sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__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 +107 -5
  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 +1 -2
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  13. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  15. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  17. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  18. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  19. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  20. sequenzo/multidomain/cat.py +0 -53
  21. sequenzo/multidomain/idcd.py +0 -1
  22. sequenzo/openmp_setup.py +233 -0
  23. sequenzo/visualization/plot_transition_matrix.py +21 -22
  24. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  25. sequenzo-0.1.19.dist-info/RECORD +272 -0
  26. sequenzo/dissimilarity_measures/setup.py +0 -35
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  169. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  171. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  172. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  173. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  174. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  175. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  176. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  177. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  178. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  179. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  180. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  181. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  182. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  183. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  184. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  185. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  186. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  187. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  188. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  189. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  190. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  191. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  192. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  197. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  198. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  199. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  200. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  201. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  202. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  203. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  206. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  207. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  208. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  209. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  210. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  211. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  212. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  213. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
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  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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@@ -1,181 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPARSEPRODUCT_H
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- #define EIGEN_SPARSEPRODUCT_H
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-
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- namespace Eigen {
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-
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- /** \returns an expression of the product of two sparse matrices.
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- * By default a conservative product preserving the symbolic non zeros is performed.
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- * The automatic pruning of the small values can be achieved by calling the pruned() function
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- * in which case a totally different product algorithm is employed:
19
- * \code
20
- * C = (A*B).pruned(); // suppress numerical zeros (exact)
21
- * C = (A*B).pruned(ref);
22
- * C = (A*B).pruned(ref,epsilon);
23
- * \endcode
24
- * where \c ref is a meaningful non zero reference value.
25
