sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-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.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-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.cp310-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.cp310-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp310-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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@@ -1,722 +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) 2008-2014 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_BINARY_OP_H
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- #define EIGEN_SPARSE_CWISE_BINARY_OP_H
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-
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- namespace Eigen {
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-
15
- // Here we have to handle 3 cases:
16
- // 1 - sparse op dense
17
- // 2 - dense op sparse
18
- // 3 - sparse op sparse
19
- // We also need to implement a 4th iterator for:
20
- // 4 - dense op dense
21
- // Finally, we also need to distinguish between the product and other operations :
22
- // configuration returned mode
23
- // 1 - sparse op dense product sparse
24
- // generic dense
25
- // 2 - dense op sparse product sparse
26
- // generic dense
27
- // 3 - sparse op sparse product sparse
28
- // generic sparse
29
- // 4 - dense op dense product dense
30
- // generic dense
31
- //
32
- // TODO to ease compiler job, we could specialize product/quotient with a scalar
33
- // and fallback to cwise-unary evaluator using bind1st_op and bind2nd_op.
34
-
35
- template<typename BinaryOp, typename Lhs, typename Rhs>
36
- class CwiseBinaryOpImpl<BinaryOp, Lhs, Rhs, Sparse>
37
- : public SparseMatrixBase<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
38
- {
39
- public:
40
- typedef CwiseBinaryOp<BinaryOp, Lhs, Rhs> Derived;
41
- typedef SparseMatrixBase<Derived> Base;
42
- EIGEN_SPARSE_PUBLIC_INTERFACE(Derived)
43
- CwiseBinaryOpImpl()
44
- {
45
- EIGEN_STATIC_ASSERT((
46
- (!internal::is_same<typename internal::traits<Lhs>::StorageKind,
47
- typename internal::traits<Rhs>::StorageKind>::value)
48
- || ((internal::evaluator<Lhs>::Flags&RowMajorBit) == (internal::evaluator<Rhs>::Flags&RowMajorBit))),
49
- THE_STORAGE_ORDER_OF_BOTH_SIDES_MUST_MATCH);
50
- }
51
- };
52
-
53
- namespace internal {
54
-
55
-
56
- // Generic "sparse OP sparse"
57
- template<typename XprType> struct binary_sparse_evaluator;
58
-
59
- template<typename BinaryOp, typename Lhs, typename Rhs>
60
- struct binary_evaluator<CwiseBinaryOp<BinaryOp, Lhs, Rhs>, IteratorBased, IteratorBased>
61
- : evaluator_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
62
- {
63
- protected:
64
- typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
65
- typedef typename evaluator<Rhs>::InnerIterator RhsIterator;
66
- typedef CwiseBinaryOp<BinaryOp, Lhs, Rhs> XprType;
67
- typedef typename traits<XprType>::Scalar Scalar;
68
- typedef typename XprType::StorageIndex StorageIndex;
69
- public:
70
-
71
- class InnerIterator
72
- {
73
- public:
74
-
75
- EIGEN_STRONG_INLINE InnerIterator(const binary_evaluator& aEval, Index outer)
76
- : m_lhsIter(aEval.m_lhsImpl,outer), m_rhsIter(aEval.m_rhsImpl,outer), m_functor(aEval.m_functor)
77
- {
78
- this->operator++();
79
- }
80
-
81
- EIGEN_STRONG_INLINE InnerIterator& operator++()
82
- {
83
