sequenzo 0.1.18__cp311-cp311-win_amd64.whl → 0.1.20__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,150 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPARSE_CWISE_UNARY_OP_H
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- #define EIGEN_SPARSE_CWISE_UNARY_OP_H
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-
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- namespace Eigen {
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-
15
- namespace internal {
16
-
17
- template<typename UnaryOp, typename ArgType>
18
- struct unary_evaluator<CwiseUnaryOp<UnaryOp,ArgType>, IteratorBased>
19
- : public evaluator_base<CwiseUnaryOp<UnaryOp,ArgType> >
20
- {
21
- public:
22
- typedef CwiseUnaryOp<UnaryOp, ArgType> XprType;
23
-
24
- class InnerIterator;
25
-
26
- enum {
27
- CoeffReadCost = int(evaluator<ArgType>::CoeffReadCost) + int(functor_traits<UnaryOp>::Cost),
28
- Flags = XprType::Flags
29
- };
30
-
31
- explicit unary_evaluator(const XprType& op) : m_functor(op.functor()), m_argImpl(op.nestedExpression())
32
- {
33
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<UnaryOp>::Cost);
34
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
35
- }
36
-
37
- inline Index nonZerosEstimate() const {
38
- return m_argImpl.nonZerosEstimate();
39
- }
40
-
41
- protected:
42
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
43
-
44
- const UnaryOp m_functor;
45
- evaluator<ArgType> m_argImpl;
46
- };
47
-
48
- template<typename UnaryOp, typename ArgType>
49
- class unary_evaluator<CwiseUnaryOp<UnaryOp,ArgType>, IteratorBased>::InnerIterator
50
- : public unary_evaluator<CwiseUnaryOp<UnaryOp,ArgType>, IteratorBased>::EvalIterator
51
- {
52
- protected:
53
- typedef typename XprType::Scalar Scalar;
54
- typedef typename unary_evaluator<CwiseUnaryOp<UnaryOp,ArgType>, IteratorBased>::EvalIterator Base;
55
- public:
56
-
57
- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& unaryOp, Index outer)
58
- : Base(unaryOp.m_argImpl,outer), m_functor(unaryOp.m_functor)
59
- {}
60
-
61
- EIGEN_STRONG_INLINE InnerIterator& operator++()
62
- { Base::operator++(); return *this; }
63
-
64
- EIGEN_STRONG_INLINE Scalar value() const { return m_functor(Base::value()); }
65
-
66
- protected:
67
- const UnaryOp m_functor;
68
- private:
69
- Scalar& valueRef();
70
- };
71
-
72
- template<typename ViewOp, typename ArgType>
73
- struct unary_evaluator<CwiseUnaryView<ViewOp,ArgType>, IteratorBased>
74
- : public evaluator_base<CwiseUnaryView<ViewOp,ArgType> >
75
- {
76
- public:
77
- typedef CwiseUnaryView<ViewOp, ArgType> XprType;
78
-
79
- class InnerIterator;
80
-
81
- enum {
82
- CoeffReadCost = int(evaluator<ArgType>::CoeffReadCost) + int(functor_traits<ViewOp>::Cost),
83
- Flags = XprType::Flags
84
- };
85
-
86
- explicit unary_evaluator(const XprType& op) : m_functor(op.functor()), m_argImpl(op.nestedExpression())
87
- {
88
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<ViewOp>::Cost);
89
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
90
- }
91
-
92
- protected:
93
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
94
-
95
- const ViewOp m_functor;
96
- evaluator<ArgType> m_argImpl;
97
- };
98
-
99
- template<typename ViewOp, typename ArgType>
100
- class unary_evaluator<CwiseUnaryView<ViewOp,ArgType>, IteratorBased>::InnerIterator
101
- : public unary_evaluator<CwiseUnaryView<ViewOp,ArgType>, IteratorBased>::EvalIterator
102
- {
103
- protected:
104
- typedef typename XprType::Scalar Scalar;
105
- typedef typename unary_evaluator<CwiseUnaryView<ViewOp,ArgType>, IteratorBased>::EvalIterator Base;
106
- public:
107
-
108
- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& unaryOp, Index outer)
109
- : Base(unaryOp.m_argImpl,outer), m_functor(unaryOp.m_functor)
110
- {}
111
-
112
- EIGEN_STRONG_INLINE InnerIterator& operator++()
113
- { Base::operator++(); return *this; }
