sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,454 +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) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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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_CXX11_TENSOR_TENSOR_REF_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_REF_H
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-
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- namespace Eigen {
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-
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- namespace internal {
16
-
17
- template <typename Dimensions, typename Scalar>
18
- class TensorLazyBaseEvaluator {
19
- public:
20
- TensorLazyBaseEvaluator() : m_refcount(0) { }
21
- virtual ~TensorLazyBaseEvaluator() { }
22
-
23
- EIGEN_DEVICE_FUNC virtual const Dimensions& dimensions() const = 0;
24
- EIGEN_DEVICE_FUNC virtual const Scalar* data() const = 0;
25
-
26
- EIGEN_DEVICE_FUNC virtual const Scalar coeff(DenseIndex index) const = 0;
27
- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex index) = 0;
28
-
29
- void incrRefCount() { ++m_refcount; }
30
- void decrRefCount() { --m_refcount; }
31
- int refCount() const { return m_refcount; }
32
-
33
- private:
34
- // No copy, no assignment;
35
- TensorLazyBaseEvaluator(const TensorLazyBaseEvaluator& other);
36
- TensorLazyBaseEvaluator& operator = (const TensorLazyBaseEvaluator& other);
37
-
38
- int m_refcount;
39
- };
40
-
41
-
42
- template <typename Dimensions, typename Expr, typename Device>
43
- class TensorLazyEvaluatorReadOnly : public TensorLazyBaseEvaluator<Dimensions, typename TensorEvaluator<Expr, Device>::Scalar> {
44
- public:
45
- // typedef typename TensorEvaluator<Expr, Device>::Dimensions Dimensions;
46
- typedef typename TensorEvaluator<Expr, Device>::Scalar Scalar;
47
- typedef StorageMemory<Scalar, Device> Storage;
48
- typedef typename Storage::Type EvaluatorPointerType;
49
- typedef TensorEvaluator<Expr, Device> EvalType;
50
-
51
- TensorLazyEvaluatorReadOnly(const Expr& expr, const Device& device) : m_impl(expr, device), m_dummy(Scalar(0)) {
52
- m_dims = m_impl.dimensions();
53
- m_impl.evalSubExprsIfNeeded(NULL);
54
- }
55
- virtual ~TensorLazyEvaluatorReadOnly() {
56
- m_impl.cleanup();
57
- }
58
-
59
- EIGEN_DEVICE_FUNC virtual const Dimensions& dimensions() const {
60
- return m_dims;
61
- }
62
- EIGEN_DEVICE_FUNC virtual const Scalar* data() const {
63
- return m_impl.data();
64
- }
65
-
66
- EIGEN_DEVICE_FUNC virtual const Scalar coeff(DenseIndex index) const {
67
- return m_impl.coeff(index);
68
- }
69
- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex /*index*/) {
70
- eigen_assert(false && "can't reference the coefficient of a rvalue");
71
- return m_dummy;
72
- };
73
-
74
- protected:
75
- TensorEvaluator<Expr, Device> m_impl;
76
- Dimensions m_dims;
77
- Scalar m_dummy;
78
- };
79
-
80
- template <typename Dimensions, typename Expr, typename Device>
81
- class TensorLazyEvaluatorWritable : public TensorLazyEvaluatorReadOnly<Dimensions, Expr, Device> {
82
- public:
83
- typedef TensorLazyEvaluatorReadOnly<Dimensions, Expr, Device> Base;
84
- typedef typename Base::Scalar Scalar;
85
- typedef StorageMemory<Scalar, Device> Storage;
86
- typedef typename Storage::Type EvaluatorPointerType;
87
-
88
- TensorLazyEvaluatorWritable(const Expr& expr, const Device& device) : Base(expr, device) {
89
- }
90
- virtual ~TensorLazyEvaluatorWritable() {
91
- }
92
-
93
- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex index) {
94
- return this->m_impl.coeffRef(index);
95
- }
96
- };
97
-
98
- template <typename Dimensions, typename Expr, typename Device>
99
- class TensorLazyEvaluator : public internal::conditional<bool(internal::is_lvalue<Expr>::value),
100
- TensorLazyEvaluatorWritable<Dimensions, Expr, Device>,
101
- TensorLazyEvaluatorReadOnly<Dimensions, const Expr, Device> >::type {
102
- public:
103
- typedef typename internal::conditional<bool(internal::is_lvalue<Expr>::value),
104
- TensorLazyEvaluatorWritable<Dimensions, Expr, Device>,
105
- TensorLazyEvaluatorReadOnly<Dimensions, const Expr, Device> >::type Base;
106
- typedef typename Base::Scalar Scalar;
107
-
108
- TensorLazyEvaluator(const Expr& expr, const Device& device) : Base(expr, device) {
109
- }
110
- virtual ~TensorLazyEvaluator() {
111
- }
112
- };
113
-
114
- } // namespace internal
115
-
116
-
117
- /** \class TensorRef
118
- * \ingroup CXX11_Tensor_Module
119
- *
120
- * \brief A reference to a tensor expression
121
- * The expression will be evaluated lazily (as much as possible).
