sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-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.cp312-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp312-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.cp312-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.cp312-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp312-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp312-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp312-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp312-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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@@ -1,571 +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) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPARSE_BLOCK_H
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- #define EIGEN_SPARSE_BLOCK_H
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-
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- namespace Eigen {
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-
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- // Subset of columns or rows
16
- template<typename XprType, int BlockRows, int BlockCols>
17
- class BlockImpl<XprType,BlockRows,BlockCols,true,Sparse>
18
- : public SparseMatrixBase<Block<XprType,BlockRows,BlockCols,true> >
19
- {
20
- typedef typename internal::remove_all<typename XprType::Nested>::type _MatrixTypeNested;
21
- typedef Block<XprType, BlockRows, BlockCols, true> BlockType;
22
- public:
23
- enum { IsRowMajor = internal::traits<BlockType>::IsRowMajor };
24
- protected:
25
- enum { OuterSize = IsRowMajor ? BlockRows : BlockCols };
26
- typedef SparseMatrixBase<BlockType> Base;
27
- using Base::convert_index;
28
- public:
29
- EIGEN_SPARSE_PUBLIC_INTERFACE(BlockType)
30
-
31
- inline BlockImpl(XprType& xpr, Index i)
32
- : m_matrix(xpr), m_outerStart(convert_index(i)), m_outerSize(OuterSize)
33
- {}
34
-
35
- inline BlockImpl(XprType& xpr, Index startRow, Index startCol, Index blockRows, Index blockCols)
36
- : m_matrix(xpr), m_outerStart(convert_index(IsRowMajor ? startRow : startCol)), m_outerSize(convert_index(IsRowMajor ? blockRows : blockCols))
37
- {}
38
-
39
- EIGEN_STRONG_INLINE Index rows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
40
- EIGEN_STRONG_INLINE Index cols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
41
-
42
- Index nonZeros() const
43
- {
44
- typedef internal::evaluator<XprType> EvaluatorType;
45
- EvaluatorType matEval(m_matrix);
46
- Index nnz = 0;
47
- Index end = m_outerStart + m_outerSize.value();
48
- for(Index j=m_outerStart; j<end; ++j)
49
- for(typename EvaluatorType::InnerIterator it(matEval, j); it; ++it)
50
- ++nnz;
51
- return nnz;
52
- }
53
-
54
- inline const Scalar coeff(Index row, Index col) const
55
- {
56
- return m_matrix.coeff(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 : m_outerStart));
57
- }
58
-
59
- inline const Scalar coeff(Index index) const
60
- {
61
- return m_matrix.coeff(IsRowMajor ? m_outerStart : index, IsRowMajor ? index : m_outerStart);
62
- }
63
-
64
- inline const XprType& nestedExpression() const { return m_matrix; }
65
- inline XprType& nestedExpression() { return m_matrix; }
66
- Index startRow() const { return IsRowMajor ? m_outerStart : 0; }
67
- Index startCol() const { return IsRowMajor ? 0 : m_outerStart; }
68
- Index blockRows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
69
- Index blockCols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
70
-
71
- protected:
72
-
73
- typename internal::ref_selector<XprType>::non_const_type m_matrix;
74
- Index m_outerStart;
75
- const internal::variable_if_dynamic<Index, OuterSize> m_outerSize;
76
-
77
- protected:
78
- // Disable assignment with clear error message.