114
-
115
- EIGEN_STRONG_INLINE Scalar value() const { return m_functor(Base::value()); }
116
- EIGEN_STRONG_INLINE Scalar& valueRef() { return m_functor(Base::valueRef()); }
117
-
118
- protected:
119
- const ViewOp m_functor;
120
- };
121
-
122
- } // end namespace internal
123
-
124
- template<typename Derived>
125
- EIGEN_STRONG_INLINE Derived&
126
- SparseMatrixBase<Derived>::operator*=(const Scalar& other)
127
- {
128
- typedef typename internal::evaluator<Derived>::InnerIterator EvalIterator;
129
- internal::evaluator<Derived> thisEval(derived());
130
- for (Index j=0; j<outerSize(); ++j)
131
- for (EvalIterator i(thisEval,j); i; ++i)
132
- i.valueRef() *= other;
133
- return derived();
134
- }
135
-
136
- template<typename Derived>
137
- EIGEN_STRONG_INLINE Derived&
138
- SparseMatrixBase<Derived>::operator/=(const Scalar& other)
139
- {
140
- typedef typename internal::evaluator<Derived>::InnerIterator EvalIterator;
141
- internal::evaluator<Derived> thisEval(derived());
142
- for (Index j=0; j<outerSize(); ++j)
143
- for (EvalIterator i(thisEval,j); i; ++i)
144
- i.valueRef() /= other;
145
- return derived();
146
- }
147
-
148
- } // end namespace Eigen
149
-
150
- #endif // EIGEN_SPARSE_CWISE_UNARY_OP_H
@@ -1,342 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_SPARSEDENSEPRODUCT_H
11
- #define EIGEN_SPARSEDENSEPRODUCT_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- template <> struct product_promote_storage_type<Sparse,Dense, OuterProduct> { typedef Sparse ret; };
18
- template <> struct product_promote_storage_type<Dense,Sparse, OuterProduct> { typedef Sparse ret; };
19
-
20
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType,
21
- typename AlphaType,
22
- int LhsStorageOrder = ((SparseLhsType::Flags&RowMajorBit)==RowMajorBit) ? RowMajor : ColMajor,
23
- bool ColPerCol = ((DenseRhsType::Flags&RowMajorBit)==0) || DenseRhsType::ColsAtCompileTime==1>
24
- struct sparse_time_dense_product_impl;
25
-
26
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType>
27
- struct sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, typename DenseResType::Scalar, RowMajor, true>
28
- {
29
- typedef typename internal::remove_all<SparseLhsType>::type Lhs;
30
- typedef typename internal::remove_all<DenseRhsType>::type Rhs;
31
- typedef typename internal::remove_all<DenseResType>::type Res;
32
- typedef typename evaluator<Lhs>::InnerIterator LhsInnerIterator;
33
- typedef evaluator<Lhs> LhsEval;
34
- static void run(const SparseLhsType& lhs, const DenseRhsType& rhs, DenseResType& res, const typename Res::Scalar& alpha)
35
- {
36
- LhsEval lhsEval(lhs);
37
-
38
- Index n = lhs.outerSize();
39
- #ifdef EIGEN_HAS_OPENMP
40
- Eigen::initParallel();
41
- Index threads = Eigen::nbThreads();
42
- #endif
43
-
44
- for(Index c=0; c<rhs.cols(); ++c)
45
- {
46
- #ifdef EIGEN_HAS_OPENMP
47
- // This 20000 threshold has been found experimentally on 2D and 3D Poisson problems.
48
- // It basically represents the minimal amount of work to be done to be worth it.
49
- if(threads>1 && lhsEval.nonZerosEstimate() > 20000)
50
- {
51
- #pragma omp parallel for schedule(dynamic,(n+threads*4-1)/(threads*4)) num_threads(threads)
52
- for(Index i=0; i<n; ++i)
53
- processRow(lhsEval,rhs,res,alpha,i,c);
54
- }
55
- else
56
- #endif
57
- {
58
- for(Index i=0; i<n; ++i)
59
- processRow(lhsEval,rhs,res,alpha,i,c);
60
- }
61
- }
62
- }
63
-
64
- static void processRow(const LhsEval& lhsEval, const DenseRhsType& rhs, DenseResType& res, const typename Res::Scalar& alpha, Index i, Index col)
65
- {
66
- typename Res::Scalar tmp(0);
67
- for(LhsInnerIterator it(lhsEval,i); it ;++it)
68
- tmp += it.value() * rhs.coeff(it.index(),col);
69
- res.coeffRef(i,col) += alpha * tmp;
70
- }
71
-
72
- };
73
-
74
- // FIXME: what is the purpose of the following specialization? Is it for the BlockedSparse format?