- * */
26
- template<typename Derived>
27
- template<typename OtherDerived>
28
- inline const Product<Derived,OtherDerived,AliasFreeProduct>
29
- SparseMatrixBase<Derived>::operator*(const SparseMatrixBase<OtherDerived> &other) const
30
- {
31
- return Product<Derived,OtherDerived,AliasFreeProduct>(derived(), other.derived());
32
- }
33
-
34
- namespace internal {
35
-
36
- // sparse * sparse
37
- template<typename Lhs, typename Rhs, int ProductType>
38
- struct generic_product_impl<Lhs, Rhs, SparseShape, SparseShape, ProductType>
39
- {
40
- template<typename Dest>
41
- static void evalTo(Dest& dst, const Lhs& lhs, const Rhs& rhs)
42
- {
43
- evalTo(dst, lhs, rhs, typename evaluator_traits<Dest>::Shape());
44
- }
45
-
46
- // dense += sparse * sparse
47
- template<typename Dest,typename ActualLhs>
48
- static void addTo(Dest& dst, const ActualLhs& lhs, const Rhs& rhs, typename enable_if<is_same<typename evaluator_traits<Dest>::Shape,DenseShape>::value,int*>::type* = 0)
49
- {
50
- typedef typename nested_eval<ActualLhs,Dynamic>::type LhsNested;
51
- typedef typename nested_eval<Rhs,Dynamic>::type RhsNested;
52
- LhsNested lhsNested(lhs);
53
- RhsNested rhsNested(rhs);
54
- internal::sparse_sparse_to_dense_product_selector<typename remove_all<LhsNested>::type,
55
- typename remove_all<RhsNested>::type, Dest>::run(lhsNested,rhsNested,dst);
56
- }
57
-
58
- // dense -= sparse * sparse
59
- template<typename Dest>
60
- static void subTo(Dest& dst, const Lhs& lhs, const Rhs& rhs, typename enable_if<is_same<typename evaluator_traits<Dest>::Shape,DenseShape>::value,int*>::type* = 0)
61
- {
62
- addTo(dst, -lhs, rhs);
63
- }
64
-
65
- protected:
66
-
67
- // sparse = sparse * sparse
68
- template<typename Dest>
69
- static void evalTo(Dest& dst, const Lhs& lhs, const Rhs& rhs, SparseShape)
70
- {
71
- typedef typename nested_eval<Lhs,Dynamic>::type LhsNested;
72
- typedef typename nested_eval<Rhs,Dynamic>::type RhsNested;
73
- LhsNested lhsNested(lhs);
74
- RhsNested rhsNested(rhs);
75
- internal::conservative_sparse_sparse_product_selector<typename remove_all<LhsNested>::type,
76
- typename remove_all<RhsNested>::type, Dest>::run(lhsNested,rhsNested,dst);
77
- }
78
-
79
- // dense = sparse * sparse
80
- template<typename Dest>
81
- static void evalTo(Dest& dst, const Lhs& lhs, const Rhs& rhs, DenseShape)
82
- {
83
- dst.setZero();
84
- addTo(dst, lhs, rhs);
85
- }
86
- };
87
-
88
- // sparse * sparse-triangular
89
- template<typename Lhs, typename Rhs, int ProductType>
90
- struct generic_product_impl<Lhs, Rhs, SparseShape, SparseTriangularShape, ProductType>
91
- : public generic_product_impl<Lhs, Rhs, SparseShape, SparseShape, ProductType>
92
- {};
93
-
94
- // sparse-triangular * sparse
95
- template<typename Lhs, typename Rhs, int ProductType>
96
- struct generic_product_impl<Lhs, Rhs, SparseTriangularShape, SparseShape, ProductType>
97
- : public generic_product_impl<Lhs, Rhs, SparseShape, SparseShape, ProductType>
98
- {};
99
-
100
- // dense = sparse-product (can be sparse*sparse, sparse*perm, etc.)
101
- template< typename DstXprType, typename Lhs, typename Rhs>
102
- struct Assignment<DstXprType, Product<Lhs,Rhs,AliasFreeProduct>, internal::assign_op<typename DstXprType::Scalar,typename Product<Lhs,Rhs,AliasFreeProduct>::Scalar>, Sparse2Dense>
103
- {
104
- typedef Product<Lhs,Rhs,AliasFreeProduct> SrcXprType;
105
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> &)
106
- {
107
- Index dstRows = src.rows();
108
- Index dstCols = src.cols();
109
- if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
110
- dst.resize(dstRows, dstCols);
111
-
112
- generic_product_impl<Lhs, Rhs>::evalTo(dst,src.lhs(),src.rhs());
113
- }
114
- };
115
-
116
- // dense += sparse-product (can be sparse*sparse, sparse*perm, etc.)
117
- template< typename DstXprType, typename Lhs, typename Rhs>
118
- struct Assignment<DstXprType, Product<Lhs,Rhs,AliasFreeProduct>, internal::add_assign_op<typename DstXprType::Scalar,typename Product<Lhs,Rhs,AliasFreeProduct>::Scalar>, Sparse2Dense>
119
- {
120
- typedef Product<Lhs,Rhs,AliasFreeProduct> SrcXprType;
121
- static void run(DstXprType &dst, const SrcXprType &src, const internal::add_assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> &)
122
- {
123
- generic_product_impl<Lhs, Rhs>::addTo(dst,src.lhs(),src.rhs());
124
- }
125
- };
126
-
127
- // dense -= sparse-product (can be sparse*sparse, sparse*perm, etc.)