- if (m_lhsIter && m_rhsIter && (m_lhsIter.index() == m_rhsIter.index()))
84
- {
85
- m_id = m_lhsIter.index();
86
- m_value = m_functor(m_lhsIter.value(), m_rhsIter.value());
87
- ++m_lhsIter;
88
- ++m_rhsIter;
89
- }
90
- else if (m_lhsIter && (!m_rhsIter || (m_lhsIter.index() < m_rhsIter.index())))
91
- {
92
- m_id = m_lhsIter.index();
93
- m_value = m_functor(m_lhsIter.value(), Scalar(0));
94
- ++m_lhsIter;
95
- }
96
- else if (m_rhsIter && (!m_lhsIter || (m_lhsIter.index() > m_rhsIter.index())))
97
- {
98
- m_id = m_rhsIter.index();
99
- m_value = m_functor(Scalar(0), m_rhsIter.value());
100
- ++m_rhsIter;
101
- }
102
- else
103
- {
104
- m_value = Scalar(0); // this is to avoid a compilation warning
105
- m_id = -1;
106
- }
107
- return *this;
108
- }
109
-
110
- EIGEN_STRONG_INLINE Scalar value() const { return m_value; }
111
-
112
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
113
- EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
114
- EIGEN_STRONG_INLINE Index row() const { return Lhs::IsRowMajor ? m_lhsIter.row() : index(); }
115
- EIGEN_STRONG_INLINE Index col() const { return Lhs::IsRowMajor ? index() : m_lhsIter.col(); }
116
-
117
- EIGEN_STRONG_INLINE operator bool() const { return m_id>=0; }
118
-
119
- protected:
120
- LhsIterator m_lhsIter;
121
- RhsIterator m_rhsIter;
122
- const BinaryOp& m_functor;
123
- Scalar m_value;
124
- StorageIndex m_id;
125
- };
126
-
127
-
128
- enum {
129
- CoeffReadCost = int(evaluator<Lhs>::CoeffReadCost) + int(evaluator<Rhs>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
130
- Flags = XprType::Flags
131
- };
132
-
133
- explicit binary_evaluator(const XprType& xpr)
134
- : m_functor(xpr.functor()),
135
- m_lhsImpl(xpr.lhs()),
136
- m_rhsImpl(xpr.rhs())
137
- {
138
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
139
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
140
- }
141
-
142
- inline Index nonZerosEstimate() const {
143
- return m_lhsImpl.nonZerosEstimate() + m_rhsImpl.nonZerosEstimate();
144
- }
145
-
146
- protected:
147
- const BinaryOp m_functor;
148
- evaluator<Lhs> m_lhsImpl;
149
- evaluator<Rhs> m_rhsImpl;
150
- };
151
-
152
- // dense op sparse
153
- template<typename BinaryOp, typename Lhs, typename Rhs>
154
- struct binary_evaluator<CwiseBinaryOp<BinaryOp, Lhs, Rhs>, IndexBased, IteratorBased>
155
- : evaluator_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
156
- {
157
- protected:
158
- typedef typename evaluator<Rhs>::InnerIterator RhsIterator;
159
- typedef CwiseBinaryOp<BinaryOp, Lhs, Rhs> XprType;
160
- typedef typename traits<XprType>::Scalar Scalar;
161
- typedef typename XprType::StorageIndex StorageIndex;
162
- public:
163
-
164
- class InnerIterator
165
- {
166
- enum { IsRowMajor = (int(Rhs::Flags)&RowMajorBit)==RowMajorBit };
167
- public:
168
-
169
- EIGEN_STRONG_INLINE InnerIterator(const binary_evaluator& aEval, Index outer)
170
- : m_lhsEval(aEval.m_lhsImpl), m_rhsIter(aEval.m_rhsImpl,outer), m_functor(aEval.m_functor), m_value(0), m_id(-1), m_innerSize(aEval.m_expr.rhs().innerSize())
171
- {
172
- this->operator++();
173
- }
174
-
175
- EIGEN_STRONG_INLINE InnerIterator& operator++()
176
- {
177
- ++m_id;
178
- if(m_id<m_innerSize)
179
- {
180
- Scalar lhsVal = m_lhsEval.coeff(IsRowMajor?m_rhsIter.outer():m_id,
181
- IsRowMajor?m_id:m_rhsIter.outer());
182
- if(m_rhsIter && m_rhsIter.index()==m_id)
183
- {
184
- m_value = m_functor(lhsVal, m_rhsIter.value());
185
- ++m_rhsIter;
186
- }
187
- else
188
