sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-win_amd64.whl

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

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

@@ -1,88 +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_SOLVER_VECTOR_H
-#define EIGEN_PACKED_TRIANGULAR_SOLVER_VECTOR_H
-
-namespace internal {
-
-template<typename LhsScalar, typename RhsScalar, typename Index, int Side, int Mode, bool Conjugate, int StorageOrder>
-struct packed_triangular_solve_vector;
-
-// forward and backward substitution, row-major, rhs is a vector
-template<typename LhsScalar, typename RhsScalar, typename Index, int Mode, bool Conjugate>
-struct packed_triangular_solve_vector<LhsScalar, RhsScalar, Index, OnTheLeft, Mode, Conjugate, RowMajor>
-{
-  enum {
-    IsLower = (Mode&Lower)==Lower
-  };
-  static void run(Index size, const LhsScalar* lhs, RhsScalar* rhs)
-  {
-    internal::conj_if<Conjugate> cj;
-    typedef Map<const Matrix<LhsScalar,Dynamic,1> > LhsMap;
-    typedef typename conj_expr_if<Conjugate,LhsMap>::type ConjLhsType;
-
-    lhs += IsLower ? 0 : (size*(size+1)>>1)-1;
-    for(Index pi=0; pi<size; ++pi)
-    {
-      Index i = IsLower ? pi : size-pi-1;
-      Index s = IsLower ? 0 : 1;
-      if (pi>0)
-	rhs[i] -= (ConjLhsType(LhsMap(lhs+s,pi))
-	    .cwiseProduct(Map<const Matrix<RhsScalar,Dynamic,1> >(rhs+(IsLower ? 0 : i+1),pi))).sum();
-      if (!(Mode & UnitDiag))
-	rhs[i] /= cj(lhs[IsLower ? i : 0]);
-      IsLower ? lhs += pi+1 : lhs -= pi+2;
-    }
-  }
-};
-
-// forward and backward substitution, column-major, rhs is a vector
-template<typename LhsScalar, typename RhsScalar, typename Index, int Mode, bool Conjugate>
-struct packed_triangular_solve_vector<LhsScalar, RhsScalar, Index, OnTheLeft, Mode, Conjugate, ColMajor>
-{
-  enum {
-    IsLower = (Mode&Lower)==Lower
-  };
-  static void run(Index size, const LhsScalar* lhs, RhsScalar* rhs)
-  {
-    internal::conj_if<Conjugate> cj;
-    typedef Map<const Matrix<LhsScalar,Dynamic,1> > LhsMap;
-    typedef typename conj_expr_if<Conjugate,LhsMap>::type ConjLhsType;
-
-    lhs += IsLower ? 0 : size*(size-1)>>1;
-    for(Index pi=0; pi<size; ++pi)
-    {
-      Index i = IsLower ? pi : size-pi-1;
-      Index r = size - pi - 1;
-      if (!(Mode & UnitDiag))
-	rhs[i] /= cj(lhs[IsLower ? 0 : i]);
-      if (r>0)
-	Map<Matrix<RhsScalar,Dynamic,1> >(rhs+(IsLower? i+1 : 0),r) -=
-	    rhs[i] * ConjLhsType(LhsMap(lhs+(IsLower? 1 : 0),r));
-      IsLower ? lhs += size-pi : lhs -= r;
-    }
-  }
-};
-
-template<typename LhsScalar, typename RhsScalar, typename Index, int Mode, bool Conjugate, int StorageOrder>
-struct packed_triangular_solve_vector<LhsScalar, RhsScalar, Index, OnTheRight, Mode, Conjugate, StorageOrder>
-{
-  static void run(Index size, const LhsScalar* lhs, RhsScalar* rhs)
-  {
-    packed_triangular_solve_vector<LhsScalar,RhsScalar,Index,OnTheLeft,
-	((Mode&Upper)==Upper ? Lower : Upper) | (Mode&UnitDiag),
-	Conjugate,StorageOrder==RowMajor?ColMajor:RowMajor
-      >::run(size, lhs, rhs);
-  }
-};
-
-} // end namespace internal
-
-#endif // EIGEN_PACKED_TRIANGULAR_SOLVER_VECTOR_H

sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h

@@ -1,57 +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_RANK2UPDATE_H
-#define EIGEN_RANK2UPDATE_H
-
-namespace internal {
-
-/* Optimized selfadjoint matrix += alpha * uv' + conj(alpha)*vu'
- * This is the low-level version of SelfadjointRank2Update.h
- */
-template<typename Scalar, typename Index, int UpLo>
-struct rank2_update_selector
-{
-  static void run(Index size, Scalar* mat, Index stride, const Scalar* u, const Scalar* v, Scalar alpha)
-  {
-    typedef Map<const Matrix<Scalar,Dynamic,1> > OtherMap;
-    for (Index i=0; i<size; ++i)
-    {
-      Map<Matrix<Scalar,Dynamic,1> >(mat+stride*i+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1)) +=
-      numext::conj(alpha) * numext::conj(u[i]) * OtherMap(v+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1))
-                + alpha * numext::conj(v[i]) * OtherMap(u+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1));
-    }
-  }
-};
-
-/* Optimized selfadjoint matrix += alpha * uv' + conj(alpha)*vu'
- * The matrix is in packed form.
- */
-template<typename Scalar, typename Index, int UpLo>
-struct packed_rank2_update_selector
-{
-  static void run(Index size, Scalar* mat, const Scalar* u, const Scalar* v, Scalar alpha)
-  {
-    typedef Map<const Matrix<Scalar,Dynamic,1> > OtherMap;
-    Index offset = 0;
-    for (Index i=0; i<size; ++i)
-    {
-      Map<Matrix<Scalar,Dynamic,1> >(mat+offset, UpLo==Lower ? size-i : (i+1)) +=
-      numext::conj(alpha) * numext::conj(u[i]) * OtherMap(v+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1))
-                + alpha * numext::conj(v[i]) * OtherMap(u+(UpLo==Lower ? i : 0), UpLo==Lower ? size-i : (i+1));
-      //FIXME This should be handled outside.
-      mat[offset+(UpLo==Lower ? 0 : i)] = numext::real(mat[offset+(UpLo==Lower ? 0 : i)]);
-      offset += UpLo==Lower ? size-i : (i+1);
-    }
-  }
-};
-
-} // end namespace internal
-
-#endif // EIGEN_RANK2UPDATE_H