128
- template< typename DstXprType, typename Lhs, typename Rhs>
129
- struct Assignment<DstXprType, Product<Lhs,Rhs,AliasFreeProduct>, internal::sub_assign_op<typename DstXprType::Scalar,typename Product<Lhs,Rhs,AliasFreeProduct>::Scalar>, Sparse2Dense>
130
- {
131
- typedef Product<Lhs,Rhs,AliasFreeProduct> SrcXprType;
132
- static void run(DstXprType &dst, const SrcXprType &src, const internal::sub_assign_op<typename DstXprType::Scalar,typename SrcXprType::Scalar> &)
133
- {
134
- generic_product_impl<Lhs, Rhs>::subTo(dst,src.lhs(),src.rhs());
135
- }
136
- };
137
-
138
- template<typename Lhs, typename Rhs, int Options>
139
- struct unary_evaluator<SparseView<Product<Lhs, Rhs, Options> >, IteratorBased>
140
- : public evaluator<typename Product<Lhs, Rhs, DefaultProduct>::PlainObject>
141
- {
142
- typedef SparseView<Product<Lhs, Rhs, Options> > XprType;
143
- typedef typename XprType::PlainObject PlainObject;
144
- typedef evaluator<PlainObject> Base;
145
-
146
- explicit unary_evaluator(const XprType& xpr)
147
- : m_result(xpr.rows(), xpr.cols())
148
- {
149
- using std::abs;
150
- ::new (static_cast<Base*>(this)) Base(m_result);
151
- typedef typename nested_eval<Lhs,Dynamic>::type LhsNested;
152
- typedef typename nested_eval<Rhs,Dynamic>::type RhsNested;
153
- LhsNested lhsNested(xpr.nestedExpression().lhs());
154
- RhsNested rhsNested(xpr.nestedExpression().rhs());
155
-
156
- internal::sparse_sparse_product_with_pruning_selector<typename remove_all<LhsNested>::type,
157
- typename remove_all<RhsNested>::type, PlainObject>::run(lhsNested,rhsNested,m_result,
158
- abs(xpr.reference())*xpr.epsilon());
159
- }
160
-
161
- protected:
162
- PlainObject m_result;
163
- };
164
-
165
- } // end namespace internal
166
-
167
- // sparse matrix = sparse-product (can be sparse*sparse, sparse*perm, etc.)
168
- template<typename Scalar, int _Options, typename _StorageIndex>
169
- template<typename Lhs, typename Rhs>
170
- SparseMatrix<Scalar,_Options,_StorageIndex>& SparseMatrix<Scalar,_Options,_StorageIndex>::operator=(const Product<Lhs,Rhs,AliasFreeProduct>& src)
171
- {
172
- // std::cout << "in Assignment : " << DstOptions << "\n";
173
- SparseMatrix dst(src.rows(),src.cols());
174
- internal::generic_product_impl<Lhs, Rhs>::evalTo(dst,src.lhs(),src.rhs());
175
- this->swap(dst);
176
- return *this;
177
- }
178
-
179
- } // end namespace Eigen
180
-
181
- #endif // EIGEN_SPARSEPRODUCT_H
@@ -1,49 +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_SPARSEREDUX_H
11
- #define EIGEN_SPARSEREDUX_H
12
-
13
- namespace Eigen {
14
-
15
- template<typename Derived>
16
- typename internal::traits<Derived>::Scalar
17
- SparseMatrixBase<Derived>::sum() const
18
- {
19
- eigen_assert(rows()>0 && cols()>0 && "you are using a non initialized matrix");
20
- Scalar res(0);
21
- internal::evaluator<Derived> thisEval(derived());
22
- for (Index j=0; j<outerSize(); ++j)
23
- for (typename internal::evaluator<Derived>::InnerIterator iter(thisEval,j); iter; ++iter)
24
- res += iter.value();
25
- return res;
26
- }
27
-
28
- template<typename _Scalar, int _Options, typename _Index>
29
- typename internal::traits<SparseMatrix<_Scalar,_Options,_Index> >::Scalar
30
- SparseMatrix<_Scalar,_Options,_Index>::sum() const
31
- {
32
- eigen_assert(rows()>0 && cols()>0 && "you are using a non initialized matrix");
33
- if(this->isCompressed())
34
- return Matrix<Scalar,1,Dynamic>::Map(m_data.valuePtr(), m_data.size()).sum();
35
- else
36
- return Base::sum();
37
- }
38
-
39
- template<typename _Scalar, int _Options, typename _Index>
40
- typename internal::traits<SparseVector<_Scalar,_Options, _Index> >::Scalar
41
- SparseVector<_Scalar,_Options,_Index>::sum() const
42
- {
43
- eigen_assert(rows()>0 && cols()>0 && "you are using a non initialized matrix");
44
- return Matrix<Scalar,1,Dynamic>::Map(m_data.valuePtr(), m_data.size()).sum();
45
- }
46
-
47
- } // end namespace Eigen
48
-
49
- #endif // EIGEN_SPARSEREDUX_H
@@ -1,397 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 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_SPARSE_REF_H
11
- #define EIGEN_SPARSE_REF_H