- m_value = m_functor(lhsVal, Scalar(0));
189
- }
190
-
191
- return *this;
192
- }
193
-
194
- EIGEN_STRONG_INLINE Scalar value() const { eigen_internal_assert(m_id<m_innerSize); return m_value; }
195
-
196
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
197
- EIGEN_STRONG_INLINE Index outer() const { return m_rhsIter.outer(); }
198
- EIGEN_STRONG_INLINE Index row() const { return IsRowMajor ? m_rhsIter.outer() : m_id; }
199
- EIGEN_STRONG_INLINE Index col() const { return IsRowMajor ? m_id : m_rhsIter.outer(); }
200
-
201
- EIGEN_STRONG_INLINE operator bool() const { return m_id<m_innerSize; }
202
-
203
- protected:
204
- const evaluator<Lhs> &m_lhsEval;
205
- RhsIterator m_rhsIter;
206
- const BinaryOp& m_functor;
207
- Scalar m_value;
208
- StorageIndex m_id;
209
- StorageIndex m_innerSize;
210
- };
211
-
212
-
213
- enum {
214
- CoeffReadCost = int(evaluator<Lhs>::CoeffReadCost) + int(evaluator<Rhs>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
215
- Flags = XprType::Flags
216
- };
217
-
218
- explicit binary_evaluator(const XprType& xpr)
219
- : m_functor(xpr.functor()),
220
- m_lhsImpl(xpr.lhs()),
221
- m_rhsImpl(xpr.rhs()),
222
- m_expr(xpr)
223
- {
224
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
225
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
226
- }
227
-
228
- inline Index nonZerosEstimate() const {
229
- return m_expr.size();
230
- }
231
-
232
- protected:
233
- const BinaryOp m_functor;
234
- evaluator<Lhs> m_lhsImpl;
235
- evaluator<Rhs> m_rhsImpl;
236
- const XprType &m_expr;
237
- };
238
-
239
- // sparse op dense
240
- template<typename BinaryOp, typename Lhs, typename Rhs>
241
- struct binary_evaluator<CwiseBinaryOp<BinaryOp, Lhs, Rhs>, IteratorBased, IndexBased>
242
- : evaluator_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
243
- {
244
- protected:
245
- typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
246
- typedef CwiseBinaryOp<BinaryOp, Lhs, Rhs> XprType;
247
- typedef typename traits<XprType>::Scalar Scalar;
248
- typedef typename XprType::StorageIndex StorageIndex;
249
- public:
250
-
251
- class InnerIterator
252
- {
253
- enum { IsRowMajor = (int(Lhs::Flags)&RowMajorBit)==RowMajorBit };
254
- public:
255
-
256
- EIGEN_STRONG_INLINE InnerIterator(const binary_evaluator& aEval, Index outer)
257
- : m_lhsIter(aEval.m_lhsImpl,outer), m_rhsEval(aEval.m_rhsImpl), m_functor(aEval.m_functor), m_value(0), m_id(-1), m_innerSize(aEval.m_expr.lhs().innerSize())
258
- {
259
- this->operator++();
260
- }
261
-
262
- EIGEN_STRONG_INLINE InnerIterator& operator++()
263
- {
264
- ++m_id;
265
- if(m_id<m_innerSize)
266
- {
267
- Scalar rhsVal = m_rhsEval.coeff(IsRowMajor?m_lhsIter.outer():m_id,
268
- IsRowMajor?m_id:m_lhsIter.outer());
269
- if(m_lhsIter && m_lhsIter.index()==m_id)
270
- {
271
- m_value = m_functor(m_lhsIter.value(), rhsVal);
272
- ++m_lhsIter;
273
- }
274
- else
275
- m_value = m_functor(Scalar(0),rhsVal);
276
- }
277
-
278
- return *this;
279
- }
280
-
281
- EIGEN_STRONG_INLINE Scalar value() const { eigen_internal_assert(m_id<m_innerSize); return m_value; }
282
-
283
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_id; }
284
- EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
285
- EIGEN_STRONG_INLINE Index row() const { return IsRowMajor ? m_lhsIter.outer() : m_id; }
286
- EIGEN_STRONG_INLINE Index col() const { return IsRowMajor ? m_id : m_lhsIter.outer(); }
287
-
288
