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

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,124 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 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_SPARSESOLVERBASE_H
11
- #define EIGEN_SPARSESOLVERBASE_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- /** \internal
18
- * Helper functions to solve with a sparse right-hand-side and result.
19
- * The rhs is decomposed into small vertical panels which are solved through dense temporaries.
20
- */
21
- template<typename Decomposition, typename Rhs, typename Dest>
22
- typename enable_if<Rhs::ColsAtCompileTime!=1 && Dest::ColsAtCompileTime!=1>::type
23
- solve_sparse_through_dense_panels(const Decomposition &dec, const Rhs& rhs, Dest &dest)
24
- {
25
- EIGEN_STATIC_ASSERT((Dest::Flags&RowMajorBit)==0,THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES);
26
- typedef typename Dest::Scalar DestScalar;
27
- // we process the sparse rhs per block of NbColsAtOnce columns temporarily stored into a dense matrix.
28
- static const Index NbColsAtOnce = 4;
29
- Index rhsCols = rhs.cols();
30
- Index size = rhs.rows();
31
- // the temporary matrices do not need more columns than NbColsAtOnce:
32
- Index tmpCols = (std::min)(rhsCols, NbColsAtOnce);
33
- Eigen::Matrix<DestScalar,Dynamic,Dynamic> tmp(size,tmpCols);
34
- Eigen::Matrix<DestScalar,Dynamic,Dynamic> tmpX(size,tmpCols);
35
- for(Index k=0; k<rhsCols; k+=NbColsAtOnce)
36
- {
37
- Index actualCols = std::min<Index>(rhsCols-k, NbColsAtOnce);
38
- tmp.leftCols(actualCols) = rhs.middleCols(k,actualCols);
39
- tmpX.leftCols(actualCols) = dec.solve(tmp.leftCols(actualCols));
40
- dest.middleCols(k,actualCols) = tmpX.leftCols(actualCols).sparseView();
41
- }
42
- }
43
-
44
- // Overload for vector as rhs
45
- template<typename Decomposition, typename Rhs, typename Dest>
46
- typename enable_if<Rhs::ColsAtCompileTime==1 || Dest::ColsAtCompileTime==1>::type
47
- solve_sparse_through_dense_panels(const Decomposition &dec, const Rhs& rhs, Dest &dest)
48
- {
49
- typedef typename Dest::Scalar DestScalar;
50
- Index size = rhs.rows();
51
- Eigen::Matrix<DestScalar,Dynamic,1> rhs_dense(rhs);
52
- Eigen::Matrix<DestScalar,Dynamic,1> dest_dense(size);
53
- dest_dense = dec.solve(rhs_dense);
54
- dest = dest_dense.sparseView();
55
- }
56
-
57
- } // end namespace internal
58
-
59
- /** \class SparseSolverBase
60
- * \ingroup SparseCore_Module
61
- * \brief A base class for sparse solvers
62
- *
63
- * \tparam Derived the actual type of the solver.
64
- *
65
- */
66
- template<typename Derived>
67
- class SparseSolverBase : internal::noncopyable
68
- {
69
- public:
70
-
71
- /** Default constructor */
72
- SparseSolverBase()
73
- : m_isInitialized(false)
74
- {}
75
-
76
- ~SparseSolverBase()
77
- {}
78
-
79
- Derived& derived() { return *static_cast<Derived*>(this); }
80
- const Derived& derived() const { return *static_cast<const Derived*>(this); }
81
-
82
- /** \returns an expression of the solution x of \f$ A x = b \f$ using the current decomposition of A.
83
- *
84
- * \sa compute()
85
- */
86
- template<typename Rhs>
87
- inline const Solve<Derived, Rhs>
88
- solve(const MatrixBase<Rhs>& b) const
89
- {
90
- eigen_assert(m_isInitialized && "Solver is not initialized.");
91
- eigen_assert(derived().rows()==b.rows() && "solve(): invalid number of rows of the right hand side matrix b");
92
- return Solve<Derived, Rhs>(derived(), b.derived());
93
- }
94
-
95
- /** \returns an expression of the solution x of \f$ A x = b \f$ using the current decomposition of A.
