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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@@ -1,115 +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) 2008-2016 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2006-2008 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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- // This file is a base class plugin containing common coefficient wise functions.
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-
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- /** \returns an expression of the difference of \c *this and \a other
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- *
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- * \note If you want to substract a given scalar from all coefficients, see Cwise::operator-().
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- *
17
- * \sa class CwiseBinaryOp, operator-=()
18
- */
19
- EIGEN_MAKE_CWISE_BINARY_OP(operator-,difference)
20
-
21
- /** \returns an expression of the sum of \c *this and \a other
22
- *
23
- * \note If you want to add a given scalar to all coefficients, see Cwise::operator+().
24
- *
25
- * \sa class CwiseBinaryOp, operator+=()
26
- */
27
- EIGEN_MAKE_CWISE_BINARY_OP(operator+,sum)
28
-
29
- /** \returns an expression of a custom coefficient-wise operator \a func of *this and \a other
30
- *
31
- * The template parameter \a CustomBinaryOp is the type of the functor
32
- * of the custom operator (see class CwiseBinaryOp for an example)
33
- *
34
- * Here is an example illustrating the use of custom functors:
35
- * \include class_CwiseBinaryOp.cpp
36
- * Output: \verbinclude class_CwiseBinaryOp.out
37
- *
38
- * \sa class CwiseBinaryOp, operator+(), operator-(), cwiseProduct()
39
- */
40
- template<typename CustomBinaryOp, typename OtherDerived>
41
- EIGEN_DEVICE_FUNC
42
- EIGEN_STRONG_INLINE const CwiseBinaryOp<CustomBinaryOp, const Derived, const OtherDerived>
43
- binaryExpr(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other, const CustomBinaryOp& func = CustomBinaryOp()) const
44
- {
45
- return CwiseBinaryOp<CustomBinaryOp, const Derived, const OtherDerived>(derived(), other.derived(), func);
46
- }
47
-
48
-
49
- #ifndef EIGEN_PARSED_BY_DOXYGEN
50
- EIGEN_MAKE_SCALAR_BINARY_OP(operator*,product)
51
- #else
52
- /** \returns an expression of \c *this scaled by the scalar factor \a scalar
53
- *
54
- * \tparam T is the scalar type of \a scalar. It must be compatible with the scalar type of the given expression.
55
- */
56
- template<typename T>
57
- const CwiseBinaryOp<internal::scalar_product_op<Scalar,T>,Derived,Constant<T> > operator*(const T& scalar) const;
58
- /** \returns an expression of \a expr scaled by the scalar factor \a scalar
59
- *
60
- * \tparam T is the scalar type of \a scalar. It must be compatible with the scalar type of the given expression.
61
- */
62
- template<typename T> friend
63
- const CwiseBinaryOp<internal::scalar_product_op<T,Scalar>,Constant<T>,Derived> operator*(const T& scalar, const StorageBaseType& expr);
64
- #endif
65
-
66
-
67
-
68
- #ifndef EIGEN_PARSED_BY_DOXYGEN
69
- EIGEN_MAKE_SCALAR_BINARY_OP_ONTHERIGHT(operator/,quotient)
70
- #else
71
- /** \returns an expression of \c *this divided by the scalar value \a scalar
72
- *
73
- * \tparam T is the scalar type of \a scalar. It must be compatible with the scalar type of the given expression.
74
- */
75
- template<typename T>
76
- const CwiseBinaryOp<internal::scalar_quotient_op<Scalar,T>,Derived,Constant<T> > operator/(const T& scalar) const;
77
- #endif
78
-
79
- /** \returns an expression of the coefficient-wise boolean \b and operator of \c *this and \a other
80
- *
81
- * \warning this operator is for expression of bool only.