- EIGEN_STRONG_INLINE operator bool() const { return m_id<m_innerSize; }
289
-
290
- protected:
291
- LhsIterator m_lhsIter;
292
- const evaluator<Rhs> &m_rhsEval;
293
- const BinaryOp& m_functor;
294
- Scalar m_value;
295
- StorageIndex m_id;
296
- StorageIndex m_innerSize;
297
- };
298
-
299
-
300
- enum {
301
- CoeffReadCost = int(evaluator<Lhs>::CoeffReadCost) + int(evaluator<Rhs>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
302
- Flags = XprType::Flags
303
- };
304
-
305
- explicit binary_evaluator(const XprType& xpr)
306
- : m_functor(xpr.functor()),
307
- m_lhsImpl(xpr.lhs()),
308
- m_rhsImpl(xpr.rhs()),
309
- m_expr(xpr)
310
- {
311
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
312
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
313
- }
314
-
315
- inline Index nonZerosEstimate() const {
316
- return m_expr.size();
317
- }
318
-
319
- protected:
320
- const BinaryOp m_functor;
321
- evaluator<Lhs> m_lhsImpl;
322
- evaluator<Rhs> m_rhsImpl;
323
- const XprType &m_expr;
324
- };
325
-
326
- template<typename T,
327
- typename LhsKind = typename evaluator_traits<typename T::Lhs>::Kind,
328
- typename RhsKind = typename evaluator_traits<typename T::Rhs>::Kind,
329
- typename LhsScalar = typename traits<typename T::Lhs>::Scalar,
330
- typename RhsScalar = typename traits<typename T::Rhs>::Scalar> struct sparse_conjunction_evaluator;
331
-
332
- // "sparse .* sparse"
333
- template<typename T1, typename T2, typename Lhs, typename Rhs>
334
- struct binary_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs>, IteratorBased, IteratorBased>
335
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> >
336
- {
337
- typedef CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> XprType;
338
- typedef sparse_conjunction_evaluator<XprType> Base;
339
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
340
- };
341
- // "dense .* sparse"
342
- template<typename T1, typename T2, typename Lhs, typename Rhs>
343
- struct binary_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs>, IndexBased, IteratorBased>
344
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> >
345
- {
346
- typedef CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> XprType;
347
- typedef sparse_conjunction_evaluator<XprType> Base;
348
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
349
- };
350
- // "sparse .* dense"
351
- template<typename T1, typename T2, typename Lhs, typename Rhs>
352
- struct binary_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs>, IteratorBased, IndexBased>
353
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> >
354
- {
355
- typedef CwiseBinaryOp<scalar_product_op<T1,T2>, Lhs, Rhs> XprType;
356
- typedef sparse_conjunction_evaluator<XprType> Base;
357
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
358
- };
359
-
360
- // "sparse ./ dense"
361
- template<typename T1, typename T2, typename Lhs, typename Rhs>
362
- struct binary_evaluator<CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs>, IteratorBased, IndexBased>
363
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs> >
364
- {
365
- typedef CwiseBinaryOp<scalar_quotient_op<T1,T2>, Lhs, Rhs> XprType;
366
- typedef sparse_conjunction_evaluator<XprType> Base;
367
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
368
- };
369
-
370
- // "sparse && sparse"
371
- template<typename Lhs, typename Rhs>
372
- struct binary_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs>, IteratorBased, IteratorBased>