75
- // -> let's disable it for now as it is conflicting with generic scalar*matrix and matrix*scalar operators
76
- // template<typename T1, typename T2/*, int _Options, typename _StrideType*/>
77
- // struct ScalarBinaryOpTraits<T1, Ref<T2/*, _Options, _StrideType*/> >
78
- // {
79
- // enum {
80
- // Defined = 1
81
- // };
82
- // typedef typename CwiseUnaryOp<scalar_multiple2_op<T1, typename T2::Scalar>, T2>::PlainObject ReturnType;
83
- // };
84
-
85
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType, typename AlphaType>
86
- struct sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, AlphaType, ColMajor, true>
87
- {
88
- typedef typename internal::remove_all<SparseLhsType>::type Lhs;
89
- typedef typename internal::remove_all<DenseRhsType>::type Rhs;
90
- typedef typename internal::remove_all<DenseResType>::type Res;
91
- typedef evaluator<Lhs> LhsEval;
92
- typedef typename LhsEval::InnerIterator LhsInnerIterator;
93
- static void run(const SparseLhsType& lhs, const DenseRhsType& rhs, DenseResType& res, const AlphaType& alpha)
94
- {
95
- LhsEval lhsEval(lhs);
96
- for(Index c=0; c<rhs.cols(); ++c)
97
- {
98
- for(Index j=0; j<lhs.outerSize(); ++j)
99
- {
100
- // typename Res::Scalar rhs_j = alpha * rhs.coeff(j,c);
101
- typename ScalarBinaryOpTraits<AlphaType, typename Rhs::Scalar>::ReturnType rhs_j(alpha * rhs.coeff(j,c));
102
- for(LhsInnerIterator it(lhsEval,j); it ;++it)
103
- res.coeffRef(it.index(),c) += it.value() * rhs_j;
104
- }
105
- }
106
- }
107
- };
108
-
109
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType>
110
- struct sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, typename DenseResType::Scalar, RowMajor, false>
111
- {
112
- typedef typename internal::remove_all<SparseLhsType>::type Lhs;
113
- typedef typename internal::remove_all<DenseRhsType>::type Rhs;
114
- typedef typename internal::remove_all<DenseResType>::type Res;
115
- typedef evaluator<Lhs> LhsEval;
116
- typedef typename LhsEval::InnerIterator LhsInnerIterator;
117
- static void run(const SparseLhsType& lhs, const DenseRhsType& rhs, DenseResType& res, const typename Res::Scalar& alpha)
118
- {
119
- Index n = lhs.rows();
120
- LhsEval lhsEval(lhs);
121
-
122
- #ifdef EIGEN_HAS_OPENMP
123
- Eigen::initParallel();
124
- Index threads = Eigen::nbThreads();
125
- // This 20000 threshold has been found experimentally on 2D and 3D Poisson problems.
126
- // It basically represents the minimal amount of work to be done to be worth it.