96
- *
97
- * \sa compute()
98
- */
99
- template<typename Rhs>
100
- inline const Solve<Derived, Rhs>
101
- solve(const SparseMatrixBase<Rhs>& b) const
102
- {
103
- eigen_assert(m_isInitialized && "Solver is not initialized.");
104
- eigen_assert(derived().rows()==b.rows() && "solve(): invalid number of rows of the right hand side matrix b");
105
- return Solve<Derived, Rhs>(derived(), b.derived());
106
- }
107
-
108
- #ifndef EIGEN_PARSED_BY_DOXYGEN
109
- /** \internal default implementation of solving with a sparse rhs */
110
- template<typename Rhs,typename Dest>
111
- void _solve_impl(const SparseMatrixBase<Rhs> &b, SparseMatrixBase<Dest> &dest) const
112
- {
113
- internal::solve_sparse_through_dense_panels(derived(), b.derived(), dest.derived());
114
- }
115
- #endif // EIGEN_PARSED_BY_DOXYGEN
116
-
117
- protected:
118
-
119
- mutable bool m_isInitialized;
120
- };
121
-
122
- } // end namespace Eigen
123
-
124
- #endif // EIGEN_SPARSESOLVERBASE_H
@@ -1,198 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2014 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_SPARSESPARSEPRODUCTWITHPRUNING_H
11
- #define EIGEN_SPARSESPARSEPRODUCTWITHPRUNING_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
-
18
- // perform a pseudo in-place sparse * sparse product assuming all matrices are col major
19
- template<typename Lhs, typename Rhs, typename ResultType>
20
- static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance)
21
- {
22
- // return sparse_sparse_product_with_pruning_impl2(lhs,rhs,res);
23
-
24
- typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
25
- typedef typename remove_all<ResultType>::type::Scalar ResScalar;
26
- typedef typename remove_all<Lhs>::type::StorageIndex StorageIndex;
27
-
28
- // make sure to call innerSize/outerSize since we fake the storage order.
29
- Index rows = lhs.innerSize();
30
- Index cols = rhs.outerSize();
31
- //Index size = lhs.outerSize();
32
- eigen_assert(lhs.outerSize() == rhs.innerSize());
33
-
34
- // allocate a temporary buffer
35
- AmbiVector<ResScalar,StorageIndex> tempVector(rows);
36
-
37
- // mimics a resizeByInnerOuter:
38
- if(ResultType::IsRowMajor)
39
- res.resize(cols, rows);
40
- else
41
- res.resize(rows, cols);
42
-
43
- evaluator<Lhs> lhsEval(lhs);
44
- evaluator<Rhs> rhsEval(rhs);
45
-
46
- // estimate the number of non zero entries
47
- // given a rhs column containing Y non zeros, we assume that the respective Y columns
48
- // of the lhs differs in average of one non zeros, thus the number of non zeros for
49
- // the product of a rhs column with the lhs is X+Y where X is the average number of non zero
50
- // per column of the lhs.