122
- *
123
- */
124
- template<typename PlainObjectType> class TensorRef : public TensorBase<TensorRef<PlainObjectType> >
125
- {
126
- public:
127
- typedef TensorRef<PlainObjectType> Self;
128
- typedef typename PlainObjectType::Base Base;
129
- typedef typename Eigen::internal::nested<Self>::type Nested;
130
- typedef typename internal::traits<PlainObjectType>::StorageKind StorageKind;
131
- typedef typename internal::traits<PlainObjectType>::Index Index;
132
- typedef typename internal::traits<PlainObjectType>::Scalar Scalar;
133
- typedef typename NumTraits<Scalar>::Real RealScalar;
134
- typedef typename Base::CoeffReturnType CoeffReturnType;
135
- typedef Scalar* PointerType;
136
- typedef PointerType PointerArgType;
137
-
138
- static const Index NumIndices = PlainObjectType::NumIndices;
139
- typedef typename PlainObjectType::Dimensions Dimensions;
140
-
141
- enum {
142
- IsAligned = false,
143
- PacketAccess = false,
144
- BlockAccess = false,
145
- PreferBlockAccess = false,
146
- Layout = PlainObjectType::Layout,
147
- CoordAccess = false, // to be implemented
148
- RawAccess = false
149
- };
150
-
151
- //===- Tensor block evaluation strategy (see TensorBlock.h) -----------===//
152
- typedef internal::TensorBlockNotImplemented TensorBlock;
153
- //===------------------------------------------------------------------===//
154
-
155
- EIGEN_STRONG_INLINE TensorRef() : m_evaluator(NULL) {
156
- }
157
-
158
- template <typename Expression>
159
- EIGEN_STRONG_INLINE TensorRef(const Expression& expr) : m_evaluator(new internal::TensorLazyEvaluator<Dimensions, Expression, DefaultDevice>(expr, DefaultDevice())) {
160
- m_evaluator->incrRefCount();
161
- }
162
-
163
- template <typename Expression>
164
- EIGEN_STRONG_INLINE TensorRef& operator = (const Expression& expr) {
165
- unrefEvaluator();
166
- m_evaluator = new internal::TensorLazyEvaluator<Dimensions, Expression, DefaultDevice>(expr, DefaultDevice());
167
- m_evaluator->incrRefCount();
168
- return *this;
169
- }
170
-
171
- ~TensorRef() {
172
- unrefEvaluator();
173
- }
174
-
175
- TensorRef(const TensorRef& other) : m_evaluator(other.m_evaluator) {
176
- eigen_assert(m_evaluator->refCount() > 0);
177
- m_evaluator->incrRefCount();
178
- }
179
-
180
- TensorRef& operator = (const TensorRef& other) {
181
- if (this != &other) {
182
- unrefEvaluator();
183
- m_evaluator = other.m_evaluator;
184
- eigen_assert(m_evaluator->refCount() > 0);
185
- m_evaluator->incrRefCount();
186
- }
187
- return *this;
188
- }
189
-
190
- EIGEN_DEVICE_FUNC
191
- EIGEN_STRONG_INLINE Index rank() const { return m_evaluator->dimensions().size(); }
192
- EIGEN_DEVICE_FUNC
193
- EIGEN_STRONG_INLINE Index dimension(Index n) const { return m_evaluator->dimensions()[n]; }
194
- EIGEN_DEVICE_FUNC
195
- EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_evaluator->dimensions(); }
196
- EIGEN_DEVICE_FUNC
197
- EIGEN_STRONG_INLINE Index size() const { return m_evaluator->dimensions().TotalSize(); }
198
- EIGEN_DEVICE_FUNC
199
- EIGEN_STRONG_INLINE const Scalar* data() const { return m_evaluator->data(); }
200
-
201
- EIGEN_DEVICE_FUNC
202
- EIGEN_STRONG_INLINE const Scalar operator()(Index index) const
203
- {
204
- return m_evaluator->coeff(index);
205
- }
206
-
207
- #if EIGEN_HAS_VARIADIC_TEMPLATES
208
- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
209
- EIGEN_STRONG_INLINE const Scalar operator()(Index firstIndex, IndexTypes... otherIndices) const
210
- {
211
- const std::size_t num_indices = (sizeof...(otherIndices) + 1);
212
- const array<Index, num_indices> indices{{firstIndex, otherIndices...}};
213
- return coeff(indices);
214
- }
