEN_CWISE_BINARY_RETURN_TYPE(Derived,OtherDerived,product)
-cwiseProduct(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return EIGEN_CWISE_BINARY_RETURN_TYPE(Derived,OtherDerived,product)(derived(), other.derived());
-}
-
-/** \returns an expression of the coefficient-wise == operator of *this and \a other
-  *
-  * \warning this performs an exact comparison, which is generally a bad idea with floating-point types.
-  * In order to check for equality between two vectors or matrices with floating-point coefficients, it is
-  * generally a far better idea to use a fuzzy comparison as provided by isApprox() and
-  * isMuchSmallerThan().
-  *
-  * Example: \include MatrixBase_cwiseEqual.cpp
-  * Output: \verbinclude MatrixBase_cwiseEqual.out
-  *
-  * \sa cwiseNotEqual(), isApprox(), isMuchSmallerThan()
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-inline const CwiseBinaryOp<numext::equal_to<Scalar>, const Derived, const OtherDerived>
-cwiseEqual(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return CwiseBinaryOp<numext::equal_to<Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
-}
-
-/** \returns an expression of the coefficient-wise != operator of *this and \a other
-  *
-  * \warning this performs an exact comparison, which is generally a bad idea with floating-point types.
-  * In order to check for equality between two vectors or matrices with floating-point coefficients, it is
-  * generally a far better idea to use a fuzzy comparison as provided by isApprox() and
-  * isMuchSmallerThan().
-  *
-  * Example: \include MatrixBase_cwiseNotEqual.cpp
-  * Output: \verbinclude MatrixBase_cwiseNotEqual.out
-  *
-  * \sa cwiseEqual(), isApprox(), isMuchSmallerThan()
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-inline const CwiseBinaryOp<numext::not_equal_to<Scalar>, const Derived, const OtherDerived>
-cwiseNotEqual(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return CwiseBinaryOp<numext::not_equal_to<Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
-}
-
-/** \returns an expression of the coefficient-wise min of *this and \a other
-  *
-  * Example: \include MatrixBase_cwiseMin.cpp
-  * Output: \verbinclude MatrixBase_cwiseMin.out
-  *
-  * \sa class CwiseBinaryOp, max()
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_min_op<Scalar,Scalar>, const Derived, const OtherDerived>
-cwiseMin(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return CwiseBinaryOp<internal::scalar_min_op<Scalar,Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
-}
-
-/** \returns an expression of the coefficient-wise min of *this and scalar \a other
-  *
-  * \sa class CwiseBinaryOp, min()
-  */
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_min_op<Scalar,Scalar>, const Derived, const ConstantReturnType>
-cwiseMin(const Scalar &other) const
-{
-  return cwiseMin(Derived::Constant(rows(), cols(), other));
-}
-
-/** \returns an expression of the coefficient-wise max of *this and \a other
-  *
-  * Example: \include MatrixBase_cwiseMax.cpp
-  * Output: \verbinclude MatrixBase_cwiseMax.out
-  *
-  * \sa class CwiseBinaryOp, min()
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_max_op<Scalar,Scalar>, const Derived, const OtherDerived>
-cwiseMax(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return CwiseBinaryOp<internal::scalar_max_op<Scalar,Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
-}
-
-/** \returns an expression of the coefficient-wise max of *this and scalar \a other
-  *
-  * \sa class CwiseBinaryOp, min()
-  */
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_max_op<Scalar,Scalar>, const Derived, const ConstantReturnType>
-cwiseMax(const Scalar &other) const
-{
-  return cwiseMax(Derived::Constant(rows(), cols(), other));
-}
-
-
-/** \returns an expression of the coefficient-wise quotient of *this and \a other
-  *
-  * Example: \include MatrixBase_cwiseQuotient.cpp
-  * Output: \verbinclude MatrixBase_cwiseQuotient.out
-  *
-  * \sa class CwiseBinaryOp, cwiseProduct(), cwiseInverse()
-  */
-template<typename OtherDerived>
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_quotient_op<Scalar>, const Derived, const OtherDerived>
-cwiseQuotient(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
-{
-  return CwiseBinaryOp<internal::scalar_quotient_op<Scalar>, const Derived, const OtherDerived>(derived(), other.derived());
-}
-
-typedef CwiseBinaryOp<internal::scalar_cmp_op<Scalar,Scalar,internal::cmp_EQ>, const Derived, const ConstantReturnType> CwiseScalarEqualReturnType;
-
-/** \returns an expression of the coefficient-wise == operator of \c *this and a scalar \a s
-  *
-  * \warning this performs an exact comparison, which is generally a bad idea with floating-point types.