82
- *
83
- * Example: \include Cwise_boolean_and.cpp
84
- * Output: \verbinclude Cwise_boolean_and.out
85
- *
86
- * \sa operator||(), select()
87
- */
88
- template<typename OtherDerived>
89
- EIGEN_DEVICE_FUNC
90
- inline const CwiseBinaryOp<internal::scalar_boolean_and_op, const Derived, const OtherDerived>
91
- operator&&(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
92
- {
93
- EIGEN_STATIC_ASSERT((internal::is_same<bool,Scalar>::value && internal::is_same<bool,typename OtherDerived::Scalar>::value),
94
- THIS_METHOD_IS_ONLY_FOR_EXPRESSIONS_OF_BOOL);
95
- return CwiseBinaryOp<internal::scalar_boolean_and_op, const Derived, const OtherDerived>(derived(),other.derived());
96
- }
97
-
98
- /** \returns an expression of the coefficient-wise boolean \b or operator of \c *this and \a other
99
- *
100
- * \warning this operator is for expression of bool only.
101
- *
102
- * Example: \include Cwise_boolean_or.cpp
103
- * Output: \verbinclude Cwise_boolean_or.out
104
- *
105
- * \sa operator&&(), select()
106
- */
107
- template<typename OtherDerived>
108
- EIGEN_DEVICE_FUNC
109
- inline const CwiseBinaryOp<internal::scalar_boolean_or_op, const Derived, const OtherDerived>
110
- operator||(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const
111
- {
112
- EIGEN_STATIC_ASSERT((internal::is_same<bool,Scalar>::value && internal::is_same<bool,typename OtherDerived::Scalar>::value),
113
- THIS_METHOD_IS_ONLY_FOR_EXPRESSIONS_OF_BOOL);
114
- return CwiseBinaryOp<internal::scalar_boolean_or_op, const Derived, const OtherDerived>(derived(),other.derived());
115
- }
@@ -1,177 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- // Copyright (C) 2006-2008 Benoit Jacob <jacob.benoit.1@gmail.com>
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- // This file is a base class plugin containing common coefficient wise functions.
12
-
13
- #ifndef EIGEN_PARSED_BY_DOXYGEN
14
-
15
- /** \internal the return type of conjugate() */
16
- typedef typename internal::conditional<NumTraits<Scalar>::IsComplex,
17
- const CwiseUnaryOp<internal::scalar_conjugate_op<Scalar>, const Derived>,
18
- const Derived&
19
- >::type ConjugateReturnType;
20
- /** \internal the return type of real() const */
21
- typedef typename internal::conditional<NumTraits<Scalar>::IsComplex,
22
- const CwiseUnaryOp<internal::scalar_real_op<Scalar>, const Derived>,
23
- const Derived&
24
- >::type RealReturnType;
25
- /** \internal the return type of real() */
26
- typedef typename internal::conditional<NumTraits<Scalar>::IsComplex,
27
- CwiseUnaryView<internal::scalar_real_ref_op<Scalar>, Derived>,
28
- Derived&
29
- >::type NonConstRealReturnType;
30
- /** \internal the return type of imag() const */
31
- typedef CwiseUnaryOp<internal::scalar_imag_op<Scalar>, const Derived> ImagReturnType;
32
- /** \internal the return type of imag() */
33
- typedef CwiseUnaryView<internal::scalar_imag_ref_op<Scalar>, Derived> NonConstImagReturnType;
34
-
35
- typedef CwiseUnaryOp<internal::scalar_opposite_op<Scalar>, const Derived> NegativeReturnType;
36
-
37
- #endif // not EIGEN_PARSED_BY_DOXYGEN
38
-
39
- /// \returns an expression of the opposite of \c *this
40
- ///
41
- EIGEN_DOC_UNARY_ADDONS(operator-,opposite)
42
- ///
43
- EIGEN_DEVICE_FUNC
44
- inline const NegativeReturnType
45
- operator-() const { return NegativeReturnType(derived()); }
46
-
47
-
48
- template<class NewType> struct CastXpr { typedef typename internal::cast_return_type<Derived,const CwiseUnaryOp<internal::scalar_cast_op<Scalar, NewType>, const Derived> >::type Type; };
49
-
50
- /// \returns an expression of \c *this with the \a Scalar type casted to
51
- /// \a NewScalar.