127
- if(threads>1 && lhsEval.nonZerosEstimate()*rhs.cols() > 20000)
128
- {
129
- #pragma omp parallel for schedule(dynamic,(n+threads*4-1)/(threads*4)) num_threads(threads)
130
- for(Index i=0; i<n; ++i)
131
- processRow(lhsEval,rhs,res,alpha,i);
132
- }
133
- else
134
- #endif
135
- {
136
- for(Index i=0; i<n; ++i)
137
- processRow(lhsEval, rhs, res, alpha, i);
138
- }
139
- }
140
-
141
- static void processRow(const LhsEval& lhsEval, const DenseRhsType& rhs, Res& res, const typename Res::Scalar& alpha, Index i)
142
- {
143
- typename Res::RowXpr res_i(res.row(i));
144
- for(LhsInnerIterator it(lhsEval,i); it ;++it)
145
- res_i += (alpha*it.value()) * rhs.row(it.index());
146
- }
147
- };
148
-
149
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType>
150
- struct sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, typename DenseResType::Scalar, ColMajor, false>
151
- {
152
- typedef typename internal::remove_all<SparseLhsType>::type Lhs;
153
- typedef typename internal::remove_all<DenseRhsType>::type Rhs;
154
- typedef typename internal::remove_all<DenseResType>::type Res;
155
- typedef typename evaluator<Lhs>::InnerIterator LhsInnerIterator;
156
- static void run(const SparseLhsType& lhs, const DenseRhsType& rhs, DenseResType& res, const typename Res::Scalar& alpha)
157
- {
158
- evaluator<Lhs> lhsEval(lhs);
159
- for(Index j=0; j<lhs.outerSize(); ++j)
160
- {
161
- typename Rhs::ConstRowXpr rhs_j(rhs.row(j));
162
- for(LhsInnerIterator it(lhsEval,j); it ;++it)
163
- res.row(it.index()) += (alpha*it.value()) * rhs_j;
164
- }
165
- }
166
- };
167
-
168
- template<typename SparseLhsType, typename DenseRhsType, typename DenseResType,typename AlphaType>
169
- inline void sparse_time_dense_product(const SparseLhsType& lhs, const DenseRhsType& rhs, DenseResType& res, const AlphaType& alpha)
170
- {
171
- sparse_time_dense_product_impl<SparseLhsType,DenseRhsType,DenseResType, AlphaType>::run(lhs, rhs, res, alpha);
172
- }
173
-
174
- } // end namespace internal
175
-
176
- namespace internal {
177
-
178
- template<typename Lhs, typename Rhs, int ProductType>
179
- struct generic_product_impl<Lhs, Rhs, SparseShape, DenseShape, ProductType>
180
- : generic_product_impl_base<Lhs,Rhs,generic_product_impl<Lhs,Rhs,SparseShape,DenseShape,ProductType> >
181
- {
182
- typedef typename Product<Lhs,Rhs>::Scalar Scalar;
183
-
184
- template<typename Dest>
185
- static void scaleAndAddTo(Dest& dst, const Lhs& lhs, const Rhs& rhs, const Scalar& alpha)
186
- {
187
- typedef typename nested_eval<Lhs,((Rhs::Flags&RowMajorBit)==0) ? 1 : Rhs::ColsAtCompileTime>::type LhsNested;
188
- typedef typename nested_eval<Rhs,((Lhs::Flags&RowMajorBit)==0) ? 1 : Dynamic>::type RhsNested;
189
- LhsNested lhsNested(lhs);
190
- RhsNested rhsNested(rhs);
191
- internal::sparse_time_dense_product(lhsNested, rhsNested, dst, alpha);
192
- }
193
- };
194
-
195
- template<typename Lhs, typename Rhs, int ProductType>
196
- struct generic_product_impl<Lhs, Rhs, SparseTriangularShape, DenseShape, ProductType>
197
- : generic_product_impl<Lhs, Rhs, SparseShape, DenseShape, ProductType>
198
- {};
199
-
200
- template<typename Lhs, typename Rhs, int ProductType>
201
- struct generic_product_impl<Lhs, Rhs, DenseShape, SparseShape, ProductType>
202
- : generic_product_impl_base<Lhs,Rhs,generic_product_impl<Lhs,Rhs,DenseShape,SparseShape,ProductType> >
203
- {
204
- typedef typename Product<Lhs,Rhs>::Scalar Scalar;
205
-
206
- template<typename Dst>
207
- static void scaleAndAddTo(Dst& dst, const Lhs& lhs, const Rhs& rhs, const Scalar& alpha)
208
- {
209
- typedef typename nested_eval<Lhs,((Rhs::Flags&RowMajorBit)==0) ? Dynamic : 1>::type LhsNested;
210
- typedef typename nested_eval<Rhs,((Lhs::Flags&RowMajorBit)==RowMajorBit) ? 1 : Lhs::RowsAtCompileTime>::type RhsNested;
211
- LhsNested lhsNested(lhs);
212
- RhsNested rhsNested(rhs);
213
-
214
- // transpose everything
215
- Transpose<Dst> dstT(dst);
216
- internal::sparse_time_dense_product(rhsNested.transpose(), lhsNested.transpose(), dstT, alpha);
217
- }
218
- };
219
-
220
- template<typename Lhs, typename Rhs, int ProductType>
221
- struct generic_product_impl<Lhs, Rhs, DenseShape, SparseTriangularShape, ProductType>
222
- : generic_product_impl<Lhs, Rhs, DenseShape, SparseShape, ProductType>
223
- {};
224
-
225
- template<typename LhsT, typename RhsT, bool NeedToTranspose>
226
- struct sparse_dense_outer_product_evaluator
227
- {
228
- protected:
229
- typedef typename conditional<NeedToTranspose,RhsT,LhsT>::type Lhs1;
230
- typedef typename conditional<NeedToTranspose,LhsT,RhsT>::type ActualRhs;
231
- typedef Product<LhsT,RhsT,DefaultProduct> ProdXprType;
232
-
233
- // if the actual left-hand side is a dense vector,
234
- // then build a sparse-view so that we can seamlessly iterate over it.