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

@@ -1,175 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2009-2015 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_BLAS_COMMON_H
-#define EIGEN_BLAS_COMMON_H
-
-#ifdef __GNUC__
-# if __GNUC__<5
-// GCC < 5.0 does not like the global Scalar typedef
-// we just keep shadow-warnings disabled permanently
-#  define EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
-# endif
-#endif
-
-#include "../Eigen/Core"
-#include "../Eigen/Jacobi"
-
-#include <complex>
-
-#ifndef SCALAR
-#error the token SCALAR must be defined to compile this file
-#endif
-
-#include "../Eigen/src/misc/blas.h"
-
-#define NOTR    0
-#define TR      1
-#define ADJ     2
-
-#define LEFT    0
-#define RIGHT   1
-
-#define UP      0
-#define LO      1
-
-#define NUNIT   0
-#define UNIT    1
-
-#define INVALID 0xff
-
-#define OP(X)   (   ((X)=='N' || (X)=='n') ? NOTR   \
-                  : ((X)=='T' || (X)=='t') ? TR     \
-                  : ((X)=='C' || (X)=='c') ? ADJ    \
-                  : INVALID)
-
-#define SIDE(X) (   ((X)=='L' || (X)=='l') ? LEFT   \
-                  : ((X)=='R' || (X)=='r') ? RIGHT  \
-                  : INVALID)
-
-#define UPLO(X) (   ((X)=='U' || (X)=='u') ? UP     \
-                  : ((X)=='L' || (X)=='l') ? LO     \
-                  : INVALID)
-
-#define DIAG(X) (   ((X)=='N' || (X)=='n') ? NUNIT  \
-                  : ((X)=='U' || (X)=='u') ? UNIT   \
-                  : INVALID)
-
-
-inline bool check_op(const char* op)
-{
-  return OP(*op)!=0xff;
-}
-
-inline bool check_side(const char* side)
-{
-  return SIDE(*side)!=0xff;
-}
-
-inline bool check_uplo(const char* uplo)
-{
-  return UPLO(*uplo)!=0xff;
-}
-
-
-namespace Eigen {
-#include "BandTriangularSolver.h"
-#include "GeneralRank1Update.h"
-#include "PackedSelfadjointProduct.h"
-#include "PackedTriangularMatrixVector.h"
-#include "PackedTriangularSolverVector.h"
-#include "Rank2Update.h"
-}
-
-using namespace Eigen;
-
-typedef SCALAR Scalar;
-typedef NumTraits<Scalar>::Real RealScalar;
-typedef std::complex<RealScalar> Complex;
-
-enum
-{
-  IsComplex = Eigen::NumTraits<SCALAR>::IsComplex,
-  Conj = IsComplex
-};
-
-typedef Matrix<Scalar,Dynamic,Dynamic,ColMajor> PlainMatrixType;
-typedef Map<Matrix<Scalar,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> > MatrixType;
-typedef Map<const Matrix<Scalar,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> > ConstMatrixType;
-typedef Map<Matrix<Scalar,Dynamic,1>, 0, InnerStride<Dynamic> > StridedVectorType;
-typedef Map<Matrix<Scalar,Dynamic,1> > CompactVectorType;
-
-template<typename T>
-Map<Matrix<T,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> >
-matrix(T* data, int rows, int cols, int stride)
-{
-  return Map<Matrix<T,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> >(data, rows, cols, OuterStride<>(stride));
-}
-
-template<typename T>
-Map<const Matrix<T,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> >
-matrix(const T* data, int rows, int cols, int stride)
-{
-  return Map<const Matrix<T,Dynamic,Dynamic,ColMajor>, 0, OuterStride<> >(data, rows, cols, OuterStride<>(stride));
-}
-
-template<typename T>
-Map<Matrix<T,Dynamic,1>, 0, InnerStride<Dynamic> > make_vector(T* data, int size, int incr)
-{
-  return Map<Matrix<T,Dynamic,1>, 0, InnerStride<Dynamic> >(data, size, InnerStride<Dynamic>(incr));
-}
-
-template<typename T>
-Map<const Matrix<T,Dynamic,1>, 0, InnerStride<Dynamic> > make_vector(const T* data, int size, int incr)
-{
-  return Map<const Matrix<T,Dynamic,1>, 0, InnerStride<Dynamic> >(data, size, InnerStride<Dynamic>(incr));
-}
-
-template<typename T>
-Map<Matrix<T,Dynamic,1> > make_vector(T* data, int size)
-{
-  return Map<Matrix<T,Dynamic,1> >(data, size);
-}
-
-template<typename T>
-Map<const Matrix<T,Dynamic,1> > make_vector(const T* data, int size)
-{
-  return Map<const Matrix<T,Dynamic,1> >(data, size);
-}
-
-template<typename T>
-T* get_compact_vector(T* x, int n, int incx)
-{
-  if(incx==1)
-    return x;
-
-  typename Eigen::internal::remove_const<T>::type* ret = new Scalar[n];
-  if(incx<0) make_vector(ret,n) = make_vector(x,n,-incx).reverse();
-  else       make_vector(ret,n) = make_vector(x,n, incx);
-  return ret;
-}
-
-template<typename T>
-T* copy_back(T* x_cpy, T* x, int n, int incx)
-{
-  if(x_cpy==x)
-    return 0;
-
-  if(incx<0) make_vector(x,n,-incx).reverse() = make_vector(x_cpy,n);
-  else       make_vector(x,n, incx)           = make_vector(x_cpy,n);
-  return x_cpy;
-}
-
-#ifndef EIGEN_BLAS_FUNC_SUFFIX
-#define EIGEN_BLAS_FUNC_SUFFIX _
-#endif
-
-#define EIGEN_BLAS_FUNC(X) EIGEN_CAT(SCALAR_SUFFIX, EIGEN_CAT(X, EIGEN_BLAS_FUNC_SUFFIX))
-
-#endif // EIGEN_BLAS_COMMON_H

sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h

@@ -1,24 +0,0 @@
-/* This contains a limited subset of the typedefs exposed by f2c
-   for use by the Eigen BLAS C-only implementation.
-*/
-
-#ifndef __EIGEN_DATATYPES_H__
-#define __EIGEN_DATATYPES_H__
-
-typedef int integer;
-typedef unsigned int uinteger;
-typedef float real;
-typedef double doublereal;
-typedef struct { real r, i; } complex;
-typedef struct { doublereal r, i; } doublecomplex;
-typedef int ftnlen;
-typedef int logical;
-
-#define abs(x) ((x) >= 0 ? (x) : -(x))
-#define dabs(x) (doublereal)abs(x)
-#define min(a,b) ((a) <= (b) ? (a) : (b))
-#define max(a,b) ((a) >= (b) ? (a) : (b))
-#define dmin(a,b) (doublereal)min(a,b)
-#define dmax(a,b) (doublereal)max(a,b)
-
-#endif