sequenzo 0.1.18__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-311-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +107 -5
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  8. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-311-darwin.so +0 -0
  10. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  11. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  13. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  15. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  17. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-darwin.so +0 -0
  18. sequenzo/multidomain/cat.py +0 -53
  19. sequenzo/multidomain/idcd.py +0 -1
  20. sequenzo/openmp_setup.py +233 -0
  21. sequenzo/visualization/plot_transition_matrix.py +21 -22
  22. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  23. sequenzo-0.1.19.dist-info/RECORD +215 -0
  24. sequenzo/dissimilarity_measures/setup.py +0 -35
  25. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  26. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  167. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  168. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  169. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  170. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  171. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  172. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  173. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  174. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  175. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  176. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  177. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  182. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  183. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  184. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  185. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  186. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  187. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  188. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
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@@ -1,232 +0,0 @@
1
- // 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 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2008 Benoit Jacob <jacob.benoit.1@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_PARAMETRIZEDLINE_H
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- #define EIGEN_PARAMETRIZEDLINE_H
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-
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- namespace Eigen {
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-
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- /** \geometry_module \ingroup Geometry_Module
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- *
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- * \class ParametrizedLine
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- *
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- * \brief A parametrized line
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- *
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- * A parametrized line is defined by an origin point \f$ \mathbf{o} \f$ and a unit
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- * direction vector \f$ \mathbf{d} \f$ such that the line corresponds to
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- * the set \f$ l(t) = \mathbf{o} + t \mathbf{d} \f$, \f$ t \in \mathbf{R} \f$.
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- *
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- * \tparam _Scalar the scalar type, i.e., the type of the coefficients
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- * \tparam _AmbientDim the dimension of the ambient space, can be a compile time value or Dynamic.
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- */
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- template <typename _Scalar, int _AmbientDim, int _Options>
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- class ParametrizedLine
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- {
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- public:
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- EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_AmbientDim)
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- enum {
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- AmbientDimAtCompileTime = _AmbientDim,
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- Options = _Options
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- };
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- typedef _Scalar Scalar;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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- typedef Eigen::Index Index; ///< \deprecated since Eigen 3.3
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- typedef Matrix<Scalar,AmbientDimAtCompileTime,1,Options> VectorType;
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-
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- /** Default constructor without initialization */
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- EIGEN_DEVICE_FUNC inline ParametrizedLine() {}
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-
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- template<int OtherOptions>
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- EIGEN_DEVICE_FUNC ParametrizedLine(const ParametrizedLine<Scalar,AmbientDimAtCompileTime,OtherOptions>& other)
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- : m_origin(other.origin()), m_direction(other.direction())
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- {}
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-
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- /** Constructs a dynamic-size line with \a _dim the dimension
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- * of the ambient space */
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- EIGEN_DEVICE_FUNC inline explicit ParametrizedLine(Index _dim) : m_origin(_dim), m_direction(_dim) {}
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-
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- /** Initializes a parametrized line of direction \a direction and origin \a origin.
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- * \warning the vector direction is assumed to be normalized.
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- */
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- EIGEN_DEVICE_FUNC ParametrizedLine(const VectorType& origin, const VectorType& direction)
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- : m_origin(origin), m_direction(direction) {}
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-
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- template <int OtherOptions>
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- EIGEN_DEVICE_FUNC explicit ParametrizedLine(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane);
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-
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- /** Constructs a parametrized line going from \a p0 to \a p1. */
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- EIGEN_DEVICE_FUNC static inline ParametrizedLine Through(const VectorType& p0, const VectorType& p1)
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- { return ParametrizedLine(p0, (p1-p0).normalized()); }
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-
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- EIGEN_DEVICE_FUNC ~ParametrizedLine() {}
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-
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- /** \returns the dimension in which the line holds */
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- EIGEN_DEVICE_FUNC inline Index dim() const { return m_direction.size(); }
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-
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- EIGEN_DEVICE_FUNC const VectorType& origin() const { return m_origin; }
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- EIGEN_DEVICE_FUNC VectorType& origin() { return m_origin; }
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-
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- EIGEN_DEVICE_FUNC const VectorType& direction() const { return m_direction; }
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- EIGEN_DEVICE_FUNC VectorType& direction() { return m_direction; }
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-
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- /** \returns the squared distance of a point \a p to its projection onto the line \c *this.