235
- typedef typename conditional<is_same<typename internal::traits<Lhs1>::StorageKind,Sparse>::value,
236
- Lhs1, SparseView<Lhs1> >::type ActualLhs;
237
- typedef typename conditional<is_same<typename internal::traits<Lhs1>::StorageKind,Sparse>::value,
238
- Lhs1 const&, SparseView<Lhs1> >::type LhsArg;
239
-
240
- typedef evaluator<ActualLhs> LhsEval;
241
- typedef evaluator<ActualRhs> RhsEval;
242
- typedef typename evaluator<ActualLhs>::InnerIterator LhsIterator;
243
- typedef typename ProdXprType::Scalar Scalar;
244
-
245
- public:
246
- enum {
247
- Flags = NeedToTranspose ? RowMajorBit : 0,
248
- CoeffReadCost = HugeCost
249
- };
250
-
251
- class InnerIterator : public LhsIterator
252
- {
253
- public:
254
- InnerIterator(const sparse_dense_outer_product_evaluator &xprEval, Index outer)
255
- : LhsIterator(xprEval.m_lhsXprImpl, 0),
256
- m_outer(outer),
257
- m_empty(false),
258
- m_factor(get(xprEval.m_rhsXprImpl, outer, typename internal::traits<ActualRhs>::StorageKind() ))
259
- {}
260
-
261
- EIGEN_STRONG_INLINE Index outer() const { return m_outer; }
262
- EIGEN_STRONG_INLINE Index row() const { return NeedToTranspose ? m_outer : LhsIterator::index(); }
263
- EIGEN_STRONG_INLINE Index col() const { return NeedToTranspose ? LhsIterator::index() : m_outer; }
264
-
265
- EIGEN_STRONG_INLINE Scalar value() const { return LhsIterator::value() * m_factor; }
266
- EIGEN_STRONG_INLINE operator bool() const { return LhsIterator::operator bool() && (!m_empty); }
267
-
268
- protected:
269
- Scalar get(const RhsEval &rhs, Index outer, Dense = Dense()) const
270
- {
271
- return rhs.coeff(outer);
272
- }
273
-
274
- Scalar get(const RhsEval &rhs, Index outer, Sparse = Sparse())
275
- {
276
- typename RhsEval::InnerIterator it(rhs, outer);
277
- if (it && it.index()==0 && it.value()!=Scalar(0))
278
- return it.value();
279
- m_empty = true;
280
- return Scalar(0);
281
- }
282
-
283
- Index m_outer;
284
- bool m_empty;
285
- Scalar m_factor;
286
- };
287
-
288
- sparse_dense_outer_product_evaluator(const Lhs1 &lhs, const ActualRhs &rhs)
289
- : m_lhs(lhs), m_lhsXprImpl(m_lhs), m_rhsXprImpl(rhs)
290
- {
291
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
292
- }
293
-
294
- // transpose case
295
- sparse_dense_outer_product_evaluator(const ActualRhs &rhs, const Lhs1 &lhs)
296
- : m_lhs(lhs), m_lhsXprImpl(m_lhs), m_rhsXprImpl(rhs)
297
- {
298
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
299
- }
300
-
301
- protected:
302
- const LhsArg m_lhs;
303
- evaluator<ActualLhs> m_lhsXprImpl;
304
- evaluator<ActualRhs> m_rhsXprImpl;
305
- };
306
-
307
- // sparse * dense outer product
308
- template<typename Lhs, typename Rhs>
309
- struct product_evaluator<Product<Lhs, Rhs, DefaultProduct>, OuterProduct, SparseShape, DenseShape>
310
- : sparse_dense_outer_product_evaluator<Lhs,Rhs, Lhs::IsRowMajor>
311
- {
312
- typedef sparse_dense_outer_product_evaluator<Lhs,Rhs, Lhs::IsRowMajor> Base;
313
-
314
- typedef Product<Lhs, Rhs> XprType;
315
- typedef typename XprType::PlainObject PlainObject;
316
-
317
- explicit product_evaluator(const XprType& xpr)
318
- : Base(xpr.lhs(), xpr.rhs())
319
- {}
320
-
321
- };
322
-
323
- template<typename Lhs, typename Rhs>
324
- struct product_evaluator<Product<Lhs, Rhs, DefaultProduct>, OuterProduct, DenseShape, SparseShape>
325
- : sparse_dense_outer_product_evaluator<Lhs,Rhs, Rhs::IsRowMajor>
326
- {
327
- typedef sparse_dense_outer_product_evaluator<Lhs,Rhs, Rhs::IsRowMajor> Base;
328
-
329
- typedef Product<Lhs, Rhs> XprType;
330
- typedef typename XprType::PlainObject PlainObject;
331
-
332
- explicit product_evaluator(const XprType& xpr)
333
- : Base(xpr.lhs(), xpr.rhs())
334
- {}
335
-
336
- };
337
-
338
- } // end namespace internal
339
-
340
- } // end namespace Eigen
341
-
342
- #endif // EIGEN_SPARSEDENSEPRODUCT_H
@@ -1,138 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPARSE_DIAGONAL_PRODUCT_H
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- #define EIGEN_SPARSE_DIAGONAL_PRODUCT_H
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-
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- namespace Eigen {
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-
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- // The product of a diagonal matrix with a sparse matrix can be easily
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- // implemented using expression template.
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- // We have two consider very different cases:
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- // 1 - diag * row-major sparse
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- // => each inner vector <=> scalar * sparse vector product
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- // => so we can reuse CwiseUnaryOp::InnerIterator
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- // 2 - diag * col-major sparse
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- // => each inner vector <=> densevector * sparse vector cwise product
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- // => again, we can reuse specialization of CwiseBinaryOp::InnerIterator
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- // for that particular case