79
- // Note that simply removing operator= yields compilation errors with ICC+MSVC
80
- template<typename T>
81
- BlockImpl& operator=(const T&)
82
- {
83
- EIGEN_STATIC_ASSERT(sizeof(T)==0, THIS_SPARSE_BLOCK_SUBEXPRESSION_IS_READ_ONLY);
84
- return *this;
85
- }
86
- };
87
-
88
-
89
- /***************************************************************************
90
- * specialization for SparseMatrix
91
- ***************************************************************************/
92
-
93
- namespace internal {
94
-
95
- template<typename SparseMatrixType, int BlockRows, int BlockCols>
96
- class sparse_matrix_block_impl
97
- : public SparseCompressedBase<Block<SparseMatrixType,BlockRows,BlockCols,true> >
98
- {
99
- typedef typename internal::remove_all<typename SparseMatrixType::Nested>::type _MatrixTypeNested;
100
- typedef Block<SparseMatrixType, BlockRows, BlockCols, true> BlockType;
101
- typedef SparseCompressedBase<Block<SparseMatrixType,BlockRows,BlockCols,true> > Base;
102
- using Base::convert_index;
103
- public:
104
- enum { IsRowMajor = internal::traits<BlockType>::IsRowMajor };
105
- EIGEN_SPARSE_PUBLIC_INTERFACE(BlockType)
106
- protected:
107
- typedef typename Base::IndexVector IndexVector;
108
- enum { OuterSize = IsRowMajor ? BlockRows : BlockCols };
109
- public:
110
-
111
- inline sparse_matrix_block_impl(SparseMatrixType& xpr, Index i)
112
- : m_matrix(xpr), m_outerStart(convert_index(i)), m_outerSize(OuterSize)
113
- {}
114
-
115
- inline sparse_matrix_block_impl(SparseMatrixType& xpr, Index startRow, Index startCol, Index blockRows, Index blockCols)
116
- : m_matrix(xpr), m_outerStart(convert_index(IsRowMajor ? startRow : startCol)), m_outerSize(convert_index(IsRowMajor ? blockRows : blockCols))
117
- {}
118
-
119
- template<typename OtherDerived>
120
- inline BlockType& operator=(const SparseMatrixBase<OtherDerived>& other)
121
- {
122
- typedef typename internal::remove_all<typename SparseMatrixType::Nested>::type _NestedMatrixType;
123
- _NestedMatrixType& matrix = m_matrix;
124
- // This assignment is slow if this vector set is not empty
125
- // and/or it is not at the end of the nonzeros of the underlying matrix.
126
-
127
- // 1 - eval to a temporary to avoid transposition and/or aliasing issues
128
- Ref<const SparseMatrix<Scalar, IsRowMajor ? RowMajor : ColMajor, StorageIndex> > tmp(other.derived());
129
- eigen_internal_assert(tmp.outerSize()==m_outerSize.value());
130
-
131
- // 2 - let's check whether there is enough allocated memory
132
- Index nnz = tmp.nonZeros();
133
- Index start = m_outerStart==0 ? 0 : m_matrix.outerIndexPtr()[m_outerStart]; // starting position of the current block
134
- Index end = m_matrix.outerIndexPtr()[m_outerStart+m_outerSize.value()]; // ending position of the current block
135
- Index block_size = end - start; // available room in the current block
136
- Index tail_size = m_matrix.outerIndexPtr()[m_matrix.outerSize()] - end;
137
-
138
- Index free_size = m_matrix.isCompressed()
139
- ? Index(matrix.data().allocatedSize()) + block_size
140
- : block_size;
141
-
142
- Index tmp_start = tmp.outerIndexPtr()[0];
143
-
144
- bool update_trailing_pointers = false;
145
- if(nnz>free_size)
146
- {
147
- // realloc manually to reduce copies
148
- typename SparseMatrixType::Storage newdata(m_matrix.data().allocatedSize() - block_size + nnz);
149
-
150
- internal::smart_copy(m_matrix.valuePtr(), m_matrix.valuePtr() + start, newdata.valuePtr());
151
- internal::smart_copy(m_matrix.innerIndexPtr(), m_matrix.innerIndexPtr() + start, newdata.indexPtr());
152
-
153
- internal::smart_copy(tmp.valuePtr() + tmp_start, tmp.valuePtr() + tmp_start + nnz, newdata.valuePtr() + start);