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- * \sa distance()
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- */
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- EIGEN_DEVICE_FUNC RealScalar squaredDistance(const VectorType& p) const
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- {
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- VectorType diff = p - origin();
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- return (diff - direction().dot(diff) * direction()).squaredNorm();
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- }
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- /** \returns the distance of a point \a p to its projection onto the line \c *this.
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- * \sa squaredDistance()
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- */
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- EIGEN_DEVICE_FUNC RealScalar distance(const VectorType& p) const { EIGEN_USING_STD(sqrt) return sqrt(squaredDistance(p)); }
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-
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- /** \returns the projection of a point \a p onto the line \c *this. */
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- EIGEN_DEVICE_FUNC VectorType projection(const VectorType& p) const
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- { return origin() + direction().dot(p-origin()) * direction(); }
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-
96
- EIGEN_DEVICE_FUNC VectorType pointAt(const Scalar& t) const;
97
-
98
- template <int OtherOptions>
99
- EIGEN_DEVICE_FUNC Scalar intersectionParameter(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const;
100
-
101
- template <int OtherOptions>
102
- EIGEN_DEVICE_FUNC Scalar intersection(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const;
103
-
104
- template <int OtherOptions>
105
- EIGEN_DEVICE_FUNC VectorType intersectionPoint(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const;
106
-
107
- /** Applies the transformation matrix \a mat to \c *this and returns a reference to \c *this.
108
- *
109
- * \param mat the Dim x Dim transformation matrix
110
- * \param traits specifies whether the matrix \a mat represents an #Isometry
111
- * or a more generic #Affine transformation. The default is #Affine.
112
- */
113
- template<typename XprType>
114
- EIGEN_DEVICE_FUNC inline ParametrizedLine& transform(const MatrixBase<XprType>& mat, TransformTraits traits = Affine)
115
- {
116
- if (traits==Affine)
117
- direction() = (mat * direction()).normalized();
118
- else if (traits==Isometry)
119
- direction() = mat * direction();
120
- else
121
- {
122
- eigen_assert(0 && "invalid traits value in ParametrizedLine::transform()");
123
- }
124
- origin() = mat * origin();
125
- return *this;
126
- }
127
-
128
- /** Applies the transformation \a t to \c *this and returns a reference to \c *this.
129
- *
130
- * \param t the transformation of dimension Dim
131
- * \param traits specifies whether the transformation \a t represents an #Isometry
132
- * or a more generic #Affine transformation. The default is #Affine.
133
- * Other kind of transformations are not supported.
134
- */
135
- template<int TrOptions>
136
- EIGEN_DEVICE_FUNC inline ParametrizedLine& transform(const Transform<Scalar,AmbientDimAtCompileTime,Affine,TrOptions>& t,
137
- TransformTraits traits = Affine)
138
- {
139
- transform(t.linear(), traits);
140
- origin() += t.translation();
141
- return *this;
142
- }
143
-
144
- /** \returns \c *this with scalar type casted to \a NewScalarType
145
- *
146
- * Note that if \a NewScalarType is equal to the current scalar type of \c *this
147
- * then this function smartly returns a const reference to \c *this.