373
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> >
374
- {
375
- typedef CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> XprType;
376
- typedef sparse_conjunction_evaluator<XprType> Base;
377
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
378
- };
379
- // "dense && sparse"
380
- template<typename Lhs, typename Rhs>
381
- struct binary_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs>, IndexBased, IteratorBased>
382
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> >
383
- {
384
- typedef CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> XprType;
385
- typedef sparse_conjunction_evaluator<XprType> Base;
386
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
387
- };
388
- // "sparse && dense"
389
- template<typename Lhs, typename Rhs>
390
- struct binary_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs>, IteratorBased, IndexBased>
391
- : sparse_conjunction_evaluator<CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> >
392
- {
393
- typedef CwiseBinaryOp<scalar_boolean_and_op, Lhs, Rhs> XprType;
394
- typedef sparse_conjunction_evaluator<XprType> Base;
395
- explicit binary_evaluator(const XprType& xpr) : Base(xpr) {}
396
- };
397
-
398
- // "sparse ^ sparse"
399
- template<typename XprType>
400
- struct sparse_conjunction_evaluator<XprType, IteratorBased, IteratorBased>
401
- : evaluator_base<XprType>
402
- {
403
- protected:
404
- typedef typename XprType::Functor BinaryOp;
405
- typedef typename XprType::Lhs LhsArg;
406
- typedef typename XprType::Rhs RhsArg;
407
- typedef typename evaluator<LhsArg>::InnerIterator LhsIterator;
408
- typedef typename evaluator<RhsArg>::InnerIterator RhsIterator;
409
- typedef typename XprType::StorageIndex StorageIndex;
410
- typedef typename traits<XprType>::Scalar Scalar;
411
- public:
412
-
413
- class InnerIterator
414
- {
415
- public:
416
-
417
- EIGEN_STRONG_INLINE InnerIterator(const sparse_conjunction_evaluator& aEval, Index outer)
418
- : m_lhsIter(aEval.m_lhsImpl,outer), m_rhsIter(aEval.m_rhsImpl,outer), m_functor(aEval.m_functor)
419
- {
420
- while (m_lhsIter && m_rhsIter && (m_lhsIter.index() != m_rhsIter.index()))
421
- {
422
- if (m_lhsIter.index() < m_rhsIter.index())
423
- ++m_lhsIter;
424
- else
425
- ++m_rhsIter;
426
- }
427
- }
428
-
429
- EIGEN_STRONG_INLINE InnerIterator& operator++()
430
- {
431
- ++m_lhsIter;
432
- ++m_rhsIter;
433
- while (m_lhsIter && m_rhsIter && (m_lhsIter.index() != m_rhsIter.index()))
434
- {
435
- if (m_lhsIter.index() < m_rhsIter.index())
436
- ++m_lhsIter;
437
- else
438
- ++m_rhsIter;
439
- }
440
- return *this;
441
- }
442
-
443
- EIGEN_STRONG_INLINE Scalar value() const { return m_functor(m_lhsIter.value(), m_rhsIter.value()); }
444
-
445
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_lhsIter.index(); }
446
- EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
447
- EIGEN_STRONG_INLINE Index row() const { return m_lhsIter.row(); }
448
- EIGEN_STRONG_INLINE Index col() const { return m_lhsIter.col(); }
449
-
450
- EIGEN_STRONG_INLINE operator bool() const { return (m_lhsIter && m_rhsIter); }
451
-
452
- protected:
453
- LhsIterator m_lhsIter;
454
- RhsIterator m_rhsIter;
455
- const BinaryOp& m_functor;
456
- };
457
-
458
-
459
- enum {
460
- CoeffReadCost = int(evaluator<LhsArg>::CoeffReadCost) + int(evaluator<RhsArg>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
461
- Flags = XprType::Flags
462
- };
463
-
464