-  * In order to check for equality between two vectors or matrices with floating-point coefficients, it is
-  * generally a far better idea to use a fuzzy comparison as provided by isApprox() and
-  * isMuchSmallerThan().
-  *
-  * \sa cwiseEqual(const MatrixBase<OtherDerived> &) const
-  */
-EIGEN_DEVICE_FUNC
-inline const CwiseScalarEqualReturnType
-cwiseEqual(const Scalar& s) const
-{
-  return CwiseScalarEqualReturnType(derived(), Derived::Constant(rows(), cols(), s), internal::scalar_cmp_op<Scalar,Scalar,internal::cmp_EQ>());
-}

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h

@@ -1,95 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
-//
-// 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/.
-
-// This file is included into the body of the base classes supporting matrix specific coefficient-wise functions.
-// This include MatrixBase and SparseMatrixBase.
-
-
-typedef CwiseUnaryOp<internal::scalar_abs_op<Scalar>, const Derived> CwiseAbsReturnType;
-typedef CwiseUnaryOp<internal::scalar_abs2_op<Scalar>, const Derived> CwiseAbs2ReturnType;
-typedef CwiseUnaryOp<internal::scalar_arg_op<Scalar>, const Derived> CwiseArgReturnType;
-typedef CwiseUnaryOp<internal::scalar_sqrt_op<Scalar>, const Derived> CwiseSqrtReturnType;
-typedef CwiseUnaryOp<internal::scalar_sign_op<Scalar>, const Derived> CwiseSignReturnType;
-typedef CwiseUnaryOp<internal::scalar_inverse_op<Scalar>, const Derived> CwiseInverseReturnType;
-
-/// \returns an expression of the coefficient-wise absolute value of \c *this
-///
-/// Example: \include MatrixBase_cwiseAbs.cpp
-/// Output: \verbinclude MatrixBase_cwiseAbs.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseAbs,absolute value)
-///
-/// \sa cwiseAbs2()
-///
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseAbsReturnType
-cwiseAbs() const { return CwiseAbsReturnType(derived()); }
-
-/// \returns an expression of the coefficient-wise squared absolute value of \c *this
-///
-/// Example: \include MatrixBase_cwiseAbs2.cpp
-/// Output: \verbinclude MatrixBase_cwiseAbs2.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseAbs2,squared absolute value)
-///
-/// \sa cwiseAbs()
-///
-EIGEN_DEVICE_FUNC
-EIGEN_STRONG_INLINE const CwiseAbs2ReturnType
-cwiseAbs2() const { return CwiseAbs2ReturnType(derived()); }
-
-/// \returns an expression of the coefficient-wise square root of *this.
-///
-/// Example: \include MatrixBase_cwiseSqrt.cpp
-/// Output: \verbinclude MatrixBase_cwiseSqrt.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseSqrt,square-root)
-///
-/// \sa cwisePow(), cwiseSquare()
-///
-EIGEN_DEVICE_FUNC
-inline const CwiseSqrtReturnType
-cwiseSqrt() const { return CwiseSqrtReturnType(derived()); }
-
-/// \returns an expression of the coefficient-wise signum of *this.
-///
-/// Example: \include MatrixBase_cwiseSign.cpp
-/// Output: \verbinclude MatrixBase_cwiseSign.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseSign,sign function)
-///
-EIGEN_DEVICE_FUNC
-inline const CwiseSignReturnType
-cwiseSign() const { return CwiseSignReturnType(derived()); }
-
-
-/// \returns an expression of the coefficient-wise inverse of *this.