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- // The two other cases are symmetric.
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-
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- namespace internal {
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-
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- enum {
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- SDP_AsScalarProduct,
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- SDP_AsCwiseProduct
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- };
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-
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- template<typename SparseXprType, typename DiagonalCoeffType, int SDP_Tag>
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- struct sparse_diagonal_product_evaluator;
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-
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- template<typename Lhs, typename Rhs, int ProductTag>
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- struct product_evaluator<Product<Lhs, Rhs, DefaultProduct>, ProductTag, DiagonalShape, SparseShape>
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- : public sparse_diagonal_product_evaluator<Rhs, typename Lhs::DiagonalVectorType, Rhs::Flags&RowMajorBit?SDP_AsScalarProduct:SDP_AsCwiseProduct>
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- {
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- typedef Product<Lhs, Rhs, DefaultProduct> XprType;
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- enum { CoeffReadCost = HugeCost, Flags = Rhs::Flags&RowMajorBit, Alignment = 0 }; // FIXME CoeffReadCost & Flags
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-
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- typedef sparse_diagonal_product_evaluator<Rhs, typename Lhs::DiagonalVectorType, Rhs::Flags&RowMajorBit?SDP_AsScalarProduct:SDP_AsCwiseProduct> Base;
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- explicit product_evaluator(const XprType& xpr) : Base(xpr.rhs(), xpr.lhs().diagonal()) {}
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- };
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-
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- template<typename Lhs, typename Rhs, int ProductTag>
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- struct product_evaluator<Product<Lhs, Rhs, DefaultProduct>, ProductTag, SparseShape, DiagonalShape>
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- : public sparse_diagonal_product_evaluator<Lhs, Transpose<const typename Rhs::DiagonalVectorType>, Lhs::Flags&RowMajorBit?SDP_AsCwiseProduct:SDP_AsScalarProduct>
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- {
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- typedef Product<Lhs, Rhs, DefaultProduct> XprType;
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- enum { CoeffReadCost = HugeCost, Flags = Lhs::Flags&RowMajorBit, Alignment = 0 }; // FIXME CoeffReadCost & Flags
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-
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- typedef sparse_diagonal_product_evaluator<Lhs, Transpose<const typename Rhs::DiagonalVectorType>, Lhs::Flags&RowMajorBit?SDP_AsCwiseProduct:SDP_AsScalarProduct> Base;
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- explicit product_evaluator(const XprType& xpr) : Base(xpr.lhs(), xpr.rhs().diagonal().transpose()) {}
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- };
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-
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- template<typename SparseXprType, typename DiagonalCoeffType>
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- struct sparse_diagonal_product_evaluator<SparseXprType, DiagonalCoeffType, SDP_AsScalarProduct>
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- {
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- protected:
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- typedef typename evaluator<SparseXprType>::InnerIterator SparseXprInnerIterator;
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- typedef typename SparseXprType::Scalar Scalar;
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-
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- public:
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- class InnerIterator : public SparseXprInnerIterator
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- {
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- public:
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- InnerIterator(const sparse_diagonal_product_evaluator &xprEval, Index outer)
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- : SparseXprInnerIterator(xprEval.m_sparseXprImpl, outer),
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- m_coeff(xprEval.m_diagCoeffImpl.coeff(outer))
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- {}
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-
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- EIGEN_STRONG_INLINE Scalar value() const { return m_coeff * SparseXprInnerIterator::value(); }
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- protected:
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- typename DiagonalCoeffType::Scalar m_coeff;