154
- internal::smart_copy(tmp.innerIndexPtr() + tmp_start, tmp.innerIndexPtr() + tmp_start + nnz, newdata.indexPtr() + start);
155
-
156
- internal::smart_copy(matrix.valuePtr()+end, matrix.valuePtr()+end + tail_size, newdata.valuePtr()+start+nnz);
157
- internal::smart_copy(matrix.innerIndexPtr()+end, matrix.innerIndexPtr()+end + tail_size, newdata.indexPtr()+start+nnz);
158
-
159
- newdata.resize(m_matrix.outerIndexPtr()[m_matrix.outerSize()] - block_size + nnz);
160
-
161
- matrix.data().swap(newdata);
162
-
163
- update_trailing_pointers = true;
164
- }
165
- else
166
- {
167
- if(m_matrix.isCompressed() && nnz!=block_size)
168
- {
169
- // no need to realloc, simply copy the tail at its respective position and insert tmp
170
- matrix.data().resize(start + nnz + tail_size);
171
-
172
- internal::smart_memmove(matrix.valuePtr()+end, matrix.valuePtr() + end+tail_size, matrix.valuePtr() + start+nnz);
173
- internal::smart_memmove(matrix.innerIndexPtr()+end, matrix.innerIndexPtr() + end+tail_size, matrix.innerIndexPtr() + start+nnz);
174
-
175
- update_trailing_pointers = true;
176
- }
177
-
178
- internal::smart_copy(tmp.valuePtr() + tmp_start, tmp.valuePtr() + tmp_start + nnz, matrix.valuePtr() + start);
179
- internal::smart_copy(tmp.innerIndexPtr() + tmp_start, tmp.innerIndexPtr() + tmp_start + nnz, matrix.innerIndexPtr() + start);
180
- }
181
-
182
- // update outer index pointers and innerNonZeros
183
- if(IsVectorAtCompileTime)
184
- {
185
- if(!m_matrix.isCompressed())
186
- matrix.innerNonZeroPtr()[m_outerStart] = StorageIndex(nnz);
187
- matrix.outerIndexPtr()[m_outerStart] = StorageIndex(start);
188
- }
189
- else
190
- {
191
- StorageIndex p = StorageIndex(start);
192
- for(Index k=0; k<m_outerSize.value(); ++k)
193
- {
194
- StorageIndex nnz_k = internal::convert_index<StorageIndex>(tmp.innerVector(k).nonZeros());
195
- if(!m_matrix.isCompressed())
196
- matrix.innerNonZeroPtr()[m_outerStart+k] = nnz_k;
197
- matrix.outerIndexPtr()[m_outerStart+k] = p;
198
- p += nnz_k;
199
- }
200
- }
201
-
202
- if(update_trailing_pointers)
203
- {
204
- StorageIndex offset = internal::convert_index<StorageIndex>(nnz - block_size);
205
- for(Index k = m_outerStart + m_outerSize.value(); k<=matrix.outerSize(); ++k)
206
- {
207
- matrix.outerIndexPtr()[k] += offset;
208
- }
209
- }
210
-
211
- return derived();
212
- }
213
-
214
- inline BlockType& operator=(const BlockType& other)
215
- {
216
- return operator=<BlockType>(other);
217
- }
218
-
219
- inline const Scalar* valuePtr() const
220
- { return m_matrix.valuePtr(); }
221
- inline Scalar* valuePtr()
222
- { return m_matrix.valuePtr(); }
223
-
224
- inline const StorageIndex* innerIndexPtr() const
225
- { return m_matrix.innerIndexPtr(); }
226
- inline StorageIndex* innerIndexPtr()
227
- { return m_matrix.innerIndexPtr(); }
228
-
229
- inline const StorageIndex* outerIndexPtr() const
230
- { return m_matrix.outerIndexPtr() + m_outerStart; }
231
- inline StorageIndex* outerIndexPtr()
232
- { return m_matrix.outerIndexPtr() + m_outerStart; }
233
-
234
- inline const StorageIndex* innerNonZeroPtr() const
235
- { return isCompressed() ? 0 : (m_matrix.innerNonZeroPtr()+m_outerStart); }
236
- inline StorageIndex* innerNonZeroPtr()
237
- { return isCompressed() ? 0 : (m_matrix.innerNonZeroPtr()+m_outerStart); }
238
-
239
- bool isCompressed() const { return m_matrix.innerNonZeroPtr()==0; }
240
-
241
- inline Scalar& coeffRef(Index row, Index col)
242
- {
243
- return m_matrix.coeffRef(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 : m_outerStart));
244
- }
245
-
246
- inline const Scalar coeff(Index row, Index col) const