148
- */
149
- template<typename NewScalarType>
150
- EIGEN_DEVICE_FUNC inline typename internal::cast_return_type<ParametrizedLine,
151
- ParametrizedLine<NewScalarType,AmbientDimAtCompileTime,Options> >::type cast() const
152
- {
153
- return typename internal::cast_return_type<ParametrizedLine,
154
- ParametrizedLine<NewScalarType,AmbientDimAtCompileTime,Options> >::type(*this);
155
- }
156
-
157
- /** Copy constructor with scalar type conversion */
158
- template<typename OtherScalarType,int OtherOptions>
159
- EIGEN_DEVICE_FUNC inline explicit ParametrizedLine(const ParametrizedLine<OtherScalarType,AmbientDimAtCompileTime,OtherOptions>& other)
160
- {
161
- m_origin = other.origin().template cast<Scalar>();
162
- m_direction = other.direction().template cast<Scalar>();
163
- }
164
-
165
- /** \returns \c true if \c *this is approximately equal to \a other, within the precision
166
- * determined by \a prec.
167
- *
168
- * \sa MatrixBase::isApprox() */
169
- EIGEN_DEVICE_FUNC bool isApprox(const ParametrizedLine& other, const typename NumTraits<Scalar>::Real& prec = NumTraits<Scalar>::dummy_precision()) const
170
- { return m_origin.isApprox(other.m_origin, prec) && m_direction.isApprox(other.m_direction, prec); }
171
-
172
- protected:
173
-
174
- VectorType m_origin, m_direction;
175
- };
176
-
177
- /** Constructs a parametrized line from a 2D hyperplane
178
- *
179
- * \warning the ambient space must have dimension 2 such that the hyperplane actually describes a line
180
- */
181
- template <typename _Scalar, int _AmbientDim, int _Options>
182
- template <int OtherOptions>
183
- EIGEN_DEVICE_FUNC inline ParametrizedLine<_Scalar, _AmbientDim,_Options>::ParametrizedLine(const Hyperplane<_Scalar, _AmbientDim,OtherOptions>& hyperplane)
184
- {
185
- EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(VectorType, 2)
186
- direction() = hyperplane.normal().unitOrthogonal();
187
- origin() = -hyperplane.normal()*hyperplane.offset();
188
- }
189
-
190
- /** \returns the point at \a t along this line
191
- */
192
- template <typename _Scalar, int _AmbientDim, int _Options>
193
- EIGEN_DEVICE_FUNC inline typename ParametrizedLine<_Scalar, _AmbientDim,_Options>::VectorType
194
- ParametrizedLine<_Scalar, _AmbientDim,_Options>::pointAt(const _Scalar& t) const
195
- {
196
- return origin() + (direction()*t);
197
- }
198
-
199
- /** \returns the parameter value of the intersection between \c *this and the given \a hyperplane
200
- */
201
- template <typename _Scalar, int _AmbientDim, int _Options>
202
- template <int OtherOptions>
203
- EIGEN_DEVICE_FUNC inline _Scalar ParametrizedLine<_Scalar, _AmbientDim,_Options>::intersectionParameter(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const
204
- {
205
- return -(hyperplane.offset()+hyperplane.normal().dot(origin()))
206
- / hyperplane.normal().dot(direction());
207
- }
208
-
209
-
210
- /** \deprecated use intersectionParameter()
211
- * \returns the parameter value of the intersection between \c *this and the given \a hyperplane
212
- */
213
- template <typename _Scalar, int _AmbientDim, int _Options>
214
- template <int OtherOptions>
215
- EIGEN_DEVICE_FUNC inline _Scalar ParametrizedLine<_Scalar, _AmbientDim,_Options>::intersection(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const
216
- {
217
- return intersectionParameter(hyperplane);
218
- }
219
-
220
- /** \returns the point of the intersection between \c *this and the given hyperplane
221
- */
222
- template <typename _Scalar, int _AmbientDim, int _Options>
223
- template <int OtherOptions>
224
- EIGEN_DEVICE_FUNC inline typename ParametrizedLine<_Scalar, _AmbientDim,_Options>::VectorType
225
- ParametrizedLine<_Scalar, _AmbientDim,_Options>::intersectionPoint(const Hyperplane<_Scalar, _AmbientDim, OtherOptions>& hyperplane) const
226
- {
227
- return pointAt(intersectionParameter(hyperplane));
228
- }
229
-
230
- } // end namespace Eigen
231
-
232
- #endif // EIGEN_PARAMETRIZEDLINE_H