- explicit sparse_conjunction_evaluator(const XprType& xpr)
465
- : m_functor(xpr.functor()),
466
- m_lhsImpl(xpr.lhs()),
467
- m_rhsImpl(xpr.rhs())
468
- {
469
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
470
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
471
- }
472
-
473
- inline Index nonZerosEstimate() const {
474
- return (std::min)(m_lhsImpl.nonZerosEstimate(), m_rhsImpl.nonZerosEstimate());
475
- }
476
-
477
- protected:
478
- const BinaryOp m_functor;
479
- evaluator<LhsArg> m_lhsImpl;
480
- evaluator<RhsArg> m_rhsImpl;
481
- };
482
-
483
- // "dense ^ sparse"
484
- template<typename XprType>
485
- struct sparse_conjunction_evaluator<XprType, IndexBased, IteratorBased>
486
- : evaluator_base<XprType>
487
- {
488
- protected:
489
- typedef typename XprType::Functor BinaryOp;
490
- typedef typename XprType::Lhs LhsArg;
491
- typedef typename XprType::Rhs RhsArg;
492
- typedef evaluator<LhsArg> LhsEvaluator;
493
- typedef typename evaluator<RhsArg>::InnerIterator RhsIterator;
494
- typedef typename XprType::StorageIndex StorageIndex;
495
- typedef typename traits<XprType>::Scalar Scalar;
496
- public:
497
-
498
- class InnerIterator
499
- {
500
- enum { IsRowMajor = (int(RhsArg::Flags)&RowMajorBit)==RowMajorBit };
501
-
502
- public:
503
-
504
- EIGEN_STRONG_INLINE InnerIterator(const sparse_conjunction_evaluator& aEval, Index outer)
505
- : m_lhsEval(aEval.m_lhsImpl), m_rhsIter(aEval.m_rhsImpl,outer), m_functor(aEval.m_functor), m_outer(outer)
506
- {}
507
-
508
- EIGEN_STRONG_INLINE InnerIterator& operator++()
509
- {
510
- ++m_rhsIter;
511
- return *this;
512
- }
513
-
514
- EIGEN_STRONG_INLINE Scalar value() const
515
- { return m_functor(m_lhsEval.coeff(IsRowMajor?m_outer:m_rhsIter.index(),IsRowMajor?m_rhsIter.index():m_outer), m_rhsIter.value()); }
516
-
517
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_rhsIter.index(); }
518
- EIGEN_STRONG_INLINE Index outer() const { return m_rhsIter.outer(); }
519
- EIGEN_STRONG_INLINE Index row() const { return m_rhsIter.row(); }
520
- EIGEN_STRONG_INLINE Index col() const { return m_rhsIter.col(); }
521
-
522
- EIGEN_STRONG_INLINE operator bool() const { return m_rhsIter; }
523
-
524
- protected:
525
- const LhsEvaluator &m_lhsEval;
526
- RhsIterator m_rhsIter;
527
- const BinaryOp& m_functor;
528
- const Index m_outer;
529
- };
530
-
531
-
532
- enum {
533
- CoeffReadCost = int(evaluator<LhsArg>::CoeffReadCost) + int(evaluator<RhsArg>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
534
- Flags = XprType::Flags
535
- };
536
-
537
- explicit sparse_conjunction_evaluator(const XprType& xpr)
538
- : m_functor(xpr.functor()),
539
- m_lhsImpl(xpr.lhs()),
540
- m_rhsImpl(xpr.rhs())
541
- {
542
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
543
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
544
- }
545
-
546
- inline Index nonZerosEstimate() const {
547
- return m_rhsImpl.nonZerosEstimate();
548
- }
549
-
550
- protected:
551
- const BinaryOp m_functor;
552
- evaluator<LhsArg> m_lhsImpl;
553
- evaluator<RhsArg> m_rhsImpl;
554
- };
555
-
556
- // "sparse ^ dense"
557
- template<typename XprType>
558
- struct sparse_conjunction_evaluator<XprType, IteratorBased, IndexBased>
559
- : evaluator_base<XprType>
560
- {
561
- protected:
562
- typedef typename XprType::Functor BinaryOp;
563
- typedef typename XprType::Lhs LhsArg;
564
- typedef typename XprType::Rhs RhsArg;
565
- typedef typename evaluator<LhsArg>::InnerIterator LhsIterator;