247
- {
248
- return m_matrix.coeff(row + (IsRowMajor ? m_outerStart : 0), col + (IsRowMajor ? 0 : m_outerStart));
249
- }
250
-
251
- inline const Scalar coeff(Index index) const
252
- {
253
- return m_matrix.coeff(IsRowMajor ? m_outerStart : index, IsRowMajor ? index : m_outerStart);
254
- }
255
-
256
- const Scalar& lastCoeff() const
257
- {
258
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(sparse_matrix_block_impl);
259
- eigen_assert(Base::nonZeros()>0);
260
- if(m_matrix.isCompressed())
261
- return m_matrix.valuePtr()[m_matrix.outerIndexPtr()[m_outerStart+1]-1];
262
- else
263
- return m_matrix.valuePtr()[m_matrix.outerIndexPtr()[m_outerStart]+m_matrix.innerNonZeroPtr()[m_outerStart]-1];
264
- }
265
-
266
- EIGEN_STRONG_INLINE Index rows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
267
- EIGEN_STRONG_INLINE Index cols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
268
-
269
- inline const SparseMatrixType& nestedExpression() const { return m_matrix; }
270
- inline SparseMatrixType& nestedExpression() { return m_matrix; }
271
- Index startRow() const { return IsRowMajor ? m_outerStart : 0; }
272
- Index startCol() const { return IsRowMajor ? 0 : m_outerStart; }
273
- Index blockRows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
274
- Index blockCols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
275
-
276
- protected:
277
-
278
- typename internal::ref_selector<SparseMatrixType>::non_const_type m_matrix;
279
- Index m_outerStart;
280
- const internal::variable_if_dynamic<Index, OuterSize> m_outerSize;
281
-
282
- };
283
-
284
- } // namespace internal
285
-
286
- template<typename _Scalar, int _Options, typename _StorageIndex, int BlockRows, int BlockCols>
287
- class BlockImpl<SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true,Sparse>
288
- : public internal::sparse_matrix_block_impl<SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols>
289
- {
290
- public:
291
- typedef _StorageIndex StorageIndex;
292
- typedef SparseMatrix<_Scalar, _Options, _StorageIndex> SparseMatrixType;
293
- typedef internal::sparse_matrix_block_impl<SparseMatrixType,BlockRows,BlockCols> Base;
294
- inline BlockImpl(SparseMatrixType& xpr, Index i)
295
- : Base(xpr, i)
296
- {}
297
-
298
- inline BlockImpl(SparseMatrixType& xpr, Index startRow, Index startCol, Index blockRows, Index blockCols)
299
- : Base(xpr, startRow, startCol, blockRows, blockCols)
300
- {}
301
-
302
- using Base::operator=;
303
- };
304
-
305
- template<typename _Scalar, int _Options, typename _StorageIndex, int BlockRows, int BlockCols>
306
- class BlockImpl<const SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true,Sparse>
307
- : public internal::sparse_matrix_block_impl<const SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols>
308
- {
309
- public:
310
- typedef _StorageIndex StorageIndex;
311
- typedef const SparseMatrix<_Scalar, _Options, _StorageIndex> SparseMatrixType;
312
- typedef internal::sparse_matrix_block_impl<SparseMatrixType,BlockRows,BlockCols> Base;
313
- inline BlockImpl(SparseMatrixType& xpr, Index i)
314
- : Base(xpr, i)
315
- {}
316
-
317
- inline BlockImpl(SparseMatrixType& xpr, Index startRow, Index startCol, Index blockRows, Index blockCols)
318
- : Base(xpr, startRow, startCol, blockRows, blockCols)
319
- {}
320
-
321
- using Base::operator=;
322
- private:
323
- template<typename Derived> BlockImpl(const SparseMatrixBase<Derived>& xpr, Index i);
324
- template<typename Derived> BlockImpl(const SparseMatrixBase<Derived>& xpr);
325
- };
326
-
327
- //----------
328
-
329
- /** Generic implementation of sparse Block expression.
330
- * Real-only.