-///
-/// Example: \include MatrixBase_cwiseInverse.cpp
-/// Output: \verbinclude MatrixBase_cwiseInverse.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseInverse,inverse)
-///
-/// \sa cwiseProduct()
-///
-EIGEN_DEVICE_FUNC
-inline const CwiseInverseReturnType
-cwiseInverse() const { return CwiseInverseReturnType(derived()); }
-
-/// \returns an expression of the coefficient-wise phase angle of \c *this
-///
-/// Example: \include MatrixBase_cwiseArg.cpp
-/// Output: \verbinclude MatrixBase_cwiseArg.out
-///
-EIGEN_DOC_UNARY_ADDONS(cwiseArg,arg)
-
-EIGEN_DEVICE_FUNC
-inline const CwiseArgReturnType
-cwiseArg() const { return CwiseArgReturnType(derived()); }

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h

@@ -1,149 +0,0 @@
-
-#ifdef EIGEN_PARSED_BY_DOXYGEN
-
-/// \returns an expression of \c *this with reshaped sizes.
-///
-/// \param nRows the number of rows in the reshaped expression, specified at either run-time or compile-time, or AutoSize
-/// \param nCols the number of columns in the reshaped expression, specified at either run-time or compile-time, or AutoSize
-/// \tparam Order specifies whether the coefficients should be processed in column-major-order (ColMajor), in row-major-order (RowMajor),
-///               or follows the \em natural order of the nested expression (AutoOrder). The default is ColMajor.
-/// \tparam NRowsType the type of the value handling the number of rows, typically Index.
-/// \tparam NColsType the type of the value handling the number of columns, typically Index.
-///
-/// Dynamic size example: \include MatrixBase_reshaped_int_int.cpp
-/// Output: \verbinclude MatrixBase_reshaped_int_int.out
-///
-/// The number of rows \a nRows and columns \a nCols can also be specified at compile-time by passing Eigen::fix<N>,
-/// or Eigen::fix<N>(n) as arguments. In the later case, \c n plays the role of a runtime fallback value in case \c N equals Eigen::Dynamic.
-/// Here is an example with a fixed number of rows and columns:
-/// \include MatrixBase_reshaped_fixed.cpp
-/// Output: \verbinclude MatrixBase_reshaped_fixed.out
-///
-/// Finally, one of the sizes parameter can be automatically deduced from the other one by passing AutoSize as in the following example:
-/// \include MatrixBase_reshaped_auto.cpp
-/// Output: \verbinclude MatrixBase_reshaped_auto.out
-/// AutoSize does preserve compile-time sizes when possible, i.e., when the sizes of the input are known at compile time \b and
-/// that the other size is passed at compile-time using Eigen::fix<N> as above.
-///
-/// \sa class Reshaped, fix, fix<N>(int)
-///
-template<int Order = ColMajor, typename NRowsType, typename NColsType>
-EIGEN_DEVICE_FUNC
-inline Reshaped<Derived,...>
-reshaped(NRowsType nRows, NColsType nCols);
-
-/// This is the const version of reshaped(NRowsType,NColsType).
-template<int Order = ColMajor, typename NRowsType, typename NColsType>
-EIGEN_DEVICE_FUNC
-inline const Reshaped<const Derived,...>
-reshaped(NRowsType nRows, NColsType nCols) const;
-
-/// \returns an expression of \c *this with columns (or rows) stacked to a linear column vector
-///
-/// \tparam Order specifies whether the coefficients should be processed in column-major-order (ColMajor), in row-major-order (RowMajor),
-///               or follows the \em natural order of the nested expression (AutoOrder). The default is ColMajor.
-///
-/// This overloads is essentially a shortcut for `A.reshaped<Order>(AutoSize,fix<1>)`.
-///
-/// - If `Order==ColMajor` (the default), then it returns a column-vector from the stacked columns of \c *this.
-/// - If `Order==RowMajor`, then it returns a column-vector from the stacked rows of \c *this.
-/// - If `Order==AutoOrder`, then it returns a column-vector with elements stacked following the storage order of \c *this.
-///   This mode is the recommended one when the particular ordering of the element is not relevant.
-///
-/// Example:
-/// \include MatrixBase_reshaped_to_vector.cpp
-/// Output: \verbinclude MatrixBase_reshaped_to_vector.out
-///
-/// If you want more control, you can still fall back to reshaped(NRowsType,NColsType).