51
- // Therefore, we have nnz(lhs*rhs) = nnz(lhs) + nnz(rhs)
52
- Index estimated_nnz_prod = lhsEval.nonZerosEstimate() + rhsEval.nonZerosEstimate();
53
-
54
- res.reserve(estimated_nnz_prod);
55
- double ratioColRes = double(estimated_nnz_prod)/(double(lhs.rows())*double(rhs.cols()));
56
- for (Index j=0; j<cols; ++j)
57
- {
58
- // FIXME:
59
- //double ratioColRes = (double(rhs.innerVector(j).nonZeros()) + double(lhs.nonZeros())/double(lhs.cols()))/double(lhs.rows());
60
- // let's do a more accurate determination of the nnz ratio for the current column j of res
61
- tempVector.init(ratioColRes);
62
- tempVector.setZero();
63
- for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
64
- {
65
- // FIXME should be written like this: tmp += rhsIt.value() * lhs.col(rhsIt.index())
66
- tempVector.restart();
67
- RhsScalar x = rhsIt.value();
68
- for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, rhsIt.index()); lhsIt; ++lhsIt)
69
- {
70
- tempVector.coeffRef(lhsIt.index()) += lhsIt.value() * x;
71
- }
72
- }
73
- res.startVec(j);
74
- for (typename AmbiVector<ResScalar,StorageIndex>::Iterator it(tempVector,tolerance); it; ++it)
75
- res.insertBackByOuterInner(j,it.index()) = it.value();
76
- }
77
- res.finalize();
78
- }
79
-
80
- template<typename Lhs, typename Rhs, typename ResultType,
81
- int LhsStorageOrder = traits<Lhs>::Flags&RowMajorBit,
82
- int RhsStorageOrder = traits<Rhs>::Flags&RowMajorBit,
83
- int ResStorageOrder = traits<ResultType>::Flags&RowMajorBit>
84
- struct sparse_sparse_product_with_pruning_selector;
85
-
86
- template<typename Lhs, typename Rhs, typename ResultType>
87
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,ColMajor>
88
- {
89
- typedef typename ResultType::RealScalar RealScalar;
90
-
91
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
92
- {
93
- typename remove_all<ResultType>::type _res(res.rows(), res.cols());
94
- internal::sparse_sparse_product_with_pruning_impl<Lhs,Rhs,ResultType>(lhs, rhs, _res, tolerance);
95
- res.swap(_res);
96
- }
97
- };
98
-
99
- template<typename Lhs, typename Rhs, typename ResultType>
100
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,RowMajor>
101
- {
102
- typedef typename ResultType::RealScalar RealScalar;
103
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
104
- {
105
- // we need a col-major matrix to hold the result
106
- typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> SparseTemporaryType;
107
- SparseTemporaryType _res(res.rows(), res.cols());
108
- internal::sparse_sparse_product_with_pruning_impl<Lhs,Rhs,SparseTemporaryType>(lhs, rhs, _res, tolerance);
109
- res = _res;
110
- }
111
- };
112
-
113
- template<typename Lhs, typename Rhs, typename ResultType>
114
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,RowMajor>
115
- {
116
- typedef typename ResultType::RealScalar RealScalar;
117
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
118
- {
119
- // let's transpose the product to get a column x column product
120
- typename remove_all<ResultType>::type _res(res.rows(), res.cols());
121
- internal::sparse_sparse_product_with_pruning_impl<Rhs,Lhs,ResultType>(rhs, lhs, _res, tolerance);
122
- res.swap(_res);
123
- }
124
- };
125
-
126
- template<typename Lhs, typename Rhs, typename ResultType>
127
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,ColMajor>
128
- {
129
- typedef typename ResultType::RealScalar RealScalar;
130
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
131
- {
132
- typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixLhs;
133
- typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixRhs;
134
- ColMajorMatrixLhs colLhs(lhs);
135
- ColMajorMatrixRhs colRhs(rhs);
136
- internal::sparse_sparse_product_with_pruning_impl<ColMajorMatrixLhs,ColMajorMatrixRhs,ResultType>(colLhs, colRhs, res, tolerance);
137
-
138
- // let's transpose the product to get a column x column product
139
- // typedef SparseMatrix<typename ResultType::Scalar> SparseTemporaryType;
140
- // SparseTemporaryType _res(res.cols(), res.rows());
141
- // sparse_sparse_product_with_pruning_impl<Rhs,Lhs,SparseTemporaryType>(rhs, lhs, _res);
142
- // res = _res.transpose();
143
- }
144
- };
145
-
146
- template<typename Lhs, typename Rhs, typename ResultType>
147
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,RowMajor>
148
- {
149
- typedef typename ResultType::RealScalar RealScalar;
150
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
151
- {
152
- typedef SparseMatrix<typename Lhs::Scalar,RowMajor,typename Lhs::StorageIndex> RowMajorMatrixLhs;
153
- RowMajorMatrixLhs rowLhs(lhs);
154
- sparse_sparse_product_with_pruning_selector<RowMajorMatrixLhs,Rhs,ResultType,RowMajor,RowMajor>(rowLhs,rhs,res,tolerance);
155
- }
156
- };
157
-
158
- template<typename Lhs, typename Rhs, typename ResultType>
159
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,RowMajor>
160
- {
161
- typedef typename ResultType::RealScalar RealScalar;
162
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
163
- {
164
- typedef SparseMatrix<typename Rhs::Scalar,RowMajor,typename Lhs::StorageIndex> RowMajorMatrixRhs;
165
- RowMajorMatrixRhs rowRhs(rhs);
166
- sparse_sparse_product_with_pruning_selector<Lhs,RowMajorMatrixRhs,ResultType,RowMajor,RowMajor,RowMajor>(lhs,rowRhs,res,tolerance);
167
- }
168
- };
169
-
170
- template<typename Lhs, typename Rhs, typename ResultType>
171
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,ColMajor>
172
- {
173
- typedef typename ResultType::RealScalar RealScalar;
174
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
175
- {
176
- typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixRhs;
177
- ColMajorMatrixRhs colRhs(rhs);
178
- internal::sparse_sparse_product_with_pruning_impl<Lhs,ColMajorMatrixRhs,ResultType>(lhs, colRhs, res, tolerance);
179
- }
180
- };
181
-
182
- template<typename Lhs, typename Rhs, typename ResultType>
183
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,ColMajor>
184
- {
185
- typedef typename ResultType::RealScalar RealScalar;
186