331
- */
332
- template<typename XprType, int BlockRows, int BlockCols, bool InnerPanel>
333
- class BlockImpl<XprType,BlockRows,BlockCols,InnerPanel,Sparse>
334
- : public SparseMatrixBase<Block<XprType,BlockRows,BlockCols,InnerPanel> >, internal::no_assignment_operator
335
- {
336
- typedef Block<XprType, BlockRows, BlockCols, InnerPanel> BlockType;
337
- typedef SparseMatrixBase<BlockType> Base;
338
- using Base::convert_index;
339
- public:
340
- enum { IsRowMajor = internal::traits<BlockType>::IsRowMajor };
341
- EIGEN_SPARSE_PUBLIC_INTERFACE(BlockType)
342
-
343
- typedef typename internal::remove_all<typename XprType::Nested>::type _MatrixTypeNested;
344
-
345
- /** Column or Row constructor
346
- */
347
- inline BlockImpl(XprType& xpr, Index i)
348
- : m_matrix(xpr),
349
- m_startRow( (BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) ? convert_index(i) : 0),
350
- m_startCol( (BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) ? convert_index(i) : 0),
351
- m_blockRows(BlockRows==1 ? 1 : xpr.rows()),
352
- m_blockCols(BlockCols==1 ? 1 : xpr.cols())
353
- {}
354
-
355
- /** Dynamic-size constructor
356
- */
357
- inline BlockImpl(XprType& xpr, Index startRow, Index startCol, Index blockRows, Index blockCols)
358
- : m_matrix(xpr), m_startRow(convert_index(startRow)), m_startCol(convert_index(startCol)), m_blockRows(convert_index(blockRows)), m_blockCols(convert_index(blockCols))
359
- {}
360
-
361
- inline Index rows() const { return m_blockRows.value(); }
362
- inline Index cols() const { return m_blockCols.value(); }
363
-
364
- inline Scalar& coeffRef(Index row, Index col)
365
- {
366
- return m_matrix.coeffRef(row + m_startRow.value(), col + m_startCol.value());
367
- }
368
-
369
- inline const Scalar coeff(Index row, Index col) const
370
- {
371
- return m_matrix.coeff(row + m_startRow.value(), col + m_startCol.value());
372
- }
373
-
374
- inline Scalar& coeffRef(Index index)
375
- {
376
- return m_matrix.coeffRef(m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index),
377
- m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0));
378
- }
379
-
380
- inline const Scalar coeff(Index index) const
381
- {
382
- return m_matrix.coeff(m_startRow.value() + (RowsAtCompileTime == 1 ? 0 : index),
383
- m_startCol.value() + (RowsAtCompileTime == 1 ? index : 0));
384
- }
385
-
386
- inline const XprType& nestedExpression() const { return m_matrix; }
387
- inline XprType& nestedExpression() { return m_matrix; }
388
- Index startRow() const { return m_startRow.value(); }
389
- Index startCol() const { return m_startCol.value(); }
390
- Index blockRows() const { return m_blockRows.value(); }
391
- Index blockCols() const { return m_blockCols.value(); }
392
-
393
- protected:
394
- // friend class internal::GenericSparseBlockInnerIteratorImpl<XprType,BlockRows,BlockCols,InnerPanel>;
395
- friend struct internal::unary_evaluator<Block<XprType,BlockRows,BlockCols,InnerPanel>, internal::IteratorBased, Scalar >;
396
-
397
- Index nonZeros() const { return Dynamic; }
398
-
399
- typename internal::ref_selector<XprType>::non_const_type m_matrix;
400
- const internal::variable_if_dynamic<Index, XprType::RowsAtCompileTime == 1 ? 0 : Dynamic> m_startRow;
401
- const internal::variable_if_dynamic<Index, XprType::ColsAtCompileTime == 1 ? 0 : Dynamic> m_startCol;
402
- const internal::variable_if_dynamic<Index, RowsAtCompileTime> m_blockRows;
403
- const internal::variable_if_dynamic<Index, ColsAtCompileTime> m_blockCols;
404
-
405
- protected:
406
- // Disable assignment with clear error message.