566
- typedef evaluator<RhsArg> RhsEvaluator;
567
- typedef typename XprType::StorageIndex StorageIndex;
568
- typedef typename traits<XprType>::Scalar Scalar;
569
- public:
570
-
571
- class InnerIterator
572
- {
573
- enum { IsRowMajor = (int(LhsArg::Flags)&RowMajorBit)==RowMajorBit };
574
-
575
- public:
576
-
577
- EIGEN_STRONG_INLINE InnerIterator(const sparse_conjunction_evaluator& aEval, Index outer)
578
- : m_lhsIter(aEval.m_lhsImpl,outer), m_rhsEval(aEval.m_rhsImpl), m_functor(aEval.m_functor), m_outer(outer)
579
- {}
580
-
581
- EIGEN_STRONG_INLINE InnerIterator& operator++()
582
- {
583
- ++m_lhsIter;
584
- return *this;
585
- }
586
-
587
- EIGEN_STRONG_INLINE Scalar value() const
588
- { return m_functor(m_lhsIter.value(),
589
- m_rhsEval.coeff(IsRowMajor?m_outer:m_lhsIter.index(),IsRowMajor?m_lhsIter.index():m_outer)); }
590
-
591
- EIGEN_STRONG_INLINE StorageIndex index() const { return m_lhsIter.index(); }
592
- EIGEN_STRONG_INLINE Index outer() const { return m_lhsIter.outer(); }
593
- EIGEN_STRONG_INLINE Index row() const { return m_lhsIter.row(); }
594
- EIGEN_STRONG_INLINE Index col() const { return m_lhsIter.col(); }
595
-
596
- EIGEN_STRONG_INLINE operator bool() const { return m_lhsIter; }
597
-
598
- protected:
599
- LhsIterator m_lhsIter;
600
- const evaluator<RhsArg> &m_rhsEval;
601
- const BinaryOp& m_functor;
602
- const Index m_outer;
603
- };
604
-
605
-
606
- enum {
607
- CoeffReadCost = int(evaluator<LhsArg>::CoeffReadCost) + int(evaluator<RhsArg>::CoeffReadCost) + int(functor_traits<BinaryOp>::Cost),
608
- Flags = XprType::Flags
609
- };
610
-
611
- explicit sparse_conjunction_evaluator(const XprType& xpr)
612
- : m_functor(xpr.functor()),
613
- m_lhsImpl(xpr.lhs()),
614
- m_rhsImpl(xpr.rhs())
615
- {
616
- EIGEN_INTERNAL_CHECK_COST_VALUE(functor_traits<BinaryOp>::Cost);
617
- EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
618
- }
619
-
620
- inline Index nonZerosEstimate() const {
621
- return m_lhsImpl.nonZerosEstimate();
622
- }
623
-
624
- protected:
625
- const BinaryOp m_functor;
626
- evaluator<LhsArg> m_lhsImpl;
627
- evaluator<RhsArg> m_rhsImpl;
628
- };
629
-
630
- }
631
-
632
- /***************************************************************************
633
- * Implementation of SparseMatrixBase and SparseCwise functions/operators
634
- ***************************************************************************/
635
-
636
- template<typename Derived>
637
- template<typename OtherDerived>
638
- Derived& SparseMatrixBase<Derived>::operator+=(const EigenBase<OtherDerived> &other)
639
- {
640
- call_assignment(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
641
- return derived();
642
- }
643
-
644
- template<typename Derived>
645
- template<typename OtherDerived>
646
- Derived& SparseMatrixBase<Derived>::operator-=(const EigenBase<OtherDerived> &other)
647
- {
648
- call_assignment(derived(), other.derived(), internal::assign_op<Scalar,typename OtherDerived::Scalar>());
649
- return derived();
650
- }
651
-
652
- template<typename Derived>
653
- template<typename OtherDerived>
654
- EIGEN_STRONG_INLINE Derived &
655
- SparseMatrixBase<Derived>::operator-=(const SparseMatrixBase<OtherDerived> &other)
656
- {
657
- return derived() = derived() - other.derived();
658
- }
659
-
660
- template<typename Derived>
661
- template<typename OtherDerived>
662
- EIGEN_STRONG_INLINE Derived &
663