52
- ///
53
- /// The template parameter \a NewScalar is the type we are casting the scalars to.
54
- ///
55
- EIGEN_DOC_UNARY_ADDONS(cast,conversion function)
56
- ///
57
- /// \sa class CwiseUnaryOp
58
- ///
59
- template<typename NewType>
60
- EIGEN_DEVICE_FUNC
61
- typename CastXpr<NewType>::Type
62
- cast() const
63
- {
64
- return typename CastXpr<NewType>::Type(derived());
65
- }
66
-
67
- /// \returns an expression of the complex conjugate of \c *this.
68
- ///
69
- EIGEN_DOC_UNARY_ADDONS(conjugate,complex conjugate)
70
- ///
71
- /// \sa <a href="group__CoeffwiseMathFunctions.html#cwisetable_conj">Math functions</a>, MatrixBase::adjoint()
72
- EIGEN_DEVICE_FUNC
73
- inline ConjugateReturnType
74
- conjugate() const
75
- {
76
- return ConjugateReturnType(derived());
77
- }
78
-
79
- /// \returns an expression of the complex conjugate of \c *this if Cond==true, returns derived() otherwise.
80
- ///
81
- EIGEN_DOC_UNARY_ADDONS(conjugate,complex conjugate)
82
- ///
83
- /// \sa conjugate()
84
- template<bool Cond>
85
- EIGEN_DEVICE_FUNC
86
- inline typename internal::conditional<Cond,ConjugateReturnType,const Derived&>::type
87
- conjugateIf() const
88
- {
89
- typedef typename internal::conditional<Cond,ConjugateReturnType,const Derived&>::type ReturnType;
90
- return ReturnType(derived());
91
- }
92
-
93
- /// \returns a read-only expression of the real part of \c *this.
94
- ///
95
- EIGEN_DOC_UNARY_ADDONS(real,real part function)
96
- ///
97
- /// \sa imag()
98
- EIGEN_DEVICE_FUNC
99
- inline RealReturnType
100
- real() const { return RealReturnType(derived()); }
101
-
102
- /// \returns an read-only expression of the imaginary part of \c *this.
103
- ///
104
- EIGEN_DOC_UNARY_ADDONS(imag,imaginary part function)
105
- ///
106
- /// \sa real()
107
- EIGEN_DEVICE_FUNC
108
- inline const ImagReturnType
109
- imag() const { return ImagReturnType(derived()); }
110
-
111
- /// \brief Apply a unary operator coefficient-wise
112
- /// \param[in] func Functor implementing the unary operator
113
- /// \tparam CustomUnaryOp Type of \a func
114
- /// \returns An expression of a custom coefficient-wise unary operator \a func of *this
115
- ///
116
- /// The function \c ptr_fun() from the C++ standard library can be used to make functors out of normal functions.
117
- ///
118
- /// Example:
119
- /// \include class_CwiseUnaryOp_ptrfun.cpp
120
- /// Output: \verbinclude class_CwiseUnaryOp_ptrfun.out
121
- ///
122
- /// Genuine functors allow for more possibilities, for instance it may contain a state.
123
- ///
124
- /// Example:
125
- /// \include class_CwiseUnaryOp.cpp
126
- /// Output: \verbinclude class_CwiseUnaryOp.out
127
- ///
128
- EIGEN_DOC_UNARY_ADDONS(unaryExpr,unary function)
129
- ///
130
- /// \sa unaryViewExpr, binaryExpr, class CwiseUnaryOp
131
- ///
132
- template<typename CustomUnaryOp>
133
- EIGEN_DEVICE_FUNC
134
- inline const CwiseUnaryOp<CustomUnaryOp, const Derived>
135
- unaryExpr(const CustomUnaryOp& func = CustomUnaryOp()) const
136
- {
137
- return CwiseUnaryOp<CustomUnaryOp, const Derived>(derived(), func);
138
- }
139
-
140
- /// \returns an expression of a custom coefficient-wise unary operator \a func of *this
141
- ///
142
- /// The template parameter \a CustomUnaryOp is the type of the functor
143
- /// of the custom unary operator.