407
- // Note that simply removing operator= yields compilation errors with ICC+MSVC
408
- template<typename T>
409
- BlockImpl& operator=(const T&)
410
- {
411
- EIGEN_STATIC_ASSERT(sizeof(T)==0, THIS_SPARSE_BLOCK_SUBEXPRESSION_IS_READ_ONLY);
412
- return *this;
413
- }
414
-
415
- };
416
-
417
- namespace internal {
418
-
419
- template<typename ArgType, int BlockRows, int BlockCols, bool InnerPanel>
420
- struct unary_evaluator<Block<ArgType,BlockRows,BlockCols,InnerPanel>, IteratorBased >
421
- : public evaluator_base<Block<ArgType,BlockRows,BlockCols,InnerPanel> >
422
- {
423
- class InnerVectorInnerIterator;
424
- class OuterVectorInnerIterator;
425
- public:
426
- typedef Block<ArgType,BlockRows,BlockCols,InnerPanel> XprType;
427
- typedef typename XprType::StorageIndex StorageIndex;
428
- typedef typename XprType::Scalar Scalar;
429
-
430
- enum {
431
- IsRowMajor = XprType::IsRowMajor,
432
-
433
- OuterVector = (BlockCols==1 && ArgType::IsRowMajor)
434
- | // FIXME | instead of || to please GCC 4.4.0 stupid warning "suggest parentheses around &&".
435
- // revert to || as soon as not needed anymore.
436
- (BlockRows==1 && !ArgType::IsRowMajor),
437
-
438
- CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
439
- Flags = XprType::Flags
440
- };
441
-
442
- typedef typename internal::conditional<OuterVector,OuterVectorInnerIterator,InnerVectorInnerIterator>::type InnerIterator;
443
-
444
- explicit unary_evaluator(const XprType& op)
445
- : m_argImpl(op.nestedExpression()), m_block(op)
446
- {}
447
-
448
- inline Index nonZerosEstimate() const {
449
- const Index nnz = m_block.nonZeros();
450
- if(nnz < 0) {
451
- // Scale the non-zero estimate for the underlying expression linearly with block size.
452
- // Return zero if the underlying block is empty.
453
- const Index nested_sz = m_block.nestedExpression().size();
454
- return nested_sz == 0 ? 0 : m_argImpl.nonZerosEstimate() * m_block.size() / nested_sz;
455
- }
456
- return nnz;
457
- }
458
-
459
- protected:
460
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
461
-
462
- evaluator<ArgType> m_argImpl;
463
- const XprType &m_block;
464
- };
465
-
466
- template<typename ArgType, int BlockRows, int BlockCols, bool InnerPanel>
467
- class unary_evaluator<Block<ArgType,BlockRows,BlockCols,InnerPanel>, IteratorBased>::InnerVectorInnerIterator
468
- : public EvalIterator
469
- {
470
- // NOTE MSVC fails to compile if we don't explicitely "import" IsRowMajor from unary_evaluator
471
- // because the base class EvalIterator has a private IsRowMajor enum too. (bug #1786)
472
- // NOTE We cannot call it IsRowMajor because it would shadow unary_evaluator::IsRowMajor
473
- enum { XprIsRowMajor = unary_evaluator::IsRowMajor };
474
- const XprType& m_block;
475
- Index m_end;
476
- public:
477
-
478
- EIGEN_STRONG_INLINE InnerVectorInnerIterator(const unary_evaluator& aEval, Index outer)
479
- : EvalIterator(aEval.m_argImpl, outer + (XprIsRowMajor ? aEval.m_block.startRow() : aEval.m_block.startCol())),
480
- m_block(aEval.m_block),
481
- m_end(XprIsRowMajor ? aEval.m_block.startCol()+aEval.m_block.blockCols() : aEval.m_block.startRow()+aEval.m_block.blockRows())
482
- {
483
- while( (EvalIterator::operator bool()) && (EvalIterator::index() < (XprIsRowMajor ? m_block.startCol() : m_block.startRow())) )
484
- EvalIterator::operator++();
485
- }
486
-
487
- inline StorageIndex index() const { return EvalIterator::index() - convert_index<StorageIndex>(XprIsRowMajor ? m_block.startCol() : m_block.startRow()); }
488
- inline Index outer() const { return EvalIterator::outer() - (XprIsRowMajor ? m_block.startRow() : m_block.startCol()); }
489
- inline Index row() const { return EvalIterator::row() - m_block.startRow(); }