-///
-/// \sa reshaped(NRowsType,NColsType), class Reshaped
-///
-template<int Order = ColMajor>
-EIGEN_DEVICE_FUNC
-inline Reshaped<Derived,...>
-reshaped();
-
-/// This is the const version of reshaped().
-template<int Order = ColMajor>
-EIGEN_DEVICE_FUNC
-inline const Reshaped<const Derived,...>
-reshaped() const;
-
-#else
-
-// This file is automatically included twice to generate const and non-const versions
-
-#ifndef EIGEN_RESHAPED_METHOD_2ND_PASS
-#define EIGEN_RESHAPED_METHOD_CONST const
-#else
-#define EIGEN_RESHAPED_METHOD_CONST
-#endif
-
-#ifndef EIGEN_RESHAPED_METHOD_2ND_PASS
-
-// This part is included once
-
-#endif
-
-template<typename NRowsType, typename NColsType>
-EIGEN_DEVICE_FUNC
-inline Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,
-                internal::get_compiletime_reshape_size<NRowsType,NColsType,SizeAtCompileTime>::value,
-                internal::get_compiletime_reshape_size<NColsType,NRowsType,SizeAtCompileTime>::value>
-reshaped(NRowsType nRows, NColsType nCols) EIGEN_RESHAPED_METHOD_CONST
-{
-  return Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,
-                  internal::get_compiletime_reshape_size<NRowsType,NColsType,SizeAtCompileTime>::value,
-                  internal::get_compiletime_reshape_size<NColsType,NRowsType,SizeAtCompileTime>::value>
-                (derived(),
-                 internal::get_runtime_reshape_size(nRows,internal::get_runtime_value(nCols),size()),
-                 internal::get_runtime_reshape_size(nCols,internal::get_runtime_value(nRows),size()));
-}
-
-template<int Order, typename NRowsType, typename NColsType>
-EIGEN_DEVICE_FUNC
-inline Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,
-                internal::get_compiletime_reshape_size<NRowsType,NColsType,SizeAtCompileTime>::value,
-                internal::get_compiletime_reshape_size<NColsType,NRowsType,SizeAtCompileTime>::value,
-                internal::get_compiletime_reshape_order<Flags,Order>::value>
-reshaped(NRowsType nRows, NColsType nCols) EIGEN_RESHAPED_METHOD_CONST
-{
-  return Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,
-                  internal::get_compiletime_reshape_size<NRowsType,NColsType,SizeAtCompileTime>::value,
-                  internal::get_compiletime_reshape_size<NColsType,NRowsType,SizeAtCompileTime>::value,
-                  internal::get_compiletime_reshape_order<Flags,Order>::value>
-                (derived(),
-                 internal::get_runtime_reshape_size(nRows,internal::get_runtime_value(nCols),size()),
-                 internal::get_runtime_reshape_size(nCols,internal::get_runtime_value(nRows),size()));
-}
-
-// Views as linear vectors
-
-EIGEN_DEVICE_FUNC
-inline Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,SizeAtCompileTime,1>
-reshaped() EIGEN_RESHAPED_METHOD_CONST
-{
-  return Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived,SizeAtCompileTime,1>(derived(),size(),1);
-}
-
-template<int Order>
-EIGEN_DEVICE_FUNC
-inline Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived, SizeAtCompileTime, 1,
-                internal::get_compiletime_reshape_order<Flags,Order>::value>
-reshaped() EIGEN_RESHAPED_METHOD_CONST
-{
-  EIGEN_STATIC_ASSERT(Order==RowMajor || Order==ColMajor || Order==AutoOrder, INVALID_TEMPLATE_PARAMETER);