144
- ///
145
- /// Example:
146
- /// \include class_CwiseUnaryOp.cpp
147
- /// Output: \verbinclude class_CwiseUnaryOp.out
148
- ///
149
- EIGEN_DOC_UNARY_ADDONS(unaryViewExpr,unary function)
150
- ///
151
- /// \sa unaryExpr, binaryExpr class CwiseUnaryOp
152
- ///
153
- template<typename CustomViewOp>
154
- EIGEN_DEVICE_FUNC
155
- inline const CwiseUnaryView<CustomViewOp, const Derived>
156
- unaryViewExpr(const CustomViewOp& func = CustomViewOp()) const
157
- {
158
- return CwiseUnaryView<CustomViewOp, const Derived>(derived(), func);
159
- }
160
-
161
- /// \returns a non const expression of the real part of \c *this.
162
- ///
163
- EIGEN_DOC_UNARY_ADDONS(real,real part function)
164
- ///
165
- /// \sa imag()
166
- EIGEN_DEVICE_FUNC
167
- inline NonConstRealReturnType
168
- real() { return NonConstRealReturnType(derived()); }
169
-
170
- /// \returns a non const expression of the imaginary part of \c *this.
171
- ///
172
- EIGEN_DOC_UNARY_ADDONS(imag,imaginary part function)
173
- ///
174
- /// \sa real()
175
- EIGEN_DEVICE_FUNC
176
- inline NonConstImagReturnType
177
- imag() { return NonConstImagReturnType(derived()); }
@@ -1,262 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2017 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
- #if !defined(EIGEN_PARSED_BY_DOXYGEN)
11
-
12
- // This file is automatically included twice to generate const and non-const versions
13
-
14
- #ifndef EIGEN_INDEXED_VIEW_METHOD_2ND_PASS
15
- #define EIGEN_INDEXED_VIEW_METHOD_CONST const
16
- #define EIGEN_INDEXED_VIEW_METHOD_TYPE ConstIndexedViewType
17
- #else
18
- #define EIGEN_INDEXED_VIEW_METHOD_CONST
19
- #define EIGEN_INDEXED_VIEW_METHOD_TYPE IndexedViewType
20
- #endif
21
-
22
- #ifndef EIGEN_INDEXED_VIEW_METHOD_2ND_PASS
23
- protected:
24
-
25
- // define some aliases to ease readability
26
-
27
- template<typename Indices>
28
- struct IvcRowType : public internal::IndexedViewCompatibleType<Indices,RowsAtCompileTime> {};
29
-
30
- template<typename Indices>
31
- struct IvcColType : public internal::IndexedViewCompatibleType<Indices,ColsAtCompileTime> {};
32
-
33
- template<typename Indices>
34
- struct IvcType : public internal::IndexedViewCompatibleType<Indices,SizeAtCompileTime> {};
35
-
36
- typedef typename internal::IndexedViewCompatibleType<Index,1>::type IvcIndex;
37
-
38
- template<typename Indices>
39
- typename IvcRowType<Indices>::type
40
- ivcRow(const Indices& indices) const {
41
- return internal::makeIndexedViewCompatible(indices, internal::variable_if_dynamic<Index,RowsAtCompileTime>(derived().rows()),Specialized);
42
- }
43
-
44
- template<typename Indices>
45
- typename IvcColType<Indices>::type
46
- ivcCol(const Indices& indices) const {
47
- return internal::makeIndexedViewCompatible(indices, internal::variable_if_dynamic<Index,ColsAtCompileTime>(derived().cols()),Specialized);
48
- }
49
-
50
- template<typename Indices>
51
- typename IvcColType<Indices>::type