12
-
13
- namespace Eigen {
14
-
15
- enum {
16
- StandardCompressedFormat = 2 /**< used by Ref<SparseMatrix> to specify whether the input storage must be in standard compressed form */
17
- };
18
-
19
- namespace internal {
20
-
21
- template<typename Derived> class SparseRefBase;
22
-
23
- template<typename MatScalar, int MatOptions, typename MatIndex, int _Options, typename _StrideType>
24
- struct traits<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
25
- : public traits<SparseMatrix<MatScalar,MatOptions,MatIndex> >
26
- {
27
- typedef SparseMatrix<MatScalar,MatOptions,MatIndex> PlainObjectType;
28
- enum {
29
- Options = _Options,
30
- Flags = traits<PlainObjectType>::Flags | CompressedAccessBit | NestByRefBit
31
- };
32
-
33
- template<typename Derived> struct match {
34
- enum {
35
- StorageOrderMatch = PlainObjectType::IsVectorAtCompileTime || Derived::IsVectorAtCompileTime || ((PlainObjectType::Flags&RowMajorBit)==(Derived::Flags&RowMajorBit)),
36
- MatchAtCompileTime = (Derived::Flags&CompressedAccessBit) && StorageOrderMatch
37
- };
38
- typedef typename internal::conditional<MatchAtCompileTime,internal::true_type,internal::false_type>::type type;
39
- };
40
-
41
- };
42
-
43
- template<typename MatScalar, int MatOptions, typename MatIndex, int _Options, typename _StrideType>
44
- struct traits<Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
45
- : public traits<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
46
- {
47
- enum {
48
- Flags = (traits<SparseMatrix<MatScalar,MatOptions,MatIndex> >::Flags | CompressedAccessBit | NestByRefBit) & ~LvalueBit
49
- };
50
- };
51
-
52
- template<typename MatScalar, int MatOptions, typename MatIndex, int _Options, typename _StrideType>
53
- struct traits<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
54
- : public traits<SparseVector<MatScalar,MatOptions,MatIndex> >
55
- {
56
- typedef SparseVector<MatScalar,MatOptions,MatIndex> PlainObjectType;
57
- enum {
58
- Options = _Options,
59
- Flags = traits<PlainObjectType>::Flags | CompressedAccessBit | NestByRefBit
60
- };
61
-
62
- template<typename Derived> struct match {
63
- enum {
64
- MatchAtCompileTime = (Derived::Flags&CompressedAccessBit) && Derived::IsVectorAtCompileTime
65
- };
66
- typedef typename internal::conditional<MatchAtCompileTime,internal::true_type,internal::false_type>::type type;
67
- };
68
-
69
- };
70
-
71
- template<typename MatScalar, int MatOptions, typename MatIndex, int _Options, typename _StrideType>
72
- struct traits<Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
73
- : public traits<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, _Options, _StrideType> >
74
- {
75
- enum {
76
- Flags = (traits<SparseVector<MatScalar,MatOptions,MatIndex> >::Flags | CompressedAccessBit | NestByRefBit) & ~LvalueBit
77
- };
78
- };
79
-
80
- template<typename Derived>
81
- struct traits<SparseRefBase<Derived> > : public traits<Derived> {};
82
-
83
- template<typename Derived> class SparseRefBase
84
- : public SparseMapBase<Derived>
85
- {
86
- public:
87
-
88
- typedef SparseMapBase<Derived> Base;
89
- EIGEN_SPARSE_PUBLIC_INTERFACE(SparseRefBase)
90
-
91
- SparseRefBase()
92
- : Base(RowsAtCompileTime==Dynamic?0:RowsAtCompileTime,ColsAtCompileTime==Dynamic?0:ColsAtCompileTime, 0, 0, 0, 0, 0)
93
- {}
94
-
95
- protected:
96
-
97
- template<typename Expression>
98
- void construct(Expression& expr)
99
- {
100
- if(expr.outerIndexPtr()==0)
101
- ::new (static_cast<Base*>(this)) Base(expr.size(), expr.nonZeros(), expr.innerIndexPtr(), expr.valuePtr());
102
- else
103
- ::new (static_cast<Base*>(this)) Base(expr.rows(), expr.cols(), expr.nonZeros(), expr.outerIndexPtr(), expr.innerIndexPtr(), expr.valuePtr(), expr.innerNonZeroPtr());
104
- }
105
- };
106
-
107
- } // namespace internal
108
-
109
-
110
- /**
111
- * \ingroup SparseCore_Module
112
- *
113
- * \brief A sparse matrix expression referencing an existing sparse expression
114
- *
115
- * \tparam SparseMatrixType the equivalent sparse matrix type of the referenced data, it must be a template instance of class SparseMatrix.