215
- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
216
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index firstIndex, IndexTypes... otherIndices)
217
- {
218
- const std::size_t num_indices = (sizeof...(otherIndices) + 1);
219
- const array<Index, num_indices> indices{{firstIndex, otherIndices...}};
220
- return coeffRef(indices);
221
- }
222
- #else
223
-
224
- EIGEN_DEVICE_FUNC
225
- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1) const
226
- {
227
- array<Index, 2> indices;
228
- indices[0] = i0;
229
- indices[1] = i1;
230
- return coeff(indices);
231
- }
232
- EIGEN_DEVICE_FUNC
233
- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2) const
234
- {
235
- array<Index, 3> indices;
236
- indices[0] = i0;
237
- indices[1] = i1;
238
- indices[2] = i2;
239
- return coeff(indices);
240
- }
241
- EIGEN_DEVICE_FUNC
242
- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2, Index i3) const
243
- {
244
- array<Index, 4> indices;
245
- indices[0] = i0;
246
- indices[1] = i1;
247
- indices[2] = i2;
248
- indices[3] = i3;
249
- return coeff(indices);
250
- }
251
- EIGEN_DEVICE_FUNC
252
- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2, Index i3, Index i4) const
253
- {
254
- array<Index, 5> indices;
255
- indices[0] = i0;
256
- indices[1] = i1;
257
- indices[2] = i2;
258
- indices[3] = i3;
259
- indices[4] = i4;
260
- return coeff(indices);
261
- }
262
- EIGEN_DEVICE_FUNC
263
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1)
264
- {
265
- array<Index, 2> indices;
266
- indices[0] = i0;
267
- indices[1] = i1;
268
- return coeffRef(indices);
269
- }
270
- EIGEN_DEVICE_FUNC
271
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1, Index i2)
272
- {
273
- array<Index, 3> indices;
274
- indices[0] = i0;
275
- indices[1] = i1;
276
- indices[2] = i2;
277
- return coeffRef(indices);
278
- }
279
- EIGEN_DEVICE_FUNC
280
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1, Index i2, Index i3)
281
- {
282
- array<Index, 4> indices;
283
- indices[0] = i0;
284
- indices[1] = i1;
285
- indices[2] = i2;
286
- indices[3] = i3;
287
- return coeffRef(indices);
288
- }
289
- EIGEN_DEVICE_FUNC
290
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1, Index i2, Index i3, Index i4)
291
- {
292
- array<Index, 5> indices;
293
- indices[0] = i0;
294
- indices[1] = i1;
295
- indices[2] = i2;
296
- indices[3] = i3;
297
- indices[4] = i4;
298
- return coeffRef(indices);
299
- }
300
- #endif
301
-
302
- template <std::size_t NumIndices> EIGEN_DEVICE_FUNC
303
- EIGEN_STRONG_INLINE const Scalar coeff(const array<Index, NumIndices>& indices) const
304
- {
305
- const Dimensions& dims = this->dimensions();
306
- Index index = 0;
307
- if (PlainObjectType::Options & RowMajor) {
308
- index += indices[0];
309
- for (size_t i = 1; i < NumIndices; ++i) {
310
- index = index * dims[i] + indices[i];
311
- }
312
- } else {
313
- index += indices[NumIndices-1];
314
- for (int i = NumIndices-2; i >= 0; --i) {
315
- index = index * dims[i] + indices[i];
316
- }
317
- }
318
- return m_evaluator->coeff(index);
319
- }
320
- template <std::size_t NumIndices> EIGEN_DEVICE_FUNC
321
- EIGEN_STRONG_INLINE Scalar& coeffRef(const array<Index, NumIndices>& indices)
322
- {
323
- const Dimensions& dims = this->dimensions();
324
- Index index = 0;
325
- if (PlainObjectType::Options & RowMajor) {
326
- index += indices[0];
327
- for (size_t i = 1; i < NumIndices; ++i) {
328
- index = index * dims[i] + indices[i];
329
- }
330
- } else {
331
- index += indices[NumIndices-1];
332
- for (int i = NumIndices-2; i >= 0; --i) {
333
- index = index * dims[i] + indices[i];
334
- }
335
- }
336
- return m_evaluator->coeffRef(index);