-  return Reshaped<EIGEN_RESHAPED_METHOD_CONST Derived, SizeAtCompileTime, 1,
-                  internal::get_compiletime_reshape_order<Flags,Order>::value>
-                (derived(), size(), 1);
-}
-
-#undef EIGEN_RESHAPED_METHOD_CONST
-
-#ifndef EIGEN_RESHAPED_METHOD_2ND_PASS
-#define EIGEN_RESHAPED_METHOD_2ND_PASS
-#include "ReshapedMethods.h"
-#undef EIGEN_RESHAPED_METHOD_2ND_PASS
-#endif
-
-#endif // EIGEN_PARSED_BY_DOXYGEN

sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h

@@ -1,97 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2011 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_BAND_TRIANGULARSOLVER_H
-#define EIGEN_BAND_TRIANGULARSOLVER_H
-
-namespace internal {
-
- /* \internal
-  * Solve Ax=b with A a band triangular matrix
-  * TODO: extend it to matrices for x abd b */
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar, int StorageOrder>
-struct band_solve_triangular_selector;
-
-
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar>
-struct band_solve_triangular_selector<Index,Mode,LhsScalar,ConjLhs,RhsScalar,RowMajor>
-{
-  typedef Map<const Matrix<LhsScalar,Dynamic,Dynamic,RowMajor>, 0, OuterStride<> > LhsMap;
-  typedef Map<Matrix<RhsScalar,Dynamic,1> > RhsMap;
-  enum { IsLower = (Mode&Lower) ? 1 : 0 };
-  static void run(Index size, Index k, const LhsScalar* _lhs, Index lhsStride, RhsScalar* _other)
-  {
-    const LhsMap lhs(_lhs,size,k+1,OuterStride<>(lhsStride));
-    RhsMap other(_other,size,1);
-    typename internal::conditional<
-                          ConjLhs,
-                          const CwiseUnaryOp<typename internal::scalar_conjugate_op<LhsScalar>,LhsMap>,
-                          const LhsMap&>
-                        ::type cjLhs(lhs);
-                        
-    for(int col=0 ; col<other.cols() ; ++col)
-    {
-      for(int ii=0; ii<size; ++ii)
-      {
-        int i = IsLower ? ii : size-ii-1;
-        int actual_k = (std::min)(k,ii);
-        int actual_start = IsLower ? k-actual_k : 1;
-        
-        if(actual_k>0)
-          other.coeffRef(i,col) -= cjLhs.row(i).segment(actual_start,actual_k).transpose()
-                                  .cwiseProduct(other.col(col).segment(IsLower ? i-actual_k : i+1,actual_k)).sum();
-
-        if((Mode&UnitDiag)==0)
-          other.coeffRef(i,col) /= cjLhs(i,IsLower ? k : 0);
-      }
-    }
-  }
-  
-};
-
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar>
-struct band_solve_triangular_selector<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ColMajor>
-{
-  typedef Map<const Matrix<LhsScalar,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> > LhsMap;
-  typedef Map<Matrix<RhsScalar,Dynamic,1> > RhsMap;
-  enum { IsLower = (Mode&Lower) ? 1 : 0 };
-  static void run(Index size, Index k, const LhsScalar* _lhs, Index lhsStride, RhsScalar* _other)
-  {
-    const LhsMap lhs(_lhs,k+1,size,OuterStride<>(lhsStride));
-    RhsMap other(_other,size,1);
-    typename internal::conditional<
-                          ConjLhs,
-                          const CwiseUnaryOp<typename internal::scalar_conjugate_op<LhsScalar>,LhsMap>,
-                          const LhsMap&>
-                        ::type cjLhs(lhs);
-                        
-    for(int col=0 ; col<other.cols() ; ++col)
-    {
-      for(int ii=0; ii<size; ++ii)