116
- * \tparam Options specifies whether the a standard compressed format is required \c Options is \c #StandardCompressedFormat, or \c 0.
117
- * The default is \c 0.
118
- *
119
- * \sa class Ref
120
- */
121
- #ifndef EIGEN_PARSED_BY_DOXYGEN
122
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
123
- class Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType >
124
- : public internal::SparseRefBase<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType > >
125
- #else
126
- template<typename SparseMatrixType, int Options>
127
- class Ref<SparseMatrixType, Options>
128
- : public SparseMapBase<Derived,WriteAccessors> // yes, that's weird to use Derived here, but that works!
129
- #endif
130
- {
131
- typedef SparseMatrix<MatScalar,MatOptions,MatIndex> PlainObjectType;
132
- typedef internal::traits<Ref> Traits;
133
- template<int OtherOptions>
134
- inline Ref(const SparseMatrix<MatScalar,OtherOptions,MatIndex>& expr);
135
- template<int OtherOptions>
136
- inline Ref(const MappedSparseMatrix<MatScalar,OtherOptions,MatIndex>& expr);
137
- public:
138
-
139
- typedef internal::SparseRefBase<Ref> Base;
140
- EIGEN_SPARSE_PUBLIC_INTERFACE(Ref)
141
-
142
-
143
- #ifndef EIGEN_PARSED_BY_DOXYGEN
144
- template<int OtherOptions>
145
- inline Ref(SparseMatrix<MatScalar,OtherOptions,MatIndex>& expr)
146
- {
147
- EIGEN_STATIC_ASSERT(bool(Traits::template match<SparseMatrix<MatScalar,OtherOptions,MatIndex> >::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
148
- eigen_assert( ((Options & int(StandardCompressedFormat))==0) || (expr.isCompressed()) );
149
- Base::construct(expr.derived());
150
- }
151
-
152
- template<int OtherOptions>
153
- inline Ref(MappedSparseMatrix<MatScalar,OtherOptions,MatIndex>& expr)
154
- {
155
- EIGEN_STATIC_ASSERT(bool(Traits::template match<SparseMatrix<MatScalar,OtherOptions,MatIndex> >::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
156
- eigen_assert( ((Options & int(StandardCompressedFormat))==0) || (expr.isCompressed()) );
157
- Base::construct(expr.derived());
158
- }
159
-
160
- template<typename Derived>
161
- inline Ref(const SparseCompressedBase<Derived>& expr)
162
- #else
163
- /** Implicit constructor from any sparse expression (2D matrix or 1D vector) */
164
- template<typename Derived>
165
- inline Ref(SparseCompressedBase<Derived>& expr)
166
- #endif
167
- {
168
- EIGEN_STATIC_ASSERT(bool(internal::is_lvalue<Derived>::value), THIS_EXPRESSION_IS_NOT_A_LVALUE__IT_IS_READ_ONLY);
169
- EIGEN_STATIC_ASSERT(bool(Traits::template match<Derived>::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
170
- eigen_assert( ((Options & int(StandardCompressedFormat))==0) || (expr.isCompressed()) );
171
- Base::construct(expr.const_cast_derived());
172
- }
173
- };
174
-
175
- // this is the const ref version
176
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
177
- class Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType>
178
- : public internal::SparseRefBase<Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
179
- {
180
- typedef SparseMatrix<MatScalar,MatOptions,MatIndex> TPlainObjectType;
181
- typedef internal::traits<Ref> Traits;
182
- public:
183
-
184
- typedef internal::SparseRefBase<Ref> Base;
185
- EIGEN_SPARSE_PUBLIC_INTERFACE(Ref)
186
-
187
- template<typename Derived>
188
- inline Ref(const SparseMatrixBase<Derived>& expr) : m_hasCopy(false)
189
- {
190
- construct(expr.derived(), typename Traits::template match<Derived>::type());
191
- }
192
-
193
- inline Ref(const Ref& other) : Base(other), m_hasCopy(false) {
194
- // copy constructor shall not copy the m_object, to avoid unnecessary malloc and copy
195
- }
196
-
197
- template<typename OtherRef>
198
- inline Ref(const RefBase<OtherRef>& other) : m_hasCopy(false) {
199
- construct(other.derived(), typename Traits::template match<OtherRef>::type());
200
- }
201
-
202
- ~Ref() {
203
- if(m_hasCopy) {
204