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
187
- {
188
- typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixLhs;
189
- ColMajorMatrixLhs colLhs(lhs);
190
- internal::sparse_sparse_product_with_pruning_impl<ColMajorMatrixLhs,Rhs,ResultType>(colLhs, rhs, res, tolerance);
191
- }
192
- };
193
-
194
- } // end namespace internal
195
-
196
- } // end namespace Eigen
197
-
198
- #endif // EIGEN_SPARSESPARSEPRODUCTWITHPRUNING_H
@@ -1,92 +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_SPARSETRANSPOSE_H
11
- #define EIGEN_SPARSETRANSPOSE_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
- template<typename MatrixType,int CompressedAccess=int(MatrixType::Flags&CompressedAccessBit)>
17
- class SparseTransposeImpl
18
- : public SparseMatrixBase<Transpose<MatrixType> >
19
- {};
20
-
21
- template<typename MatrixType>
22
- class SparseTransposeImpl<MatrixType,CompressedAccessBit>
23
- : public SparseCompressedBase<Transpose<MatrixType> >
24
- {
25
- typedef SparseCompressedBase<Transpose<MatrixType> > Base;
26
- public:
27
- using Base::derived;
28
- typedef typename Base::Scalar Scalar;
29
- typedef typename Base::StorageIndex StorageIndex;
30
-
31
- inline Index nonZeros() const { return derived().nestedExpression().nonZeros(); }
32
-
33
- inline const Scalar* valuePtr() const { return derived().nestedExpression().valuePtr(); }
34
- inline const StorageIndex* innerIndexPtr() const { return derived().nestedExpression().innerIndexPtr(); }
35
- inline const StorageIndex* outerIndexPtr() const { return derived().nestedExpression().outerIndexPtr(); }
36
- inline const StorageIndex* innerNonZeroPtr() const { return derived().nestedExpression().innerNonZeroPtr(); }
37
-
38
- inline Scalar* valuePtr() { return derived().nestedExpression().valuePtr(); }
39
- inline StorageIndex* innerIndexPtr() { return derived().nestedExpression().innerIndexPtr(); }
40
- inline StorageIndex* outerIndexPtr() { return derived().nestedExpression().outerIndexPtr(); }
41
- inline StorageIndex* innerNonZeroPtr() { return derived().nestedExpression().innerNonZeroPtr(); }
42
- };
43
- }
44
-
45
- template<typename MatrixType> class TransposeImpl<MatrixType,Sparse>
46
- : public internal::SparseTransposeImpl<MatrixType>
47
- {
48
- protected:
49
- typedef internal::SparseTransposeImpl<MatrixType> Base;
50
- };
51
-
52
- namespace internal {
53
-
54
- template<typename ArgType>
55
- struct unary_evaluator<Transpose<ArgType>, IteratorBased>
56
- : public evaluator_base<Transpose<ArgType> >
57
- {
58
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
59
- public:
60
- typedef Transpose<ArgType> XprType;
61
-
62
- inline Index nonZerosEstimate() const {
63
- return m_argImpl.nonZerosEstimate();
64
- }
65
-
66
- class InnerIterator : public EvalIterator
67
- {
68
- public:
69
- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& unaryOp, Index outer)
70
- : EvalIterator(unaryOp.m_argImpl,outer)
71
- {}
72
-
73
- Index row() const { return EvalIterator::col(); }
74
- Index col() const { return EvalIterator::row(); }
75
- };
76
-
77
- enum {
78
- CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
79
- Flags = XprType::Flags
80
- };
81
-
82
- explicit unary_evaluator(const XprType& op) :m_argImpl(op.nestedExpression()) {}
83
-
84
- protected:
85
- evaluator<ArgType> m_argImpl;
86
- };
87
-
88
- } // end namespace internal
89
-
90
- } // end namespace Eigen
91
-
92
- #endif // EIGEN_SPARSETRANSPOSE_H
@@ -1,189 +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
- // Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #ifndef EIGEN_SPARSE_TRIANGULARVIEW_H
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- #define EIGEN_SPARSE_TRIANGULARVIEW_H
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-
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- namespace Eigen {
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-
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- /** \ingroup SparseCore_Module
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- *
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- * \brief Base class for a triangular part in a \b sparse matrix
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- *
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- * This class is an abstract base class of class TriangularView, and objects of type TriangularViewImpl cannot be instantiated.
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- * It extends class TriangularView with additional methods which are available for sparse expressions only.
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- *
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- * \sa class TriangularView, SparseMatrixBase::triangularView()
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- */
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- template<typename MatrixType, unsigned int Mode> class TriangularViewImpl<MatrixType,Mode,Sparse>
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- : public SparseMatrixBase<TriangularView<MatrixType,Mode> >
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- {
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- enum { SkipFirst = ((Mode&Lower) && !(MatrixType::Flags&RowMajorBit))
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- || ((Mode&Upper) && (MatrixType::Flags&RowMajorBit)),
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- SkipLast = !SkipFirst,
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- SkipDiag = (Mode&ZeroDiag) ? 1 : 0,
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- HasUnitDiag = (Mode&UnitDiag) ? 1 : 0
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- };
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-
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- typedef TriangularView<MatrixType,Mode> TriangularViewType;
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-
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- protected:
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- // dummy solve function to make TriangularView happy.