490
- inline Index col() const { return EvalIterator::col() - m_block.startCol(); }
491
-
492
- inline operator bool() const { return EvalIterator::operator bool() && EvalIterator::index() < m_end; }
493
- };
494
-
495
- template<typename ArgType, int BlockRows, int BlockCols, bool InnerPanel>
496
- class unary_evaluator<Block<ArgType,BlockRows,BlockCols,InnerPanel>, IteratorBased>::OuterVectorInnerIterator
497
- {
498
- // NOTE see above
499
- enum { XprIsRowMajor = unary_evaluator::IsRowMajor };
500
- const unary_evaluator& m_eval;
501
- Index m_outerPos;
502
- const Index m_innerIndex;
503
- Index m_end;
504
- EvalIterator m_it;
505
- public:
506
-
507
- EIGEN_STRONG_INLINE OuterVectorInnerIterator(const unary_evaluator& aEval, Index outer)
508
- : m_eval(aEval),
509
- m_outerPos( (XprIsRowMajor ? aEval.m_block.startCol() : aEval.m_block.startRow()) ),
510
- m_innerIndex(XprIsRowMajor ? aEval.m_block.startRow() : aEval.m_block.startCol()),
511
- m_end(XprIsRowMajor ? aEval.m_block.startCol()+aEval.m_block.blockCols() : aEval.m_block.startRow()+aEval.m_block.blockRows()),
512
- m_it(m_eval.m_argImpl, m_outerPos)
513
- {
514
- EIGEN_UNUSED_VARIABLE(outer);
515
- eigen_assert(outer==0);
516
-
517
- while(m_it && m_it.index() < m_innerIndex) ++m_it;
518
- if((!m_it) || (m_it.index()!=m_innerIndex))
519
- ++(*this);
520
- }
521
-
522
- inline StorageIndex index() const { return convert_index<StorageIndex>(m_outerPos - (XprIsRowMajor ? m_eval.m_block.startCol() : m_eval.m_block.startRow())); }
523
- inline Index outer() const { return 0; }
524
- inline Index row() const { return XprIsRowMajor ? 0 : index(); }
525
- inline Index col() const { return XprIsRowMajor ? index() : 0; }
526
-
527
- inline Scalar value() const { return m_it.value(); }
528
- inline Scalar& valueRef() { return m_it.valueRef(); }
529
-
530
- inline OuterVectorInnerIterator& operator++()
531
- {
532
- // search next non-zero entry
533
- while(++m_outerPos<m_end)
534
- {
535
- // Restart iterator at the next inner-vector:
536
- m_it.~EvalIterator();
537
- ::new (&m_it) EvalIterator(m_eval.m_argImpl, m_outerPos);
538
- // search for the key m_innerIndex in the current outer-vector
539
- while(m_it && m_it.index() < m_innerIndex) ++m_it;
540
- if(m_it && m_it.index()==m_innerIndex) break;
541
- }
542
- return *this;
543
- }
544
-
545
- inline operator bool() const { return m_outerPos < m_end; }
546
- };
547
-
548
- template<typename _Scalar, int _Options, typename _StorageIndex, int BlockRows, int BlockCols>
549
- struct unary_evaluator<Block<SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true>, IteratorBased>
550
- : evaluator<SparseCompressedBase<Block<SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true> > >
551
- {
552
- typedef Block<SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true> XprType;
553
- typedef evaluator<SparseCompressedBase<XprType> > Base;
554
- explicit unary_evaluator(const XprType &xpr) : Base(xpr) {}
555
- };
556
-
557
- template<typename _Scalar, int _Options, typename _StorageIndex, int BlockRows, int BlockCols>
558
- struct unary_evaluator<Block<const SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true>, IteratorBased>
559
- : evaluator<SparseCompressedBase<Block<const SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true> > >
560
- {
561
- typedef Block<const SparseMatrix<_Scalar, _Options, _StorageIndex>,BlockRows,BlockCols,true> XprType;
562
- typedef evaluator<SparseCompressedBase<XprType> > Base;
563
- explicit unary_evaluator(const XprType &xpr) : Base(xpr) {}
564
- };
565
-
566
- } // end namespace internal
567
-
568
-
569
- } // end namespace Eigen
570
-
571
- #endif // EIGEN_SPARSE_BLOCK_H