52
- ivcSize(const Indices& indices) const {
53
- return internal::makeIndexedViewCompatible(indices, internal::variable_if_dynamic<Index,SizeAtCompileTime>(derived().size()),Specialized);
54
- }
55
-
56
- public:
57
-
58
- #endif
59
-
60
- template<typename RowIndices, typename ColIndices>
61
- struct EIGEN_INDEXED_VIEW_METHOD_TYPE {
62
- typedef IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,
63
- typename IvcRowType<RowIndices>::type,
64
- typename IvcColType<ColIndices>::type> type;
65
- };
66
-
67
- // This is the generic version
68
-
69
- template<typename RowIndices, typename ColIndices>
70
- typename internal::enable_if<internal::valid_indexed_view_overload<RowIndices,ColIndices>::value
71
- && internal::traits<typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type>::ReturnAsIndexedView,
72
- typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type >::type
73
- operator()(const RowIndices& rowIndices, const ColIndices& colIndices) EIGEN_INDEXED_VIEW_METHOD_CONST
74
- {
75
- return typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type
76
- (derived(), ivcRow(rowIndices), ivcCol(colIndices));
77
- }
78
-
79
- // The following overload returns a Block<> object
80
-
81
- template<typename RowIndices, typename ColIndices>
82
- typename internal::enable_if<internal::valid_indexed_view_overload<RowIndices,ColIndices>::value
83
- && internal::traits<typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type>::ReturnAsBlock,
84
- typename internal::traits<typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type>::BlockType>::type
85
- operator()(const RowIndices& rowIndices, const ColIndices& colIndices) EIGEN_INDEXED_VIEW_METHOD_CONST
86
- {
87
- typedef typename internal::traits<typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type>::BlockType BlockType;
88
- typename IvcRowType<RowIndices>::type actualRowIndices = ivcRow(rowIndices);
89
- typename IvcColType<ColIndices>::type actualColIndices = ivcCol(colIndices);
90
- return BlockType(derived(),
91
- internal::first(actualRowIndices),
92
- internal::first(actualColIndices),
93
- internal::size(actualRowIndices),
94
- internal::size(actualColIndices));
95
- }
96
-
97
- // The following overload returns a Scalar
98
-
99
- template<typename RowIndices, typename ColIndices>
100
- typename internal::enable_if<internal::valid_indexed_view_overload<RowIndices,ColIndices>::value
101
- && internal::traits<typename EIGEN_INDEXED_VIEW_METHOD_TYPE<RowIndices,ColIndices>::type>::ReturnAsScalar,
102
- CoeffReturnType >::type
103
- operator()(const RowIndices& rowIndices, const ColIndices& colIndices) EIGEN_INDEXED_VIEW_METHOD_CONST
104
- {
105
- return Base::operator()(internal::eval_expr_given_size(rowIndices,rows()),internal::eval_expr_given_size(colIndices,cols()));
106
- }
107
-
108
- #if EIGEN_HAS_STATIC_ARRAY_TEMPLATE
109
-
110
- // The following three overloads are needed to handle raw Index[N] arrays.