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- void solve() const;
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-
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- typedef SparseMatrixBase<TriangularViewType> Base;
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- public:
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-
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- EIGEN_SPARSE_PUBLIC_INTERFACE(TriangularViewType)
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-
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- typedef typename MatrixType::Nested MatrixTypeNested;
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- typedef typename internal::remove_reference<MatrixTypeNested>::type MatrixTypeNestedNonRef;
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- typedef typename internal::remove_all<MatrixTypeNested>::type MatrixTypeNestedCleaned;
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-
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- template<typename RhsType, typename DstType>
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE void _solve_impl(const RhsType &rhs, DstType &dst) const {
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- if(!(internal::is_same<RhsType,DstType>::value && internal::extract_data(dst) == internal::extract_data(rhs)))
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- dst = rhs;
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- this->solveInPlace(dst);
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- }
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-
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- /** Applies the inverse of \c *this to the dense vector or matrix \a other, "in-place" */
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- template<typename OtherDerived> void solveInPlace(MatrixBase<OtherDerived>& other) const;
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-
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- /** Applies the inverse of \c *this to the sparse vector or matrix \a other, "in-place" */
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- template<typename OtherDerived> void solveInPlace(SparseMatrixBase<OtherDerived>& other) const;
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-
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- };
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-
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- namespace internal {
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-
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- template<typename ArgType, unsigned int Mode>
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- struct unary_evaluator<TriangularView<ArgType,Mode>, IteratorBased>
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- : evaluator_base<TriangularView<ArgType,Mode> >
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- {
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- typedef TriangularView<ArgType,Mode> XprType;
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-
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- protected:
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-
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- typedef typename XprType::Scalar Scalar;
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- typedef typename XprType::StorageIndex StorageIndex;
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- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
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-
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- enum { SkipFirst = ((Mode&Lower) && !(ArgType::Flags&RowMajorBit))
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- || ((Mode&Upper) && (ArgType::Flags&RowMajorBit)),
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- SkipLast = !SkipFirst,
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- SkipDiag = (Mode&ZeroDiag) ? 1 : 0,
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- HasUnitDiag = (Mode&UnitDiag) ? 1 : 0
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- };
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-
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- public:
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-
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- enum {
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- CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
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- Flags = XprType::Flags
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- };
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-
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- explicit unary_evaluator(const XprType &xpr) : m_argImpl(xpr.nestedExpression()), m_arg(xpr.nestedExpression()) {}
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-
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- inline Index nonZerosEstimate() const {
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- return m_argImpl.nonZerosEstimate();
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- }
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-
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- class InnerIterator : public EvalIterator
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- {
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- typedef EvalIterator Base;
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- public:
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-
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- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& xprEval, Index outer)
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- : Base(xprEval.m_argImpl,outer), m_returnOne(false), m_containsDiag(Base::outer()<xprEval.m_arg.innerSize())
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- {
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- if(SkipFirst)
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- {