337
- }
338
-
339
- EIGEN_DEVICE_FUNC
340
- EIGEN_STRONG_INLINE const Scalar coeff(Index index) const
341
- {
342
- return m_evaluator->coeff(index);
343
- }
344
-
345
- EIGEN_DEVICE_FUNC
346
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index index)
347
- {
348
- return m_evaluator->coeffRef(index);
349
- }
350
-
351
- private:
352
- EIGEN_STRONG_INLINE void unrefEvaluator() {
353
- if (m_evaluator) {
354
- m_evaluator->decrRefCount();
355
- if (m_evaluator->refCount() == 0) {
356
- delete m_evaluator;
357
- }
358
- }
359
- }
360
-
361
- internal::TensorLazyBaseEvaluator<Dimensions, Scalar>* m_evaluator;
362
- };
363
-
364
-
365
- // evaluator for rvalues
366
- template<typename Derived, typename Device>
367
- struct TensorEvaluator<const TensorRef<Derived>, Device>
368
- {
369
- typedef typename Derived::Index Index;
370
- typedef typename Derived::Scalar Scalar;
371
- typedef typename Derived::Scalar CoeffReturnType;
372
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
373
- typedef typename Derived::Dimensions Dimensions;
374
- typedef StorageMemory<CoeffReturnType, Device> Storage;
375
- typedef typename Storage::Type EvaluatorPointerType;
376
-
377
- enum {
378
- IsAligned = false,
379
- PacketAccess = false,
380
- BlockAccess = false,
381
- PreferBlockAccess = false,
382
- Layout = TensorRef<Derived>::Layout,
383
- CoordAccess = false, // to be implemented
384
- RawAccess = false
385
- };
386
-
387
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
388
- typedef internal::TensorBlockNotImplemented TensorBlock;
389
- //===--------------------------------------------------------------------===//
390
-
391
- EIGEN_STRONG_INLINE TensorEvaluator(const TensorRef<Derived>& m, const Device&)
392
- : m_ref(m)
393
- { }
394
-
395
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_ref.dimensions(); }
396
-
397
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType) {
398
- return true;
399
- }
400
-
401
- EIGEN_STRONG_INLINE void cleanup() { }
402
-
403
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const {
404
- return m_ref.coeff(index);
405
- }
406
-
407
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) {
408
- return m_ref.coeffRef(index);
409
- }
410
-
411
- EIGEN_DEVICE_FUNC const Scalar* data() const { return m_ref.data(); }
412
-
413
- protected:
414
- TensorRef<Derived> m_ref;
415
- };
416
-
417
-
418
- // evaluator for lvalues
419
- template<typename Derived, typename Device>
420
- struct TensorEvaluator<TensorRef<Derived>, Device> : public TensorEvaluator<const TensorRef<Derived>, Device>
421
- {
422
- typedef typename Derived::Index Index;
423
- typedef typename Derived::Scalar Scalar;
424
- typedef typename Derived::Scalar CoeffReturnType;
425
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
426
- typedef typename Derived::Dimensions Dimensions;
427
-
428
- typedef TensorEvaluator<const TensorRef<Derived>, Device> Base;
429
-
430
- enum {
431
- IsAligned = false,
432
- PacketAccess = false,
433
- BlockAccess = false,
434
- PreferBlockAccess = false,
435
- RawAccess = false
436
- };
437
-
438
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
439
- typedef internal::TensorBlockNotImplemented TensorBlock;
440
- //===--------------------------------------------------------------------===//
441
-
442
- EIGEN_STRONG_INLINE TensorEvaluator(TensorRef<Derived>& m, const Device& d) : Base(m, d)
443
- { }
444
-
445
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) {
446
- return this->m_ref.coeffRef(index);
447
- }
448
- };
449
-
450
-
451
-
452
- } // end namespace Eigen
453
-
454
- #endif // EIGEN_CXX11_TENSOR_TENSOR_REF_H