111
-
112
- template<typename RowIndicesT, std::size_t RowIndicesN, typename ColIndices>
113
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const RowIndicesT (&)[RowIndicesN],typename IvcColType<ColIndices>::type>
114
- operator()(const RowIndicesT (&rowIndices)[RowIndicesN], const ColIndices& colIndices) EIGEN_INDEXED_VIEW_METHOD_CONST
115
- {
116
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const RowIndicesT (&)[RowIndicesN],typename IvcColType<ColIndices>::type>
117
- (derived(), rowIndices, ivcCol(colIndices));
118
- }
119
-
120
- template<typename RowIndices, typename ColIndicesT, std::size_t ColIndicesN>
121
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,typename IvcRowType<RowIndices>::type, const ColIndicesT (&)[ColIndicesN]>
122
- operator()(const RowIndices& rowIndices, const ColIndicesT (&colIndices)[ColIndicesN]) EIGEN_INDEXED_VIEW_METHOD_CONST
123
- {
124
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,typename IvcRowType<RowIndices>::type,const ColIndicesT (&)[ColIndicesN]>
125
- (derived(), ivcRow(rowIndices), colIndices);
126
- }
127
-
128
- template<typename RowIndicesT, std::size_t RowIndicesN, typename ColIndicesT, std::size_t ColIndicesN>
129
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const RowIndicesT (&)[RowIndicesN], const ColIndicesT (&)[ColIndicesN]>
130
- operator()(const RowIndicesT (&rowIndices)[RowIndicesN], const ColIndicesT (&colIndices)[ColIndicesN]) EIGEN_INDEXED_VIEW_METHOD_CONST
131
- {
132
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const RowIndicesT (&)[RowIndicesN],const ColIndicesT (&)[ColIndicesN]>
133
- (derived(), rowIndices, colIndices);
134
- }
135
-
136
- #endif // EIGEN_HAS_STATIC_ARRAY_TEMPLATE
137
-
138
- // Overloads for 1D vectors/arrays
139
-
140
- template<typename Indices>
141
- typename internal::enable_if<
142
- IsRowMajor && (!(internal::get_compile_time_incr<typename IvcType<Indices>::type>::value==1 || internal::is_valid_index_type<Indices>::value)),
143
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,IvcIndex,typename IvcType<Indices>::type> >::type
144
- operator()(const Indices& indices) EIGEN_INDEXED_VIEW_METHOD_CONST
145
- {
146
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
147
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,IvcIndex,typename IvcType<Indices>::type>
148
- (derived(), IvcIndex(0), ivcCol(indices));
149
- }
150
-
151
- template<typename Indices>
152
- typename internal::enable_if<
153
- (!IsRowMajor) && (!(internal::get_compile_time_incr<typename IvcType<Indices>::type>::value==1 || internal::is_valid_index_type<Indices>::value)),
154
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,typename IvcType<Indices>::type,IvcIndex> >::type
155
- operator()(const Indices& indices) EIGEN_INDEXED_VIEW_METHOD_CONST
156
- {
157
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
158
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,typename IvcType<Indices>::type,IvcIndex>
159
- (derived(), ivcRow(indices), IvcIndex(0));
160
- }
161
-
162
- template<typename Indices>
163
- typename internal::enable_if<
164
- (internal::get_compile_time_incr<typename IvcType<Indices>::type>::value==1) && (!internal::is_valid_index_type<Indices>::value) && (!symbolic::is_symbolic<Indices>::value),
165
- VectorBlock<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,internal::array_size<Indices>::value> >::type
166
- operator()(const Indices& indices) EIGEN_INDEXED_VIEW_METHOD_CONST
167
- {
168
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
169
- typename IvcType<Indices>::type actualIndices = ivcSize(indices);
170
- return VectorBlock<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,internal::array_size<Indices>::value>
171
- (derived(), internal::first(actualIndices), internal::size(actualIndices));
172
- }
173
-
174
- template<typename IndexType>
175
- typename internal::enable_if<symbolic::is_symbolic<IndexType>::value, CoeffReturnType >::type
176
- operator()(const IndexType& id) EIGEN_INDEXED_VIEW_METHOD_CONST
177
- {
178
- return Base::operator()(internal::eval_expr_given_size(id,size()));
179
- }
180
-
181