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- while((*this) && ((HasUnitDiag||SkipDiag) ? this->index()<=outer : this->index()<outer))
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- Base::operator++();
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- if(HasUnitDiag)
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- m_returnOne = m_containsDiag;
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- }
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- else if(HasUnitDiag && ((!Base::operator bool()) || Base::index()>=Base::outer()))
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- {
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- if((!SkipFirst) && Base::operator bool())
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- Base::operator++();
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- m_returnOne = m_containsDiag;
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- }
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- }
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-
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- EIGEN_STRONG_INLINE InnerIterator& operator++()
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- {
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- if(HasUnitDiag && m_returnOne)
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- m_returnOne = false;
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- else
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- {
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- Base::operator++();
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- if(HasUnitDiag && (!SkipFirst) && ((!Base::operator bool()) || Base::index()>=Base::outer()))
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- {
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- if((!SkipFirst) && Base::operator bool())
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- Base::operator++();
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- m_returnOne = m_containsDiag;
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- }
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- }
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- return *this;
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- }
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-
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- EIGEN_STRONG_INLINE operator bool() const
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- {
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- if(HasUnitDiag && m_returnOne)
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- return true;
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- if(SkipFirst) return Base::operator bool();
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- else
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- {
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- if (SkipDiag) return (Base::operator bool() && this->index() < this->outer());
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- else return (Base::operator bool() && this->index() <= this->outer());
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- }
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- }
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-
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- // inline Index row() const { return (ArgType::Flags&RowMajorBit ? Base::outer() : this->index()); }
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- // inline Index col() const { return (ArgType::Flags&RowMajorBit ? this->index() : Base::outer()); }
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- inline StorageIndex index() const
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- {
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- if(HasUnitDiag && m_returnOne) return internal::convert_index<StorageIndex>(Base::outer());
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- else return Base::index();
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- }
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- inline Scalar value() const
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- {
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- if(HasUnitDiag && m_returnOne) return Scalar(1);
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- else return Base::value();
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- }
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-
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- protected:
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- bool m_returnOne;
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- bool m_containsDiag;
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- private:
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- Scalar& valueRef();
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- };
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-
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- protected:
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- evaluator<ArgType> m_argImpl;
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- const ArgType& m_arg;
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- };
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-
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- } // end namespace internal
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-
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- template<typename Derived>
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- template<int Mode>
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- inline const TriangularView<const Derived, Mode>
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- SparseMatrixBase<Derived>::triangularView() const
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- {
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- return TriangularView<const Derived, Mode>(derived());
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- }
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_SPARSE_TRIANGULARVIEW_H