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- };
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-
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- sparse_diagonal_product_evaluator(const SparseXprType &sparseXpr, const DiagonalCoeffType &diagCoeff)
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- : m_sparseXprImpl(sparseXpr), m_diagCoeffImpl(diagCoeff)
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- {}
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-
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- Index nonZerosEstimate() const { return m_sparseXprImpl.nonZerosEstimate(); }
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-
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- protected:
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- evaluator<SparseXprType> m_sparseXprImpl;
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- evaluator<DiagonalCoeffType> m_diagCoeffImpl;
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- };
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-
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-
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- template<typename SparseXprType, typename DiagCoeffType>
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- struct sparse_diagonal_product_evaluator<SparseXprType, DiagCoeffType, SDP_AsCwiseProduct>
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- {
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- typedef typename SparseXprType::Scalar Scalar;
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- typedef typename SparseXprType::StorageIndex StorageIndex;
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-
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- typedef typename nested_eval<DiagCoeffType,SparseXprType::IsRowMajor ? SparseXprType::RowsAtCompileTime
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- : SparseXprType::ColsAtCompileTime>::type DiagCoeffNested;
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-
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- class InnerIterator
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- {
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- typedef typename evaluator<SparseXprType>::InnerIterator SparseXprIter;
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- public:
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- InnerIterator(const sparse_diagonal_product_evaluator &xprEval, Index outer)
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- : m_sparseIter(xprEval.m_sparseXprEval, outer), m_diagCoeffNested(xprEval.m_diagCoeffNested)
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- {}
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-
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- inline Scalar value() const { return m_sparseIter.value() * m_diagCoeffNested.coeff(index()); }
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- inline StorageIndex index() const { return m_sparseIter.index(); }
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- inline Index outer() const { return m_sparseIter.outer(); }
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- inline Index col() const { return SparseXprType::IsRowMajor ? m_sparseIter.index() : m_sparseIter.outer(); }
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- inline Index row() const { return SparseXprType::IsRowMajor ? m_sparseIter.outer() : m_sparseIter.index(); }
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-
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- EIGEN_STRONG_INLINE InnerIterator& operator++() { ++m_sparseIter; return *this; }
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- inline operator bool() const { return m_sparseIter; }
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-
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- protected:
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- SparseXprIter m_sparseIter;
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- DiagCoeffNested m_diagCoeffNested;
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- };
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-
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- sparse_diagonal_product_evaluator(const SparseXprType &sparseXpr, const DiagCoeffType &diagCoeff)
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- : m_sparseXprEval(sparseXpr), m_diagCoeffNested(diagCoeff)
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- {}
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-
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- Index nonZerosEstimate() const { return m_sparseXprEval.nonZerosEstimate(); }
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-
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- protected:
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- evaluator<SparseXprType> m_sparseXprEval;
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- DiagCoeffNested m_diagCoeffNested;
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- };
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-
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- } // end namespace internal
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_SPARSE_DIAGONAL_PRODUCT_H