-      {
-        int i = IsLower ? ii : size-ii-1;
-        int actual_k = (std::min)(k,size-ii-1);
-        int actual_start = IsLower ? 1 : k-actual_k;
-        
-        if((Mode&UnitDiag)==0)
-          other.coeffRef(i,col) /= cjLhs(IsLower ? 0 : k, i);
-
-        if(actual_k>0)
-          other.col(col).segment(IsLower ? i+1 : i-actual_k, actual_k)
-              -= other.coeff(i,col) * cjLhs.col(i).segment(actual_start,actual_k);
-        
-      }
-    }
-  }
-};
-
-
-} // end namespace internal
-
-#endif // EIGEN_BAND_TRIANGULARSOLVER_H

sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h

@@ -1,44 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Chen-Pang He <jdh8@ms63.hinet.net>
-//
-// 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_GENERAL_RANK1UPDATE_H
-#define EIGEN_GENERAL_RANK1UPDATE_H
-
-namespace internal {
-
-/* Optimized matrix += alpha * uv' */
-template<typename Scalar, typename Index, int StorageOrder, bool ConjLhs, bool ConjRhs>
-struct general_rank1_update;
-
-template<typename Scalar, typename Index, bool ConjLhs, bool ConjRhs>
-struct general_rank1_update<Scalar,Index,ColMajor,ConjLhs,ConjRhs>
-{
-  static void run(Index rows, Index cols, Scalar* mat, Index stride, const Scalar* u, const Scalar* v, Scalar alpha)
-  {
-    typedef Map<const Matrix<Scalar,Dynamic,1> > OtherMap;
-    typedef typename conj_expr_if<ConjLhs,OtherMap>::type ConjRhsType;
-    conj_if<ConjRhs> cj;
-
-    for (Index i=0; i<cols; ++i)
-      Map<Matrix<Scalar,Dynamic,1> >(mat+stride*i,rows) += alpha * cj(v[i]) * ConjRhsType(OtherMap(u,rows));
-  }
-};
-
-template<typename Scalar, typename Index, bool ConjLhs, bool ConjRhs>
-struct general_rank1_update<Scalar,Index,RowMajor,ConjLhs,ConjRhs>
-{
-  static void run(Index rows, Index cols, Scalar* mat, Index stride, const Scalar* u, const Scalar* v, Scalar alpha)
-  {
-    general_rank1_update<Scalar,Index,ColMajor,ConjRhs,ConjRhs>::run(rows,cols,mat,stride,u,v,alpha);
-  }
-};
-
-} // end namespace internal
-
-#endif // EIGEN_GENERAL_RANK1UPDATE_H

sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h

@@ -1,53 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Chen-Pang He <jdh8@ms63.hinet.net>
-//
-// 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_SELFADJOINT_PACKED_PRODUCT_H
-#define EIGEN_SELFADJOINT_PACKED_PRODUCT_H
-
-namespace internal {
-
-/* Optimized matrix += alpha * uv'
- * The matrix is in packed form.
- */
-template<typename Scalar, typename Index, int StorageOrder, int UpLo, bool ConjLhs, bool ConjRhs>
-struct selfadjoint_packed_rank1_update;
-
-template<typename Scalar, typename Index, int UpLo, bool ConjLhs, bool ConjRhs>
-struct selfadjoint_packed_rank1_update<Scalar,Index,ColMajor,UpLo,ConjLhs,ConjRhs>
-{
-  typedef typename NumTraits<Scalar>::Real RealScalar;
-  static void run(Index size, Scalar* mat, const Scalar* vec, RealScalar alpha)
-  {
-    typedef Map<const Matrix<Scalar,Dynamic,1> > OtherMap;
-    typedef typename conj_expr_if<ConjLhs,OtherMap>::type ConjRhsType;
-    conj_if<ConjRhs> cj;
-
-    for (Index i=0; i<size; ++i)
-    {
-      Map<Matrix<Scalar,Dynamic,1> >(mat, UpLo==Lower ? size-i : (i+1)) += alpha * cj(vec[i]) * ConjRhsType(OtherMap(vec+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1)));
-      //FIXME This should be handled outside.