- TPlainObjectType* obj = reinterpret_cast<TPlainObjectType*>(&m_storage);
205
- obj->~TPlainObjectType();
206
- }
207
- }
208
-
209
- protected:
210
-
211
- template<typename Expression>
212
- void construct(const Expression& expr,internal::true_type)
213
- {
214
- if((Options & int(StandardCompressedFormat)) && (!expr.isCompressed()))
215
- {
216
- TPlainObjectType* obj = reinterpret_cast<TPlainObjectType*>(&m_storage);
217
- ::new (obj) TPlainObjectType(expr);
218
- m_hasCopy = true;
219
- Base::construct(*obj);
220
- }
221
- else
222
- {
223
- Base::construct(expr);
224
- }
225
- }
226
-
227
- template<typename Expression>
228
- void construct(const Expression& expr, internal::false_type)
229
- {
230
- TPlainObjectType* obj = reinterpret_cast<TPlainObjectType*>(&m_storage);
231
- ::new (obj) TPlainObjectType(expr);
232
- m_hasCopy = true;
233
- Base::construct(*obj);
234
- }
235
-
236
- protected:
237
- typename internal::aligned_storage<sizeof(TPlainObjectType), EIGEN_ALIGNOF(TPlainObjectType)>::type m_storage;
238
- bool m_hasCopy;
239
- };
240
-
241
-
242
-
243
- /**
244
- * \ingroup SparseCore_Module
245
- *
246
- * \brief A sparse vector expression referencing an existing sparse vector expression
247
- *
248
- * \tparam SparseVectorType the equivalent sparse vector type of the referenced data, it must be a template instance of class SparseVector.
249
- *
250
- * \sa class Ref
251
- */
252
- #ifndef EIGEN_PARSED_BY_DOXYGEN
253
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
254
- class Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType >
255
- : public internal::SparseRefBase<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType > >
256
- #else
257
- template<typename SparseVectorType>
258
- class Ref<SparseVectorType>
259
- : public SparseMapBase<Derived,WriteAccessors>
260
- #endif
261
- {
262
- typedef SparseVector<MatScalar,MatOptions,MatIndex> PlainObjectType;
263
- typedef internal::traits<Ref> Traits;
264
- template<int OtherOptions>
265
- inline Ref(const SparseVector<MatScalar,OtherOptions,MatIndex>& expr);
266
- public:
267
-
268
- typedef internal::SparseRefBase<Ref> Base;
269
- EIGEN_SPARSE_PUBLIC_INTERFACE(Ref)
270
-
271
- #ifndef EIGEN_PARSED_BY_DOXYGEN
272
- template<int OtherOptions>
273
- inline Ref(SparseVector<MatScalar,OtherOptions,MatIndex>& expr)
274
- {
275
- EIGEN_STATIC_ASSERT(bool(Traits::template match<SparseVector<MatScalar,OtherOptions,MatIndex> >::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
276
- Base::construct(expr.derived());
277
- }
278
-
279
- template<typename Derived>
280
- inline Ref(const SparseCompressedBase<Derived>& expr)
281
- #else
282
- /** Implicit constructor from any 1D sparse vector expression */
283
- template<typename Derived>
284
- inline Ref(SparseCompressedBase<Derived>& expr)
285
- #endif
286
- {
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- EIGEN_STATIC_ASSERT(bool(internal::is_lvalue<Derived>::value), THIS_EXPRESSION_IS_NOT_A_LVALUE__IT_IS_READ_ONLY);
288
- EIGEN_STATIC_ASSERT(bool(Traits::template match<Derived>::MatchAtCompileTime), STORAGE_LAYOUT_DOES_NOT_MATCH);
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- Base::construct(expr.const_cast_derived());
290
- }
291
- };
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-
293
- // this is the const ref version
294
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
295
- class Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType>
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- : public internal::SparseRefBase<Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
297
- {
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- typedef SparseVector<MatScalar,MatOptions,MatIndex> TPlainObjectType;
299
- typedef internal::traits<Ref> Traits;
300
- public:
301
-
302
- typedef internal::SparseRefBase<Ref> Base;
303
- EIGEN_SPARSE_PUBLIC_INTERFACE(Ref)