- SparseMatrixBase<Derived>::operator+=(const SparseMatrixBase<OtherDerived>& other)
664
- {
665
- return derived() = derived() + other.derived();
666
- }
667
-
668
- template<typename Derived>
669
- template<typename OtherDerived>
670
- Derived& SparseMatrixBase<Derived>::operator+=(const DiagonalBase<OtherDerived>& other)
671
- {
672
- call_assignment_no_alias(derived(), other.derived(), internal::add_assign_op<Scalar,typename OtherDerived::Scalar>());
673
- return derived();
674
- }
675
-
676
- template<typename Derived>
677
- template<typename OtherDerived>
678
- Derived& SparseMatrixBase<Derived>::operator-=(const DiagonalBase<OtherDerived>& other)
679
- {
680
- call_assignment_no_alias(derived(), other.derived(), internal::sub_assign_op<Scalar,typename OtherDerived::Scalar>());
681
- return derived();
682
- }
683
-
684
- template<typename Derived>
685
- template<typename OtherDerived>
686
- EIGEN_STRONG_INLINE const typename SparseMatrixBase<Derived>::template CwiseProductDenseReturnType<OtherDerived>::Type
687
- SparseMatrixBase<Derived>::cwiseProduct(const MatrixBase<OtherDerived> &other) const
688
- {
689
- return typename CwiseProductDenseReturnType<OtherDerived>::Type(derived(), other.derived());
690
- }
691
-
692
- template<typename DenseDerived, typename SparseDerived>
693
- EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_sum_op<typename DenseDerived::Scalar,typename SparseDerived::Scalar>, const DenseDerived, const SparseDerived>
694
- operator+(const MatrixBase<DenseDerived> &a, const SparseMatrixBase<SparseDerived> &b)
695
- {
696
- return CwiseBinaryOp<internal::scalar_sum_op<typename DenseDerived::Scalar,typename SparseDerived::Scalar>, const DenseDerived, const SparseDerived>(a.derived(), b.derived());
697
- }
698
-
699
- template<typename SparseDerived, typename DenseDerived>
700
- EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_sum_op<typename SparseDerived::Scalar,typename DenseDerived::Scalar>, const SparseDerived, const DenseDerived>
701
- operator+(const SparseMatrixBase<SparseDerived> &a, const MatrixBase<DenseDerived> &b)
702
- {
703
- return CwiseBinaryOp<internal::scalar_sum_op<typename SparseDerived::Scalar,typename DenseDerived::Scalar>, const SparseDerived, const DenseDerived>(a.derived(), b.derived());
704
- }
705
-
706
- template<typename DenseDerived, typename SparseDerived>
707
- EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_difference_op<typename DenseDerived::Scalar,typename SparseDerived::Scalar>, const DenseDerived, const SparseDerived>
708
- operator-(const MatrixBase<DenseDerived> &a, const SparseMatrixBase<SparseDerived> &b)
709
- {
710
- return CwiseBinaryOp<internal::scalar_difference_op<typename DenseDerived::Scalar,typename SparseDerived::Scalar>, const DenseDerived, const SparseDerived>(a.derived(), b.derived());
711
- }
712
-
713
- template<typename SparseDerived, typename DenseDerived>
714
- EIGEN_STRONG_INLINE const CwiseBinaryOp<internal::scalar_difference_op<typename SparseDerived::Scalar,typename DenseDerived::Scalar>, const SparseDerived, const DenseDerived>
715
- operator-(const SparseMatrixBase<SparseDerived> &a, const MatrixBase<DenseDerived> &b)
716
- {
717
- return CwiseBinaryOp<internal::scalar_difference_op<typename SparseDerived::Scalar,typename DenseDerived::Scalar>, const SparseDerived, const DenseDerived>(a.derived(), b.derived());
718
- }
719
-
720
- } // end namespace Eigen
721
-
722
- #endif // EIGEN_SPARSE_CWISE_BINARY_OP_H