-      mat[UpLo==Lower ? 0 : i] = numext::real(mat[UpLo==Lower ? 0 : i]);
-      mat += UpLo==Lower ? size-i : (i+1);
-    }
-  }
-};
-
-template<typename Scalar, typename Index, int UpLo, bool ConjLhs, bool ConjRhs>
-struct selfadjoint_packed_rank1_update<Scalar,Index,RowMajor,UpLo,ConjLhs,ConjRhs>
-{
-  typedef typename NumTraits<Scalar>::Real RealScalar;
-  static void run(Index size, Scalar* mat, const Scalar* vec, RealScalar alpha)
-  {
-    selfadjoint_packed_rank1_update<Scalar,Index,ColMajor,UpLo==Lower?Upper:Lower,ConjRhs,ConjLhs>::run(size,mat,vec,alpha);
-  }
-};
-
-} // end namespace internal
-
-#endif // EIGEN_SELFADJOINT_PACKED_PRODUCT_H

sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h

@@ -1,79 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Chen-Pang He <jdh8@ms63.hinet.net>
-//
-// 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_PACKED_TRIANGULAR_MATRIX_VECTOR_H
-#define EIGEN_PACKED_TRIANGULAR_MATRIX_VECTOR_H
-
-namespace internal {
-
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar, bool ConjRhs, int StorageOrder>
-struct packed_triangular_matrix_vector_product;
-
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar, bool ConjRhs>
-struct packed_triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,ColMajor>
-{
-  typedef typename ScalarBinaryOpTraits<LhsScalar, RhsScalar>::ReturnType ResScalar;
-  enum {
-    IsLower     = (Mode & Lower)   ==Lower,
-    HasUnitDiag = (Mode & UnitDiag)==UnitDiag,
-    HasZeroDiag = (Mode & ZeroDiag)==ZeroDiag
-  };
-  static void run(Index size, const LhsScalar* lhs, const RhsScalar* rhs, ResScalar* res, ResScalar alpha)
-  {
-    internal::conj_if<ConjRhs> cj;
-    typedef Map<const Matrix<LhsScalar,Dynamic,1> > LhsMap;
-    typedef typename conj_expr_if<ConjLhs,LhsMap>::type ConjLhsType;
-    typedef Map<Matrix<ResScalar,Dynamic,1> > ResMap;
-
-    for (Index i=0; i<size; ++i)
-    {
-      Index s = IsLower&&(HasUnitDiag||HasZeroDiag) ? 1 : 0;
-      Index r = IsLower ? size-i: i+1;
-      if (EIGEN_IMPLIES(HasUnitDiag||HasZeroDiag, (--r)>0))
-	ResMap(res+(IsLower ? s+i : 0),r) += alpha * cj(rhs[i]) * ConjLhsType(LhsMap(lhs+s,r));
-      if (HasUnitDiag)
-	res[i] += alpha * cj(rhs[i]);
-      lhs += IsLower ? size-i: i+1;
-    }
-  };
-};
-
-template<typename Index, int Mode, typename LhsScalar, bool ConjLhs, typename RhsScalar, bool ConjRhs>
-struct packed_triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor>
-{
-  typedef typename ScalarBinaryOpTraits<LhsScalar, RhsScalar>::ReturnType ResScalar;
-  enum {
-    IsLower     = (Mode & Lower)   ==Lower,
-    HasUnitDiag = (Mode & UnitDiag)==UnitDiag,
-    HasZeroDiag = (Mode & ZeroDiag)==ZeroDiag
-  };
-  static void run(Index size, const LhsScalar* lhs, const RhsScalar* rhs, ResScalar* res, ResScalar alpha)
-  {
-    internal::conj_if<ConjRhs> cj;
-    typedef Map<const Matrix<LhsScalar,Dynamic,1> > LhsMap;
-    typedef typename conj_expr_if<ConjLhs,LhsMap>::type ConjLhsType;
-    typedef Map<const Matrix<RhsScalar,Dynamic,1> > RhsMap;
-    typedef typename conj_expr_if<ConjRhs,RhsMap>::type ConjRhsType;
-
-    for (Index i=0; i<size; ++i)
-    {
-      Index s = !IsLower&&(HasUnitDiag||HasZeroDiag) ? 1 : 0;
-      Index r = IsLower ? i+1 : size-i;
-      if (EIGEN_IMPLIES(HasUnitDiag||HasZeroDiag, (--r)>0))
-	res[i] += alpha * (ConjLhsType(LhsMap(lhs+s,r)).cwiseProduct(ConjRhsType(RhsMap(rhs+(IsLower ? 0 : s+i),r)))).sum();
-      if (HasUnitDiag)
-	res[i] += alpha * cj(rhs[i]);
-      lhs += IsLower ? i+1 : size-i;
-    }
-  };
-};
-
-} // end namespace internal
-
-#endif // EIGEN_PACKED_TRIANGULAR_MATRIX_VECTOR_H