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-
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- template<typename Derived>
306
- inline Ref(const SparseMatrixBase<Derived>& expr) : m_hasCopy(false)
307
- {
308
- construct(expr.derived(), typename Traits::template match<Derived>::type());
309
- }
310
-
311
- inline Ref(const Ref& other) : Base(other), m_hasCopy(false) {
312
- // copy constructor shall not copy the m_object, to avoid unnecessary malloc and copy
313
- }
314
-
315
- template<typename OtherRef>
316
- inline Ref(const RefBase<OtherRef>& other) : m_hasCopy(false) {
317
- construct(other.derived(), typename Traits::template match<OtherRef>::type());
318
- }
319
-
320
- ~Ref() {
321
- if(m_hasCopy) {
322
- TPlainObjectType* obj = reinterpret_cast<TPlainObjectType*>(&m_storage);
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- obj->~TPlainObjectType();
324
- }
325
- }
326
-
327
- protected:
328
-
329
- template<typename Expression>
330
- void construct(const Expression& expr,internal::true_type)
331
- {
332
- Base::construct(expr);
333
- }
334
-
335
- template<typename Expression>
336
- void construct(const Expression& expr, internal::false_type)
337
- {
338
- TPlainObjectType* obj = reinterpret_cast<TPlainObjectType*>(&m_storage);
339
- ::new (obj) TPlainObjectType(expr);
340
- m_hasCopy = true;
341
- Base::construct(*obj);
342
- }
343
-
344
- protected:
345
- typename internal::aligned_storage<sizeof(TPlainObjectType), EIGEN_ALIGNOF(TPlainObjectType)>::type m_storage;
346
- bool m_hasCopy;
347
- };
348
-
349
- namespace internal {
350
-
351
- // FIXME shall we introduce a general evaluatior_ref that we can specialize for any sparse object once, and thus remove this copy-pasta thing...
352
-
353
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
354
- struct evaluator<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
355
- : evaluator<SparseCompressedBase<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
356
- {
357
- typedef evaluator<SparseCompressedBase<Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
358
- typedef Ref<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;
359
- evaluator() : Base() {}
360
- explicit evaluator(const XprType &mat) : Base(mat) {}
361
- };
362
-
363
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
364
- struct evaluator<Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
365
- : evaluator<SparseCompressedBase<Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
366
- {
367
- typedef evaluator<SparseCompressedBase<Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
368
- typedef Ref<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;
369
- evaluator() : Base() {}
370
- explicit evaluator(const XprType &mat) : Base(mat) {}
371
- };
372
-
373
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
374
- struct evaluator<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
375
- : evaluator<SparseCompressedBase<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
376
- {
377
- typedef evaluator<SparseCompressedBase<Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
378
- typedef Ref<SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;
379
- evaluator() : Base() {}
380
- explicit evaluator(const XprType &mat) : Base(mat) {}
381
- };
382
-
383
- template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
384
- struct evaluator<Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
385
- : evaluator<SparseCompressedBase<Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
386
- {
387
- typedef evaluator<SparseCompressedBase<Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
388
- typedef Ref<const SparseVector<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;
389
- evaluator() : Base() {}
390
- explicit evaluator(const XprType &mat) : Base(mat) {}
391
- };
392
-
393
- }
394
-
395
- } // end namespace Eigen
396
-
397
- #endif // EIGEN_SPARSE_REF_H