- #if EIGEN_HAS_STATIC_ARRAY_TEMPLATE
182
-
183
- template<typename IndicesT, std::size_t IndicesN>
184
- typename internal::enable_if<IsRowMajor,
185
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,IvcIndex,const IndicesT (&)[IndicesN]> >::type
186
- operator()(const IndicesT (&indices)[IndicesN]) EIGEN_INDEXED_VIEW_METHOD_CONST
187
- {
188
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
189
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,IvcIndex,const IndicesT (&)[IndicesN]>
190
- (derived(), IvcIndex(0), indices);
191
- }
192
-
193
- template<typename IndicesT, std::size_t IndicesN>
194
- typename internal::enable_if<!IsRowMajor,
195
- IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const IndicesT (&)[IndicesN],IvcIndex> >::type
196
- operator()(const IndicesT (&indices)[IndicesN]) EIGEN_INDEXED_VIEW_METHOD_CONST
197
- {
198
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
199
- return IndexedView<EIGEN_INDEXED_VIEW_METHOD_CONST Derived,const IndicesT (&)[IndicesN],IvcIndex>
200
- (derived(), indices, IvcIndex(0));
201
- }
202
-
203
- #endif // EIGEN_HAS_STATIC_ARRAY_TEMPLATE
204
-
205
- #undef EIGEN_INDEXED_VIEW_METHOD_CONST
206
- #undef EIGEN_INDEXED_VIEW_METHOD_TYPE
207
-
208
- #ifndef EIGEN_INDEXED_VIEW_METHOD_2ND_PASS
209
- #define EIGEN_INDEXED_VIEW_METHOD_2ND_PASS
210
- #include "IndexedViewMethods.h"
211
- #undef EIGEN_INDEXED_VIEW_METHOD_2ND_PASS
212
- #endif
213
-
214
- #else // EIGEN_PARSED_BY_DOXYGEN
215
-
216
- /**
217
- * \returns a generic submatrix view defined by the rows and columns indexed \a rowIndices and \a colIndices respectively.
218
- *
219
- * Each parameter must either be:
220
- * - An integer indexing a single row or column
221
- * - Eigen::all indexing the full set of respective rows or columns in increasing order
222
- * - An ArithmeticSequence as returned by the Eigen::seq and Eigen::seqN functions
223
- * - Any %Eigen's vector/array of integers or expressions
224
- * - Plain C arrays: \c int[N]
225
- * - And more generally any type exposing the following two member functions:
226
- * \code
227
- * <integral type> operator[](<integral type>) const;
228
- * <integral type> size() const;
229
- * \endcode
230
- * where \c <integral \c type> stands for any integer type compatible with Eigen::Index (i.e. \c std::ptrdiff_t).
231
- *
232
- * The last statement implies compatibility with \c std::vector, \c std::valarray, \c std::array, many of the Range-v3's ranges, etc.
233
- *
234
- * If the submatrix can be represented using a starting position \c (i,j) and positive sizes \c (rows,columns), then this
235
- * method will returns a Block object after extraction of the relevant information from the passed arguments. This is the case
236
- * when all arguments are either:
237
- * - An integer
238
- * - Eigen::all
239
- * - An ArithmeticSequence with compile-time increment strictly equal to 1, as returned by Eigen::seq(a,b), and Eigen::seqN(a,N).
240
- *
241
- * Otherwise a more general IndexedView<Derived,RowIndices',ColIndices'> object will be returned, after conversion of the inputs
242
- * to more suitable types \c RowIndices' and \c ColIndices'.
243
- *
244
- * For 1D vectors and arrays, you better use the operator()(const Indices&) overload, which behave the same way but taking a single parameter.
245
- *
246
- * See also this <a href="https://stackoverflow.com/questions/46110917/eigen-replicate-items-along-one-dimension-without-useless-allocations">question</a> and its answer for an example of how to duplicate coefficients.
247
- *
248
- * \sa operator()(const Indices&), class Block, class IndexedView, DenseBase::block(Index,Index,Index,Index)
249
- */
250
- template<typename RowIndices, typename ColIndices>
251
- IndexedView_or_Block
252
- operator()(const RowIndices& rowIndices, const ColIndices& colIndices);
253
-
254
- /** This is an overload of operator()(const RowIndices&, const ColIndices&) for 1D vectors or arrays
255
- *
256
- * \only_for_vectors
257
- */
258
- template<typename Indices>
259
- IndexedView_or_VectorBlock
260
- operator()(const Indices& indices);
261
-
262
- #endif // EIGEN_PARSED_BY_DOXYGEN